1
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Rice AJ, Sword TT, Chengan K, Mitchell DA, Mouncey NJ, Moore SJ, Bailey CB. Cell-free synthetic biology for natural product biosynthesis and discovery. Chem Soc Rev 2025; 54:4314-4352. [PMID: 40104998 PMCID: PMC11920963 DOI: 10.1039/d4cs01198h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2024] [Indexed: 03/20/2025]
Abstract
Natural products have applications as biopharmaceuticals, agrochemicals, and other high-value chemicals. However, there are challenges in isolating natural products from their native producers (e.g. bacteria, fungi, plants). In many cases, synthetic chemistry or heterologous expression must be used to access these important molecules. The biosynthetic machinery to generate these compounds is found within biosynthetic gene clusters, primarily consisting of the enzymes that biosynthesise a range of natural product classes (including, but not limited to ribosomal and nonribosomal peptides, polyketides, and terpenoids). Cell-free synthetic biology has emerged in recent years as a bottom-up technology applied towards both prototyping pathways and producing molecules. Recently, it has been applied to natural products, both to characterise biosynthetic pathways and produce new metabolites. This review discusses the core biochemistry of cell-free synthetic biology applied to metabolite production and critiques its advantages and disadvantages compared to whole cell and/or chemical production routes. Specifically, we review the advances in cell-free biosynthesis of ribosomal peptides, analyse the rapid prototyping of natural product biosynthetic enzymes and pathways, highlight advances in novel antimicrobial discovery, and discuss the rising use of cell-free technologies in industrial biotechnology and synthetic biology.
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Affiliation(s)
- Andrew J Rice
- Department of Biochemistry, School of Medicine - Basic Sciences, Vanderbilt University Medical Research Building-IV, Nashville, Tennessee, 37232, USA
| | - Tien T Sword
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, USA
| | | | - Douglas A Mitchell
- Department of Biochemistry, School of Medicine - Basic Sciences, Vanderbilt University Medical Research Building-IV, Nashville, Tennessee, 37232, USA
- Department of Chemistry, Vanderbilt University, Medical Research Building-IV, Nashville, Tennessee, 37232, USA
| | - Nigel J Mouncey
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Simon J Moore
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.
| | - Constance B Bailey
- School of Chemistry, University of Sydney, Camperdown, NSW, 2001, Australia.
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2
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Nour El-Din H, Kettal M, Lam S, Granados Maciel J, Peters DL, Chen W. Cell-free expression system: a promising platform for bacteriophage production and engineering. Microb Cell Fact 2025; 24:42. [PMID: 39962567 PMCID: PMC11834285 DOI: 10.1186/s12934-025-02661-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2024] [Accepted: 01/21/2025] [Indexed: 02/20/2025] Open
Abstract
Cell-free expression is a technique used to synthesize proteins without utilising living cells. This technique relies mainly on the cellular machinery -ribosomes, enzymes, and other components - extracted from cells to produce proteins in vitro. Thus far, cell-free expression systems have been used for an array of biologically important purposes, such as studying protein functions and interactions, designing synthetic pathways, and producing novel proteins and enzymes. In this review article, we aim to provide bacteriophage (phage) researchers with an understanding of the cell-free expression process and the potential it holds to accelerate phage production and engineering for phage therapy and other applications. Throughout the review, we summarize the system's main steps and components, both generally and particularly for the self-assembly and engineering of phages and discuss their potential optimization for better protein and phage production. Cell-free expression systems have the potential to serve as a platform for the biosynthetic production of personalized phage therapeutics. This is an area of in vitro biosynthesis that is becoming increasingly attractive, given the current high interest in phages and their promising potential role in the fight against antimicrobial resistant infections.
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Affiliation(s)
- Hanzada Nour El-Din
- Human Health Therapeutics Research Center, National Research Council Canada, Ottawa, ON, K1N 5A2, Canada.
| | - Maryam Kettal
- Human Health Therapeutics Research Center, National Research Council Canada, Ottawa, ON, K1N 5A2, Canada
| | - Serena Lam
- Human Health Therapeutics Research Center, National Research Council Canada, Ottawa, ON, K1N 5A2, Canada
| | - José Granados Maciel
- Human Health Therapeutics Research Center, National Research Council Canada, Ottawa, ON, K1N 5A2, Canada
| | - Danielle L Peters
- Human Health Therapeutics Research Center, National Research Council Canada, Ottawa, ON, K1N 5A2, Canada
| | - Wangxue Chen
- Human Health Therapeutics Research Center, National Research Council Canada, Ottawa, ON, K1N 5A2, Canada
- Department of Biology, Brock University, St. Catharines, ON, Canada
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3
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Hunt A, Rasor BJ, Seki K, Ekas HM, Warfel KF, Karim AS, Jewett MC. Cell-Free Gene Expression: Methods and Applications. Chem Rev 2025; 125:91-149. [PMID: 39700225 PMCID: PMC11719329 DOI: 10.1021/acs.chemrev.4c00116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 07/29/2024] [Accepted: 10/21/2024] [Indexed: 12/21/2024]
Abstract
Cell-free gene expression (CFE) systems empower synthetic biologists to build biological molecules and processes outside of living intact cells. The foundational principle is that precise, complex biomolecular transformations can be conducted in purified enzyme or crude cell lysate systems. This concept circumvents mechanisms that have evolved to facilitate species survival, bypasses limitations on molecular transport across the cell wall, and provides a significant departure from traditional, cell-based processes that rely on microscopic cellular "reactors." In addition, cell-free systems are inherently distributable through freeze-drying, which allows simple distribution before rehydration at the point-of-use. Furthermore, as cell-free systems are nonliving, they provide built-in safeguards for biocontainment without the constraints attendant on genetically modified organisms. These features have led to a significant increase in the development and use of CFE systems over the past two decades. Here, we discuss recent advances in CFE systems and highlight how they are transforming efforts to build cells, control genetic networks, and manufacture biobased products.
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Affiliation(s)
- Andrew
C. Hunt
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Blake J. Rasor
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Kosuke Seki
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Holly M. Ekas
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Katherine F. Warfel
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Ashty S. Karim
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Michael C. Jewett
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry
of Life Processes Institute, Northwestern
University, Evanston, Illinois 60208, United States
- Robert
H. Lurie Comprehensive Cancer Center, Northwestern
University, Chicago, Illinois 60611, United States
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
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4
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Jilani SB, Alahuhta M, Bomble YJ, Olson DG. Cell-Free Systems Biology: Characterizing Central Metabolism of Clostridium thermocellum with a Three-Enzyme Cascade Reaction. ACS Synth Biol 2024; 13:3587-3599. [PMID: 39387698 PMCID: PMC11574923 DOI: 10.1021/acssynbio.4c00405] [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] [Received: 06/10/2024] [Revised: 08/28/2024] [Accepted: 09/27/2024] [Indexed: 10/15/2024]
Abstract
Genetic approaches have been traditionally used to understand microbial metabolism, but this process can be slow in nonmodel organisms due to limited genetic tools. An alternative approach is to study metabolism directly in the cell lysate. This avoids the need for genetic tools and is routinely used to study individual enzymatic reactions but is not generally used to study systems-level properties of metabolism. Here we demonstrate a new approach that we call "cell-free systems biology", where we use well-characterized enzymes and multienzyme cascades to serve as sources or sinks of intermediate metabolites. This allows us to isolate subnetworks within metabolism and study their systems-level properties. To demonstrate this, we worked with a three-enzyme cascade reaction that converts pyruvate to 2,3-butanediol. Although it has been previously used in cell-free systems, its pH dependence was not well characterized, limiting its utility as a sink for pyruvate. We showed that improved proton accounting allowed better prediction of pH changes and that active pH control allowed 2,3-butanediol titers of up to 2.1 M (189 g/L) from acetoin and 1.6 M (144 g/L) from pyruvate. The improved proton accounting provided a crucial insight that preventing the escape of CO2 from the system largely eliminated the need for active pH control, dramatically simplifying our experimental setup. We then used this cascade reaction to understand limits to product formation in Clostridium thermocellum, an organism with potential applications for cellulosic biofuel production. We showed that the fate of pyruvate is largely controlled by electron availability and that reactions upstream of pyruvate limit overall product formation.
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Affiliation(s)
- S Bilal Jilani
- Thayer School of Engineering at Dartmouth College, Hanover, New Hampshire 03755, United States
| | - Markus Alahuhta
- National Renewable Energy Laboratory, Biosciences Center, Golden, Colorado 80401, United States
| | - Yannick J Bomble
- National Renewable Energy Laboratory, Biosciences Center, Golden, Colorado 80401, United States
| | - Daniel G Olson
- Thayer School of Engineering at Dartmouth College, Hanover, New Hampshire 03755, United States
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5
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Lehr FX, Pavletić B, Glatter T, Heimerl T, Moeller R, Niederholtmeyer H. Enhanced assembly of bacteriophage T7 produced in cell-free reactions under simulated microgravity. NPJ Microgravity 2024; 10:30. [PMID: 38491014 PMCID: PMC10943216 DOI: 10.1038/s41526-024-00378-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/08/2024] [Indexed: 03/18/2024] Open
Abstract
On-demand biomanufacturing has the potential to improve healthcare and self-sufficiency during space missions. Cell-free transcription and translation reactions combined with DNA blueprints can produce promising therapeutics like bacteriophages and virus-like particles. However, how space conditions affect the synthesis and self-assembly of such complex multi-protein structures is unknown. Here, we characterize the cell-free production of infectious bacteriophage T7 virions under simulated microgravity. Rotation in a 2D-clinostat increased the number of infectious particles compared to static controls. Quantitative analyses by mass spectrometry, immuno-dot-blot and real-time PCR showed no significant differences in protein and DNA contents, suggesting enhanced self-assembly of T7 phages in simulated microgravity. While the effects of genuine space conditions on the cell-free synthesis and assembly of bacteriophages remain to be investigated, our findings support the vision of a cell-free synthesis-enabled "astropharmacy".
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Affiliation(s)
- François-Xavier Lehr
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
| | - Bruno Pavletić
- German Aerospace Center, Institute of Aerospace Medicine, Aerospace Microbiology, Cologne, Germany
- Technical University of Braunschweig, Faculty of Life Sciences, Braunschweig, Germany
| | - Timo Glatter
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Thomas Heimerl
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
| | - Ralf Moeller
- German Aerospace Center, Institute of Aerospace Medicine, Aerospace Microbiology, Cologne, Germany.
| | - Henrike Niederholtmeyer
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany.
- Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Straubing, Germany.
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6
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Melinek BJ, Tuck J, Probert P, Branton H, Bracewell DG. Designing of an extract production protocol for industrial application of cell-free protein synthesis technology: Building from a current best practice to a quality by design approach. ENGINEERING BIOLOGY 2023; 7:1-17. [PMID: 38094242 PMCID: PMC10715128 DOI: 10.1049/enb2.12029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 11/10/2023] [Accepted: 11/20/2023] [Indexed: 10/16/2024] Open
Abstract
Cell-Free Protein Synthesis (CFPS) has, over the past decade, seen a substantial increase in interest from both academia and industry. Applications range from fundamental research, through high-throughput screening to niche manufacture of therapeutic products. This review/perspective focuses on Quality Control in CFPS. The importance and difficulty of measuring the Raw Material Attributes (RMAs) of whole cell extract, such as constituent protein and metabolite concentrations, and of understanding and controlling these complicated enzymatic reactions is explored, for both centralised and distributed industrial production of biotherapeutics. It is suggested that a robust cell-free extract production process should produce cell extract of consistent quality; however, demonstrating this is challenging without a full understanding of the RMAs and their interaction with reaction conditions and product. Lack of technology transfer and knowledge sharing is identified as a key limiting factor in the development of CFPS. The article draws upon the experiences of industrial process specialists, discussions within the Future Targeted Healthcare Manufacturing Hub Specialist Working Groups and evidence drawn from various sources to identify sources of process variation and to propose an initial guide towards systematisation of CFPS process development and reporting. These proposals include the development of small scale screening tools, consistent reporting of selected process parameters and analytics and application of industrial thinking and manufacturability to protocol development.
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Affiliation(s)
| | - Jade Tuck
- CPIDarlingtonUK
- Merck KGaADarmstadtGermany
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7
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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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8
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Koo CW, Hershewe JM, Jewett MC, Rosenzweig AC. Cell-Free Protein Synthesis of Particulate Methane Monooxygenase into Nanodiscs. ACS Synth Biol 2022; 11:4009-4017. [PMID: 36417751 PMCID: PMC9910172 DOI: 10.1021/acssynbio.2c00366] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Particulate methane monooxygenase (pMMO) is a multi-subunit membrane metalloenzyme used by methanotrophic bacteria to convert methane to methanol. A major hurdle to studying pMMO is the lack of a recombinant expression system, precluding investigation of individual residues by mutagenesis and hampering a complete understanding of its mechanism. Here, we developed an Escherichia coli lysate-based cell-free protein synthesis (CFPS) system that can be used to express pMMO in vitro in the presence of nanodiscs. We used a SUMO fusion construct to generate the native PmoB subunit and showed that the SUMO protease (Ulp1) cleaves the protein in the reaction mixture. Using an affinity tag to isolate the complete pMMO complex, we demonstrated that the complex forms without the need for exogenous translocon machinery or chaperones, confirmed by negative stain electron microscopy. This work demonstrates the potential for using CFPS to express multi-subunit membrane-bound metalloenzymes directly into lipid bilayers.
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Affiliation(s)
- Christopher W. Koo
- Department of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Jasmine M. Hershewe
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Amy C. Rosenzweig
- Department of Molecular Biosciences and of Chemistry and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
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9
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Bruni R. High-Throughput Cell-Free Screening of Eukaryotic Membrane Proteins in Lipidic Mimetics. Curr Protoc 2022; 2:e510. [PMID: 35926131 DOI: 10.1002/cpz1.510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Membrane proteins (MPs) carry out important functions in the metabolism of cells, such as the detection of extracellular activities and the transport of small molecules across the plasma and organelle membranes. Expression of MPs for biochemical, biophysical, and structural analysis is in most cases achieved by overexpression of the desired target in an appropriate host, such as a bacterium. However, overexpression of MPs is usually toxic to the host cells and can lead to aggregation of target protein and to resistance to detergent extraction. An alternative to cell-based MP expression is cell-free (CF), or in vitro, expression. CF expression of MPs has several advantages over cell-based methods, including lack of toxicity issues, no requirement for detergent extraction, and direct incorporation of target proteins in various lipidic mimetics. This article describes a high-throughput method for the expression and purification of eukaryotic membrane proteins used in the author's lab. Basic Protocol 1 describes the selection and cloning of target genes into appropriate vectors for CF expression. Basic Protocol 2 describes the assembly of CF reactions for high-throughput screening. Basic Protocol 3 outlines methods for purification and detection of target proteins. Support Protocols 1-6 describe various accessory procedures: amplification of target, treatment of vectors to prepare them for ligation-independent cloning, and the preparation of S30 extract, T7 RNA polymerase, liposomes, and nanodiscs. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Target selection, construct design, and cloning into pET-based expression vectors Support Protocol 1: Amplification of target DNA Support Protocol 2: Preparation of ligation-independent cloning (LIC)-compatible vectors Basic Protocol 2: Assembly of small-scale cell-free reactions for high-throughput screening Support Protocol 3: Preparation of Escherichia coli S30 extract Support Protocol 4: Preparation of T7 RNA polymerase Support Protocol 5: Preparation of liposomes Support Protocol 6: Preparation of nanodiscs Basic Protocol 3: Purification and detection of cell-free reaction products.
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Affiliation(s)
- Renato Bruni
- Center on Membrane Protein Production and Analysis (COMPPÅ), New York Structural Biology Center, New York, New York
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10
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Kapoor N, Uchiyama S, Pill L, Bautista L, Sedra A, Yin L, Regan M, Chu E, Rabara T, Wong M, Davey P, Fairman J, Nizet V. Non-Native Amino Acid Click Chemistry-Based Technology for Site-Specific Polysaccharide Conjugation to a Bacterial Protein Serving as Both Carrier and Vaccine Antigen. ACS OMEGA 2022; 7:24111-24120. [PMID: 35874267 PMCID: PMC9301713 DOI: 10.1021/acsomega.1c07360] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Surface-expressed bacterial polysaccharides are important vaccine antigens but must be conjugated to a carrier protein for efficient antigen presentation and development of strong memory B cell and antibody responses, especially in young children. The commonly used protein carriers include tetanus toxoid (TT), diphtheria toxoid (DT), and its derivative CRM197, but carrier-induced epitopic suppression and bystander interference may limit the expanded use of the same carriers in the pediatric immunization schedule. Recent efforts to develop a vaccine against the major human pathogen group A Streptococcus (GAS) have sought to combine two promising vaccine antigens-the universally conserved group A cell wall carbohydrate (GAC) with the secreted toxin antigen streptolysin O (SLO) as a protein carrier; however, standard reductive amination procedures appeared to destroy function epitopes of the protein, markedly diminishing functional antibody responses. Here, we couple a cell-free protein synthesis (CFPS) platform, allowing the incorporation of non-natural amino acids into a C-terminally truncated SLO toxoid for the precise conjugation to the polyrhamnose backbone of GAC. The combined immunogen generated functional antibodies against both conserved GAS virulence factors and provided protection against systemic GAS challenges. CFPS may represent a scalable method for generating pathogen-specific carrier proteins for multivalent subunit vaccine development.
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Affiliation(s)
- Neeraj Kapoor
- Vaxcyte,
Inc., 825 Industrial
Road, Suite 300, San Carlos, California 94070, United States
| | - Satoshi Uchiyama
- Division of Host-Microbe Systems
and Therapeutics, Department of
Pediatrics and Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, 9500 Gilman Drive Mail Code 0760, La Jolla, California 92093, United States
| | - Lucy Pill
- Vaxcyte,
Inc., 825 Industrial
Road, Suite 300, San Carlos, California 94070, United States
| | - Leslie Bautista
- Vaxcyte,
Inc., 825 Industrial
Road, Suite 300, San Carlos, California 94070, United States
| | - Angie Sedra
- Vaxcyte,
Inc., 825 Industrial
Road, Suite 300, San Carlos, California 94070, United States
| | - Lu Yin
- Vaxcyte,
Inc., 825 Industrial
Road, Suite 300, San Carlos, California 94070, United States
| | - Maritoni Regan
- Vaxcyte,
Inc., 825 Industrial
Road, Suite 300, San Carlos, California 94070, United States
| | - Ellen Chu
- Vaxcyte,
Inc., 825 Industrial
Road, Suite 300, San Carlos, California 94070, United States
| | - Taylor Rabara
- Vaxcyte,
Inc., 825 Industrial
Road, Suite 300, San Carlos, California 94070, United States
| | - Melissa Wong
- Vaxcyte,
Inc., 825 Industrial
Road, Suite 300, San Carlos, California 94070, United States
| | - Peter Davey
- Vaxcyte,
Inc., 825 Industrial
Road, Suite 300, San Carlos, California 94070, United States
| | - Jeff Fairman
- Vaxcyte,
Inc., 825 Industrial
Road, Suite 300, San Carlos, California 94070, United States
| | - Victor Nizet
- Division of Host-Microbe Systems
and Therapeutics, Department of
Pediatrics and Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, 9500 Gilman Drive Mail Code 0760, La Jolla, California 92093, United States
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11
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Ramm F, Jack L, Kaser D, Schloßhauer JL, Zemella A, Kubick S. Cell-Free Systems Enable the Production of AB5 Toxins for Diagnostic Applications. Toxins (Basel) 2022; 14:toxins14040233. [PMID: 35448842 PMCID: PMC9027097 DOI: 10.3390/toxins14040233] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 12/04/2022] Open
Abstract
Cell-free protein synthesis (CFPS) represents a versatile key technology for the production of toxic proteins. As a cell lysate, rather than viable cells, is used, the toxic effects on the host organism can be circumvented. The open nature of cell-free systems allows for the addition of supplements affecting protein concentration and folding. Here, we present the cell-free synthesis and functional characterization of two AB5 toxins, namely the cholera toxin (Ctx) and the heat-labile enterotoxin (LT), using two eukaryotic cell-free systems based on Chinese hamster ovary (CHO) and Spodoptera frugiperda (Sf21) cells. Through an iterative optimization procedure, the synthesis of the individual AB5 toxins was established, and the formation of multimeric structures could be shown by autoradiography. A functional analysis was performed using cell-based assays, thereby demonstrating that the LT complex induced the characteristic cell elongation of target cells after 24 h. The LT complex induced cell death at higher concentrations, starting at an initial concentration of 5 nM. The initial toxic effects of the Ctx multimer could already be detected at 4 nM. The detection and characterization of such AB5 toxins is of utmost importance, and the monitoring of intracellular trafficking facilitates the further identification of the mechanism of action of these toxins. We showed that the B-subunit of LT (LTB) could be fluorescently labeled using an LTB-Strep fusion protein, which is a proof-of-concept for future Trojan horse applications. Further, we performed a mutational analysis of the CtxA subunit as its template was modified, and an amber stop codon was inserted into CtxA’s active site. Subsequently, a non-canonical amino acid was site-specifically incorporated using bio-orthogonal systems. Finally, a fluorescently labeled CtxA protein was produced using copper-catalyzed click reactions as well as a Staudinger ligation. As expected, the modified Ctx multimer no longer induced toxic effects. In our study, we showed that CFPS could be used to study the active centers of toxins by inserting mutations. Additionally, this methodology can be applied for the design of Trojan horses and targeted toxins, as well as enabling the intracellular trafficking of toxins as a prerequisite for the analysis of the toxin’s mechanism of action.
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Affiliation(s)
- Franziska Ramm
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany; (F.R.); (L.J.); (D.K.); (J.L.S.); (A.Z.)
- Institute of Chemistry and Biochemistry—Biochemistry, Freie Universität Berlin, Takustr. 6, 14195 Berlin, Germany
| | - Lena Jack
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany; (F.R.); (L.J.); (D.K.); (J.L.S.); (A.Z.)
| | - Danny Kaser
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany; (F.R.); (L.J.); (D.K.); (J.L.S.); (A.Z.)
| | - Jeffrey L. Schloßhauer
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany; (F.R.); (L.J.); (D.K.); (J.L.S.); (A.Z.)
- Institute of Chemistry and Biochemistry—Biochemistry, Freie Universität Berlin, Takustr. 6, 14195 Berlin, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany; (F.R.); (L.J.); (D.K.); (J.L.S.); (A.Z.)
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany; (F.R.); (L.J.); (D.K.); (J.L.S.); (A.Z.)
- Institute of Chemistry and Biochemistry—Biochemistry, Freie Universität Berlin, Takustr. 6, 14195 Berlin, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus–Senftenberg, Brandenburg Medical School Theodor Fontane and the University of Potsdam, 14476 Potsdam, Germany
- Correspondence:
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12
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Miguez AM, Zhang Y, Piorino F, Styczynski MP. Metabolic Dynamics in Escherichia coli-Based Cell-Free Systems. ACS Synth Biol 2021; 10:2252-2265. [PMID: 34478281 PMCID: PMC9807262 DOI: 10.1021/acssynbio.1c00167] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The field of metabolic engineering has yielded remarkable accomplishments in using cells to produce valuable molecules, and cell-free expression (CFE) systems have the potential to push the field even further. However, CFE systems still face some outstanding challenges, including endogenous metabolic activity that is poorly understood yet has a significant impact on CFE productivity. Here, we use metabolomics to characterize the temporal metabolic changes in CFE systems and their constituent components, including significant metabolic activity in central carbon and amino acid metabolism. We find that while changing the reaction starting state via lysate preincubation impacts protein production, it has a comparatively small impact on metabolic state. We also demonstrate that changes to lysate preparation have a larger effect on protein yield and temporal metabolic profiles, though general metabolic trends are conserved. Finally, while we improve protein production through targeted supplementation of metabolic enzymes, we show that the endogenous metabolic activity is fairly resilient to these enzymatic perturbations. Overall, this work highlights the robust nature of CFE reaction metabolism as well as the importance of understanding the complex interdependence of metabolites and proteins in CFE systems to guide optimization efforts.
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13
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Garenne D, Thompson S, Brisson A, Khakimzhan A, Noireaux V. The all-E. coliTXTL toolbox 3.0: new capabilities of a cell-free synthetic biology platform. Synth Biol (Oxf) 2021; 6:ysab017. [PMID: 34712841 PMCID: PMC8546610 DOI: 10.1093/synbio/ysab017] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/19/2021] [Accepted: 07/12/2021] [Indexed: 12/12/2022] Open
Abstract
The new generation of cell-free gene expression systems enables the prototyping and engineering of biological systems in vitro over a remarkable scope of applications and physical scales. As the utilization of DNA-directed in vitro protein synthesis expands in scope, developing more powerful cell-free transcription-translation (TXTL) platforms remains a major goal to either execute larger DNA programs or improve cell-free biomanufacturing capabilities. In this work, we report the capabilities of the all-E. coli TXTL toolbox 3.0, a multipurpose cell-free expression system specifically developed for synthetic biology. In non-fed batch-mode reactions, the synthesis of the fluorescent reporter protein eGFP (enhanced green fluorescent protein) reaches 4 mg/ml. In synthetic cells, consisting of liposomes loaded with a TXTL reaction, eGFP is produced at concentrations of >8 mg/ml when the chemical building blocks feeding the reaction diffuse through membrane channels to facilitate exchanges with the outer solution. The bacteriophage T7, encoded by a genome of 40 kb and ∼60 genes, is produced at a concentration of 1013 PFU/ml (plaque forming unit/ml). This TXTL system extends the current cell-free expression capabilities by offering unique strength and properties, for testing regulatory elements and circuits, biomanufacturing biologics or building synthetic cells.
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Affiliation(s)
- David Garenne
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
| | - Seth Thompson
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
| | - Amaury Brisson
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
| | - Aset Khakimzhan
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
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14
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Wong M, Badri A, Gasparis C, Belfort G, Koffas M. Modular optimization in metabolic engineering. Crit Rev Biochem Mol Biol 2021; 56:587-602. [PMID: 34180323 DOI: 10.1080/10409238.2021.1937928] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
There is an increasing demand for bioproducts produced by metabolically engineered microbes, such as pharmaceuticals, biofuels, biochemicals and other high value compounds. In order to meet this demand, modular optimization, the optimizing of subsections instead of the whole system, has been adopted to engineer cells to overproduce products. Research into modularity has focused on traditional approaches such as DNA, RNA, and protein-level modularity of intercellular machinery, by optimizing metabolic pathways for enhanced production. While research into these traditional approaches continues, limitations such as scale-up and time cost hold them back from wider use, while at the same time there is a shift to more novel methods, such as moving from episomal expression to chromosomal integration. Recently, nontraditional approaches such as co-culture systems and cell-free metabolic engineering (CFME) are being investigated for modular optimization. Co-culture modularity looks to optimally divide the metabolic burden between different hosts. CFME seeks to modularly optimize metabolic pathways in vitro, both speeding up the design of such systems and eliminating the issues associated with live hosts. In this review we will examine both traditional and nontraditional approaches for modular optimization, examining recent developments and discussing issues and emerging solutions for future research in metabolic engineering.
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Affiliation(s)
- Matthew Wong
- Howard P. Isermann Department of Chemical and Biological Engineering and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Abinaya Badri
- Howard P. Isermann Department of Chemical and Biological Engineering and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Christopher Gasparis
- Howard P. Isermann Department of Chemical and Biological Engineering and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Georges Belfort
- Howard P. Isermann Department of Chemical and Biological Engineering and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Mattheos Koffas
- Howard P. Isermann Department of Chemical and Biological Engineering and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
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15
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Tamiev BD, Dopp JL, Reuel NF. Anaerobic Conditioning of E. coli Cell Lysate for Enhanced In Vitro Protein Synthesis. ACS Synth Biol 2021; 10:716-723. [PMID: 33760595 DOI: 10.1021/acssynbio.0c00501] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cell-free protein expression (CFPS) from E. coli cell lysate is an established chemical biology technique. Common efforts to improve synthesis capacity, such as strain engineering and process improvements, have overlooked the opportunity to increase productivity by reducing the dependence on limited, dissolved oxygen. Here we demonstrate conditioning E. coli cells for anaerobic respiration which increases the initial protein expression rate up to 4-fold and increases titer by 50% as compared to traditional aerobic cell lysate when using sfGFP as a reporter protein in CFPS reactions run at atmospheric conditions. This enhancement is even more significant when run in an oxygen-depleted environment, where anaerobic respiration preconditioned cells increase yield when supplemented with nitrite as a terminal electron acceptor (TEA). Furthermore, we test knockout mutants to determine key proteins responsible for enhancing the anaerobically prepared CFPS lysate. Further improvements could be made in preconditioning cells by increasing expression levels of critical pathway enzymes or by screening other TEA.
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Affiliation(s)
- By Denis Tamiev
- Biochemistry, Biophysics and Molecular Biology Department, Iowa State University, Ames, Iowa 50011, United States
| | - Jared L. Dopp
- Chemical and Biological Engineering Department, Iowa State University, Ames, Iowa 50011, United States
| | - Nigel F. Reuel
- Chemical and Biological Engineering Department, Iowa State University, Ames, Iowa 50011, United States
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16
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Stamatis C, Farid SS. Process economics evaluation of cell-free synthesis for the commercial manufacture of antibody drug conjugates. Biotechnol J 2021; 16:e2000238. [PMID: 33231912 DOI: 10.1002/biot.202000238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 11/13/2020] [Indexed: 11/06/2022]
Abstract
Continuous improvements of cell-free synthesis (CFS) systems have generated interest in adopting the technology for the manufacture of biologics. This paper provides an evaluation of the manufacturing cost-effectiveness of CFS for the commercial production of antibody-drug conjugates (ADCs). The evaluation was performed using an advanced techno-economic engine (TEE) built in Python. The TEE is programmed in an object-oriented environment capable of simulating a plethora of process flowsheets and predicting size and cost metrics for the process and the facility. A case study was formulated to compare the economics of whole bioprocesses based on either a CFS system or a mammalian cell system (CHO) for the manufacture of an ADC at a range of product demands. The analysis demonstrated the potential of CFS for the commercial manufacture of biologics and identified key cost drivers related to the system. The CFS system showed an approximately 80% increase in the cost of goods compared to CHO with a significant cost attributed to the in-house manufacture of the bacterial cell extract, necessary for the CFS reaction step in the process. A sensitivity and target analysis highlighted the need for further process improvements especially in the titer for the CFS process to become more competitive against well-established systems.
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Affiliation(s)
- Christos Stamatis
- The Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering, University College London, London, UK
| | - Suzanne S Farid
- The Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering, University College London, London, UK
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17
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Abstract
Cell-free protein expression systems and lipid nanoparticle technologies are core platforms for membrane protein synthesis. The implementation of preassembled nanodiscs allows the co-translational insertion of membrane proteins into tailored lipid bilayers in the absence of any artificial hydrophobic compounds. This strategy is particularly interesting for detergent sensitive or otherwise critical membrane proteins such as G-protein-coupled receptors (GPCRs). Cell-free expression reactions are completed within a day and the formed GPCR/nanodisc particles can be purified directly out of the reaction mixture by affinity tags and without any further manipulation. The streamlined procedure reduces risk of GPCR denaturation and the sample quality can further be supported by supplying chaperones or other beneficial compounds directly into the expression reactions.GPCRs inserted into nanoparticle membranes are excellent tools for a variety of applications such as ligand screening, engineering or even structural characterization. In this chapter, we provide protocols for the reaction set-up and efficient cell-free production of functionally folded GPCRs reaching μM concentrations in the final expression reactions. We further exemplify the tuning of GPCR sample quality and discuss their application for throughput ligand screening and for the analysis of ligand-binding characteristics.
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18
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Dopp JL, Reuel NF. Simple, functional, inexpensive cell extract for in vitro prototyping of proteins with disulfide bonds. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107790] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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19
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Nelson JAD, Barnett RJ, Hunt JP, Foutz I, Welton M, Bundy BC. Hydrofoam and oxygen headspace bioreactors improve cell-free therapeutic protein production yields through enhanced oxygen transport. Biotechnol Prog 2020; 37:e3079. [PMID: 32920987 DOI: 10.1002/btpr.3079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 08/31/2020] [Accepted: 09/10/2020] [Indexed: 12/19/2022]
Abstract
Protein therapeutics are powerful tools in the fight against diabetes, cancers, growth disorders, and many other debilitating diseases. However, availability is limited due to cost and complications of production from living organisms. To make life-saving protein therapeutics more available to the world, the possibility of magistral or point-of-care protein therapeutic production has gained focus. The recent invention and optimization of lyophilized "cell-free" protein synthesis reagents and its demonstrated ability to produce highly active versions of FDA-approved cancer therapeutics have increased its potential for low-cost, single-batch, magistral medicine. Here we present for the first time the concept of increased oxygen mass transfer in small-batch, cell-free protein synthesis (CFPS) reactions through air-water foams. These "hydrofoam" reactions increased CFPS yields by up to 100%. Contrary to traditional protein synthesis using living organisms, where foam bubbles cause cell-lysis and production losses, hydrofoam CFPS reactions are "cell-free" and better tolerate foaming. Simulation and experimental results suggest that oxygen transfer is limiting in even small volume batch CFPS reactors and that the hydrofoam format improved oxygen transfer. This is further supported by CFPS reactions achieving higher yields when oxygen gas replaces air in the headspace of batch reactions. Improving CFPS yields with hydrofoam reduces the overall cost of biotherapeutic production, increasing availability to the developing world. Beyond protein therapeutic production, hydrofoam CFPS could also be used to enhance other CFPS applications including biosensing, biomanufacturing, and biocatalysis.
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Affiliation(s)
- J Andrew D Nelson
- Department of Chemical Engineering, Brigham Young University, Provo, Utah, USA
| | - R Jordan Barnett
- Department of Chemical Engineering, Brigham Young University, Provo, Utah, USA
| | - J Porter Hunt
- Department of Chemical Engineering, Brigham Young University, Provo, Utah, USA
| | - Isaac Foutz
- Department of Chemical Engineering, Brigham Young University, Provo, Utah, USA
| | - Meagan Welton
- Department of Chemical Engineering, Brigham Young University, Provo, Utah, USA
| | - Bradley C Bundy
- Department of Chemical Engineering, Brigham Young University, Provo, Utah, USA
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20
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Development of a clostridia-based cell-free system for prototyping genetic parts and metabolic pathways. Metab Eng 2020; 62:95-105. [PMID: 32540392 DOI: 10.1016/j.ymben.2020.06.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/15/2020] [Accepted: 06/07/2020] [Indexed: 02/04/2023]
Abstract
Gas fermentation by autotrophic bacteria, such as clostridia, offers a sustainable path to numerous bioproducts from a range of local, highly abundant, waste and low-cost feedstocks, such as industrial flue gases or syngas generated from biomass or municipal waste. Unfortunately, designing and engineering clostridia remains laborious and slow. The ability to prototype individual genetic part function, gene expression patterns, and biosynthetic pathway performance in vitro before implementing designs in cells could help address these bottlenecks by speeding up design. Unfortunately, a high-yielding cell-free gene expression (CFE) system from clostridia has yet to be developed. Here, we report the development and optimization of a high-yielding (236 ± 24 μg/mL) batch CFE platform from the industrially relevant anaerobe, Clostridium autoethanogenum. A key feature of the platform is that both circular and linear DNA templates can be applied directly to the CFE reaction to program protein synthesis. We demonstrate the ability to prototype gene expression, and quantitatively map aerobic cell-free metabolism in lysates from this system. We anticipate that the C. autoethanogenum CFE platform will not only expand the protein synthesis toolkit for synthetic biology, but also serve as a platform in expediting the screening and prototyping of gene regulatory elements in non-model, industrially relevant microbes.
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21
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Abstract
Cell-free systems are a widely used research tool in systems and synthetic biology and a promising platform for manufacturing of proteins and chemicals. In the past, cell-free biology was primarily used to better understand fundamental biochemical processes. Notably, E. coli cell-free extracts were used in the 1960s to decipher the sequencing of the genetic code. Since then, the transcription and translation capabilities of cell-free systems have been repeatedly optimized to improve energy efficiency and product yield. Today, cell-free systems, in combination with the rise of synthetic biology, have taken on a new role as a promising technology for just-in-time manufacturing of therapeutically important biologics and high-value small molecules. They have also been implemented at an industrial scale for the production of antibodies and cytokines. In this review, we discuss the evolution of cell-free technologies, in particular advancements in extract preparation, cell-free protein synthesis, and cell-free metabolic engineering applications. We then conclude with a discussion of the mathematical modeling of cell-free systems. Mathematical modeling of cell-free processes could be critical to addressing performance bottlenecks and estimating the costs of cell-free manufactured products.
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22
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Gregorio NE, Kao WY, Williams LC, Hight CM, Patel P, Watts KR, Oza JP. Unlocking Applications of Cell-Free Biotechnology through Enhanced Shelf Life and Productivity of E. coli Extracts. ACS Synth Biol 2020; 9:766-778. [PMID: 32083847 DOI: 10.1021/acssynbio.9b00433] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cell-free protein synthesis (CFPS) is a platform biotechnology that enables a breadth of applications. However, field applications remain limited due to the poor shelf-stability of aqueous cell extracts required for CFPS. Lyophilization of E. coli extracts improves shelf life but remains insufficient for extended storage at room temperature. To address this limitation, we mapped the chemical space of ten low-cost additives with four distinct mechanisms of action in a combinatorial manner to identify formulations capable of stabilizing lyophilized cell extract. We report three key findings: (1) unique additive formulations that maintain full productivity of cell extracts stored at 4 °C and 23 °C; (2) additive formulations that enhance extract productivity by nearly 2-fold; (3) a machine learning algorithm that provides predictive capacity for the stabilizing effects of additive formulations that were not tested experimentally. These findings provide a simple and low-cost advance toward making CFPS field-ready and cost-competitive for biomanufacturing.
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Affiliation(s)
- Nicole E. Gregorio
- Chemistry and Biochemistry Department, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Wesley Y. Kao
- Chemistry and Biochemistry Department, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Layne C. Williams
- Chemistry and Biochemistry Department, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Christopher M. Hight
- Chemistry and Biochemistry Department, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Pratish Patel
- Department of Finance, Orfalea College of Business, California Polytechnic State University, San Luis Obispo, California 93407, United States
| | - Katharine R. Watts
- Chemistry and Biochemistry Department, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Javin P. Oza
- Chemistry and Biochemistry Department, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
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23
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Niu FX, Huang YB, Shen YP, Ji LN, Liu JZ. Enhanced Production of Pinene by Using a Cell-Free System with Modular Cocatalysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:2139-2145. [PMID: 31973519 DOI: 10.1021/acs.jafc.9b07830] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
α-Pinene is an important monoterpene that is widely used as a pharmaceutical product, biofuel, and so forth. We first established a cell-free system with modular cocatalysis for the production of pinene from glucose. After optimization of the compositions of the cell-free reaction mixture using the Plackett-Burman experimental design and the path of steepest ascent, the production of pinene increased by 57%. It was found that ammonium acetate, NAD+, and NADPH are the three most important parameters for the production of pinene. Mix-and-match experiments showed that the simultaneous addition of the lysate of Escherichia coli overexpressing native 4-hydroxy-3-methylbut-2-enyl diphosphate reductase, SufBCD Fe-S cluster assembly protein, isopentenyl-diphosphate isomerase, and Pinus taeda pinene synthase improved the production of pinene. Increasing the enzyme concentration of the extract further enhanced the production of pinene to 1256.31 ± 46.12 mg/L with a productivity of 104.7 mg/L h, almost 1.2-fold faster than any system reported thus far. This study demonstrates that a cell-free system is a powerful and robust platform for biomanufacture.
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Affiliation(s)
- Fu-Xing Niu
- Institute of Synthetic Biology, MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Life Sciences , Sun Yat-Sen University , Guangzhou 510275 , China
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences , Hubei University , Wuhan 430062 , China
| | - Yuan-Bin Huang
- Institute of Synthetic Biology, MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Life Sciences , Sun Yat-Sen University , Guangzhou 510275 , China
| | - Yu-Ping Shen
- Institute of Synthetic Biology, MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Life Sciences , Sun Yat-Sen University , Guangzhou 510275 , China
| | - Liang-Nian Ji
- Institute of Synthetic Biology, MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Life Sciences , Sun Yat-Sen University , Guangzhou 510275 , China
| | - Jian-Zhong Liu
- Institute of Synthetic Biology, MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Life Sciences , Sun Yat-Sen University , Guangzhou 510275 , China
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24
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Gregorio NE, Levine MZ, Oza JP. A User's Guide to Cell-Free Protein Synthesis. Methods Protoc 2019; 2:E24. [PMID: 31164605 PMCID: PMC6481089 DOI: 10.3390/mps2010024] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/05/2019] [Accepted: 03/06/2019] [Indexed: 02/06/2023] Open
Abstract
Cell-free protein synthesis (CFPS) is a platform technology that provides new opportunities for protein expression, metabolic engineering, therapeutic development, education, and more. The advantages of CFPS over in vivo protein expression include its open system, the elimination of reliance on living cells, and the ability to focus all system energy on production of the protein of interest. Over the last 60 years, the CFPS platform has grown and diversified greatly, and it continues to evolve today. Both new applications and new types of extracts based on a variety of organisms are current areas of development. However, new users interested in CFPS may find it challenging to implement a cell-free platform in their laboratory due to the technical and functional considerations involved in choosing and executing a platform that best suits their needs. Here we hope to reduce this barrier to implementing CFPS by clarifying the similarities and differences amongst cell-free platforms, highlighting the various applications that have been accomplished in each of them, and detailing the main methodological and instrumental requirement for their preparation. Additionally, this review will help to contextualize the landscape of work that has been done using CFPS and showcase the diversity of applications that it enables.
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Affiliation(s)
- Nicole E Gregorio
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
| | - Max Z Levine
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
| | - Javin P Oza
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
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25
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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: 4.0] [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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26
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Expanding biological applications using cell-free metabolic engineering: An overview. Metab Eng 2018; 50:156-172. [PMID: 30367967 DOI: 10.1016/j.ymben.2018.09.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 09/21/2018] [Accepted: 09/22/2018] [Indexed: 11/21/2022]
Abstract
Expanding the concept of cell-free biology, implemented both with purified components and crude extracts, is continuing to deepen our appreciation of biological fundamentals while enlarging the range of applications. We are no longer intimidated by the complexity of crude extracts and complicated reaction systems with hundreds of active components, and, instead, coordinately activate and inactivate metabolic processes to focus and expand the capabilities of natural biological processes. This, in turn, dramatically increases the range of benefits offered by new products, both natural and supernatural, that were previously infeasible and/or unimaginable. This overview of cell-free metabolic engineering provides a broad range of examples and insights to guide and motivate continued research that will further expand fundamental understanding and beneficial applications. However, this survey also reveals how far we are from fully unlocking the potential offered by natural and engineered biological components and systems. This is an exciting conclusion, but metabolic engineering by itself is not sufficient. Going forward, innovative metabolic engineering must be intimately combined with creative process engineering to fully realize potential contributions toward a sustainable global civilization.
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27
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Failmezger J, Scholz S, Blombach B, Siemann-Herzberg M. Cell-Free Protein Synthesis From Fast-Growing Vibrio natriegens. Front Microbiol 2018; 9:1146. [PMID: 29910785 PMCID: PMC5992293 DOI: 10.3389/fmicb.2018.01146] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 05/14/2018] [Indexed: 12/02/2022] Open
Abstract
Vibrio natriegens constitutes one of the fastest-growing nonpathogenic bacteria and a potential novel workhorse for many biotechnological applications. Here, we report the development of a Vibrio-based cell-free protein synthesis system (CFPS). Specifically, up to 0.4 g L-1 eGFP could be successfully synthesized in small-scale batch reactions using cell-free extract obtained from fast-growing V. natriegens cultures. Versatile CFPS system characterization attained by combining the analyses of key metabolites for translation and ribosomes revealed limitations regarding rRNA stability and critical substrate consumption (e.g., amino acids). Alternatively, rRNA showed increased stability by inducing Mg2+homeostasis in the reaction. Although the enormous translation capacity of the CFPS system based on the available ribosome concentration could not yet be fully exploited, its potential was successfully demonstrated by activating an endogenous transcription unit with V. natriegensRNA polymerase (RNAP) for protein expression. This allowed the use of in vitro screening for promoter strength, a critical factor for efficient gene expression in vitro and in vivo. Three different promoters were tested and output signals corresponded well with the expected affinity for V. natriegens RNAP. This established CFPS toolbox may provide a foundation to establish V. natriegens as a valuable platform in biotechnology as well as synthetic biology.
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Cell-free protein synthesis from genomically recoded bacteria enables multisite incorporation of noncanonical amino acids. Nat Commun 2018; 9:1203. [PMID: 29572528 PMCID: PMC5865108 DOI: 10.1038/s41467-018-03469-5] [Citation(s) in RCA: 147] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 02/13/2018] [Indexed: 12/24/2022] Open
Abstract
Cell-free protein synthesis has emerged as a powerful approach for expanding the range of genetically encoded chemistry into proteins. Unfortunately, efforts to site-specifically incorporate multiple non-canonical amino acids into proteins using crude extract-based cell-free systems have been limited by release factor 1 competition. Here we address this limitation by establishing a bacterial cell-free protein synthesis platform based on genomically recoded Escherichia coli lacking release factor 1. This platform was developed by exploiting multiplex genome engineering to enhance extract performance by functionally inactivating negative effectors. Our most productive cell extracts enabled synthesis of 1,780 ± 30 mg/L superfolder green fluorescent protein. Using an optimized platform, we demonstrated the ability to introduce 40 identical p-acetyl-l-phenylalanine residues site specifically into an elastin-like polypeptide with high accuracy of incorporation ( ≥ 98%) and yield (96 ± 3 mg/L). We expect this cell-free platform to facilitate fundamental understanding and enable manufacturing paradigms for proteins with new and diverse chemistries. Cell-free protein synthesis allows for producing proteins without the need of a host organism, thus sparing the researcher experimental hassle. Here, the authors developed a cell-free synthesis method that enables incorporating non-standard amino acids in the product.
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Kapoor N, Vanjak I, Rozzelle J, Berges A, Chan W, Yin G, Tran C, Sato AK, Steiner AR, Pham TP, Birkett AJ, Long CA, Fairman J, Miura K. Malaria Derived Glycosylphosphatidylinositol Anchor Enhances Anti-Pfs25 Functional Antibodies That Block Malaria Transmission. Biochemistry 2018; 57:516-519. [PMID: 29323879 PMCID: PMC5803671 DOI: 10.1021/acs.biochem.7b01099] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
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Malaria,
one of the most common vector borne human diseases, is a major world
health issue. In 2015 alone, more than 200 million people were infected
with malaria, out of which, 429 000 died. Even though artemisinin-based
combination therapies (ACT) are highly effective at treating malaria
infections, novel efforts toward development of vaccines to prevent
transmission are still needed. Pfs25, a postfertilization stage parasite
surface antigen, is a leading transmission-blocking vaccine (TBV)
candidate. It is postulated that Pfs25 anchors to the cell membrane
using a glycosylphosphatidylinositol (GPI) linker, which itself possesses
pro-inflammatory properties. In this study, Escherichia coli derived extract (XtractCF+TM) was used in cell free protein
synthesis [CFPS] to successfully express >200 mg/L of recombinant
Pfs25 with a C-terminal non-natural amino acid (nnAA), namely, p-azidomethyl phenylalanine (pAMF), which possesses a reactive
azide group. Thereafter, a unique conjugate vaccine (CV), namely,
Pfs25-GPI was generated with dibenzocyclooctyne (DBCO) derivatized
glycan core of malaria GPI using a simple but highly efficient copper
free click chemistry reaction. In mice immunized with Pfs25 or Pfs25-GPI,
the Pfs25-GPI group showed significantly higher titers compared to
the Pfs25 group. Moreover, only purified IgGs from Pfs25-GPI group
were able to significantly block transmission of parasites to mosquitoes,
as judged by a standard membrane feeding assay [SMFA]. To our knowledge,
this is the first report of the generation of a CV using Pfs25 and
malaria specific GPI where the GPI is shown to enhance the ability
of Pfs25 to elicit transmission blocking antibodies.
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Affiliation(s)
- Neeraj Kapoor
- SutroVax, Inc. , 353 Hatch Drive, Foster City, California 94404, United States
| | - Ivana Vanjak
- SutroVax, Inc. , 353 Hatch Drive, Foster City, California 94404, United States
| | - James Rozzelle
- SutroVax, Inc. , 353 Hatch Drive, Foster City, California 94404, United States
| | - Aym Berges
- SutroVax, Inc. , 353 Hatch Drive, Foster City, California 94404, United States
| | - Wei Chan
- SutroVax, Inc. , 353 Hatch Drive, Foster City, California 94404, United States
| | - Gang Yin
- Sutro Biopharma , 310 Utah, South San Francisco, California 94080, United States
| | - Cuong Tran
- Sutro Biopharma , 310 Utah, South San Francisco, California 94080, United States
| | - Aaron K Sato
- Sutro Biopharma , 310 Utah, South San Francisco, California 94080, United States
| | - Alexander R Steiner
- Sutro Biopharma , 310 Utah, South San Francisco, California 94080, United States
| | - Thao P Pham
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health , Rockville, Maryland 20852, United States
| | - Ashley J Birkett
- PATH's Malaria Vaccine Initiative (MVI) , Washington, D.C. 20001 United States
| | - Carole A Long
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health , Rockville, Maryland 20852, United States
| | - Jeff Fairman
- SutroVax, Inc. , 353 Hatch Drive, Foster City, California 94404, United States
| | - Kazutoyo Miura
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health , Rockville, Maryland 20852, United States
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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: 3.4] [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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31
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Wang P, Chang AY, Novosad V, Chupin VV, Schaller RD, Rozhkova EA. Cell-Free Synthetic Biology Chassis for Nanocatalytic Photon-to-Hydrogen Conversion. ACS NANO 2017; 11:6739-6745. [PMID: 28602073 DOI: 10.1021/acsnano.7b01142] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We report on an entirely man-made nano-bio architecture fabricated through noncovalent assembly of a cell-free expressed transmembrane proton pump and TiO2 semiconductor nanoparticles as an efficient nanophotocatalyst for H2 evolution. The system produces hydrogen at a turnover of about 240 μmol of H2 (μmol protein)-1 h-1 and 17.74 mmol of H2 (μmol protein)-1 h-1 under monochromatic green and white light, respectively, at ambient conditions, in water at neutral pH and room temperature, with methanol as a sacrificial electron donor. Robustness and flexibility of this approach allow for systemic manipulation at the nanoparticle-bio interface toward directed evolution of energy transformation materials and artificial systems.
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Affiliation(s)
- Peng Wang
- Center for Nanoscale Materials, Argonne National Laboratory , 9700 South Cass Avenue, Argonne, Illinois 60439-4855, United States
- State Key Laboratory of Crystal Materials, Shandong University , Jinan, Shandong 250100, People's Republic of China
| | - Angela Y Chang
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Valentyn Novosad
- Materials Science Division, Argonne National Laboratory , Argonne, Illinois 60439-4855, United States
| | - Vladimir V Chupin
- Laboratory Chemistry and Physics of Lipids, Department of General and Applied Physics, Moscow Institute of Physics and Technology , Dolgoprudny, Moscow Region 141701, Russia
| | - Richard D Schaller
- Center for Nanoscale Materials, Argonne National Laboratory , 9700 South Cass Avenue, Argonne, Illinois 60439-4855, United States
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Elena A Rozhkova
- Center for Nanoscale Materials, Argonne National Laboratory , 9700 South Cass Avenue, Argonne, Illinois 60439-4855, United States
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32
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Moore SJ, MacDonald JT, Freemont PS. Cell-free synthetic biology for in vitro prototype engineering. Biochem Soc Trans 2017; 45:785-791. [PMID: 28620040 PMCID: PMC5473021 DOI: 10.1042/bst20170011] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 03/24/2017] [Accepted: 03/31/2017] [Indexed: 12/21/2022]
Abstract
Cell-free transcription-translation is an expanding field in synthetic biology as a rapid prototyping platform for blueprinting the design of synthetic biological devices. Exemplar efforts include translation of prototype designs into medical test kits for on-site identification of viruses (Zika and Ebola), while gene circuit cascades can be tested, debugged and re-designed within rapid turnover times. Coupled with mathematical modelling, this discipline lends itself towards the precision engineering of new synthetic life. The next stages of cell-free look set to unlock new microbial hosts that remain slow to engineer and unsuited to rapid iterative design cycles. It is hoped that the development of such systems will provide new tools to aid the transition from cell-free prototype designs to functioning synthetic genetic circuits and engineered natural product pathways in living cells.
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Affiliation(s)
- Simon J Moore
- Department of Medicine, Centre for Synthetic Biology and Innovation, South Kensington Campus, London, U.K
| | - James T MacDonald
- Department of Medicine, Centre for Synthetic Biology and Innovation, South Kensington Campus, London, U.K
| | - Paul S Freemont
- Department of Medicine, Centre for Synthetic Biology and Innovation, South Kensington Campus, London, U.K.
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33
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Karim AS, Jewett MC. A cell-free framework for rapid biosynthetic pathway prototyping and enzyme discovery. Metab Eng 2016; 36:116-126. [PMID: 26996382 DOI: 10.1016/j.ymben.2016.03.002] [Citation(s) in RCA: 160] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 02/12/2016] [Accepted: 03/10/2016] [Indexed: 10/22/2022]
Abstract
Speeding up design-build-test (DBT) cycles is a fundamental challenge facing biochemical engineering. To address this challenge, we report a new cell-free protein synthesis driven metabolic engineering (CFPS-ME) framework for rapid biosynthetic pathway prototyping. In our framework, cell-free cocktails for synthesizing target small molecules are assembled in a mix-and-match fashion from crude cell lysates either containing selectively enriched pathway enzymes from heterologous overexpression or directly producing pathway enzymes in lysates by CFPS. As a model, we apply our approach to n-butanol biosynthesis showing that Escherichia coli lysates support a highly active 17-step CoA-dependent n-butanol pathway in vitro. The elevated degree of flexibility in the cell-free environment allows us to manipulate physiochemical conditions, access enzymatic nodes, discover new enzymes, and prototype enzyme sets with linear DNA templates to study pathway performance. We anticipate that CFPS-ME will facilitate efforts to define, manipulate, and understand metabolic pathways for accelerated DBT cycles without the need to reengineer organisms.
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Affiliation(s)
- Ashty S Karim
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Tech E-136, Evanston, IL 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Tech E-136, Evanston, IL 60208, USA; Chemistry of Life Processes Institute, 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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34
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Zemella A, Thoring L, Hoffmeister C, Kubick S. Cell-Free Protein Synthesis: Pros and Cons of Prokaryotic and Eukaryotic Systems. Chembiochem 2015; 16:2420-31. [PMID: 26478227 PMCID: PMC4676933 DOI: 10.1002/cbic.201500340] [Citation(s) in RCA: 159] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Indexed: 01/07/2023]
Abstract
From its start as a small-scale in vitro system to study fundamental translation processes, cell-free protein synthesis quickly rose to become a potent platform for the high-yield production of proteins. In contrast to classical in vivo protein expression, cell-free systems do not need time-consuming cloning steps, and the open nature provides easy manipulation of reaction conditions as well as high-throughput potential. Especially for the synthesis of difficult to express proteins, such as toxic and transmembrane proteins, cell-free systems are of enormous interest. The modification of the genetic code to incorporate non-canonical amino acids into the target protein in particular provides enormous potential in biotechnology and pharmaceutical research and is in the focus of many cell-free projects. Many sophisticated cell-free systems for manifold applications have been established. This review describes the recent advances in cell-free protein synthesis and details the expanding applications in this field.
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Affiliation(s)
- Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Lena Thoring
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Christian Hoffmeister
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany.
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35
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Lysate of engineered Escherichia coli supports high-level conversion of glucose to 2,3-butanediol. Metab Eng 2015; 32:133-142. [PMID: 26428449 DOI: 10.1016/j.ymben.2015.09.015] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 08/19/2015] [Accepted: 09/18/2015] [Indexed: 01/04/2023]
Abstract
Cell-free metabolic engineering (CFME) is emerging as a powerful approach for the production of target molecules and pathway debugging. Unfortunately, high cofactor costs, limited cofactor and energy regeneration, and low volumetric productivities hamper the widespread use and practical implementation of CFME technology. To address these challenges, we have developed a cell-free system that harnesses ensembles of catalytic proteins prepared from crude lysates, or extracts, of cells to fuel highly active heterologous metabolic conversions. As a model pathway, we selected conversion of glucose to 2,3-butanediol (2,3-BD), a medium level commodity chemical with many industrial applications. Specifically, we engineered a single strain of Escherichia coli to express three pathway enzymes necessary to make meso-2,3-BD (m2,3-BD). We then demonstrated that lysates from this strain, with addition of glucose and catalytic amounts of cofactors NAD+ and ATP, can produce m2,3-BD. Endogenous glycolytic enzymes convert glucose to pyruvate, the starting intermediate for m2,3-BD synthesis. Strikingly, with no strain optimization, we observed a maximal synthesis rate of m2,3-BD of 11.3 ± 0.1 g/L/h with a theoretical yield of 71% (0.36 g m2,3-BD/g glucose) in batch reactions. Titers reached 82 ± 8 g/L m2,3-BD in a 30 h fed-batch reaction. Our results highlight the ability for high-level co-factor regeneration in cell-free lysates. Further, they suggest exciting opportunities to use lysate-based systems to rapidly prototype metabolic pathways and carry out molecular transformations when bioconversion yields (g product/L), productivities (g product/L/h), or cellular toxicity limit commercial feasibility of whole-cell fermentation.
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36
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Robust production of recombinant phosphoproteins using cell-free protein synthesis. Nat Commun 2015; 6:8168. [PMID: 26350765 PMCID: PMC4566161 DOI: 10.1038/ncomms9168] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 07/25/2015] [Indexed: 01/18/2023] Open
Abstract
Understanding the functional and structural consequences of site-specific protein phosphorylation has remained limited by our inability to produce phosphoproteins at high yields. Here we address this limitation by developing a cell-free protein synthesis (CFPS) platform that employs crude extracts from a genomically recoded strain of Escherichia coli for site-specific, co-translational incorporation of phosphoserine into proteins. We apply this system to the robust production of up to milligram quantities of human MEK1 kinase. Then, we recapitulate a physiological signalling cascade in vitro to evaluate the contributions of site-specific phosphorylation of mono- and doubly phosphorylated forms on MEK1 activity. We discover that only one phosphorylation event is necessary and sufficient for MEK1 activity. Our work sets the stage for using CFPS as a rapid high-throughput technology platform for direct expression of programmable phosphoproteins containing multiple phosphorylated residues. This work will facilitate study of phosphorylation-dependent structure–function relationships, kinase signalling networks and kinase inhibitor drugs. The inability to produce recombinant phosphoproteins has hindered research into their structure and function. Here the authors develop a cell-free protein synthesis platform to site-specifically incorporate phosphoserine into proteins at high yields, and recapitulate a MEK1 kinase signalling cascade.
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37
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Hong SH, Kwon YC, Martin RW, Des Soye BJ, de Paz AM, Swonger KN, Ntai I, Kelleher NL, Jewett MC. Improving cell-free protein synthesis through genome engineering of Escherichia coli lacking release factor 1. Chembiochem 2015; 16:844-53. [PMID: 25737329 DOI: 10.1002/cbic.201402708] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Indexed: 12/12/2022]
Abstract
Site-specific incorporation of non-standard amino acids (NSAAs) into proteins opens the way to novel biological insights and applications in biotechnology. Here, we describe the development of a high yielding cell-free protein synthesis (CFPS) platform for NSAA incorporation from crude extracts of genomically recoded Escherichia coli lacking release factor 1. We used genome engineering to construct synthetic organisms that, upon cell lysis, lead to improved extract performance. We targeted five potential negative effectors to be disabled: the nuclease genes rna, rnb, csdA, mazF, and endA. Using our most productive extract from strain MCJ.559 (csdA(-) endA(-)), we synthesized 550±40 μg mL(-1) of modified superfolder green fluorescent protein containing p-acetyl-L-phenylalanine. This yield was increased to ∼1300 μg mL(-1) when using a semicontinuous method. Our work has implications for using whole genome editing for CFPS strain development, expanding the chemistry of biological systems, and cell-free synthetic biology.
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Affiliation(s)
- Seok Hoon Hong
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Tech E-136, Evanston, IL 60208 (USA)
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38
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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: 0.9] [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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Liguori L, Marques B, Villegas-Méndez A, Rothe R, Lenormand JL. Production of membrane proteins using cell–free expression systems. Expert Rev Proteomics 2014; 4:79-90. [PMID: 17288517 DOI: 10.1586/14789450.4.1.79] [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] [Indexed: 11/08/2022]
Abstract
Different overexpression systems are widely used in the laboratory to produce proteins in a reasonable amount for functional and structural studies. However, to optimize these systems without modifying the cellular functions of the living organism remains a challenging task. Cell-free expression systems have become a convenient method for the high-throughput expression of recombinant proteins, and great effort has been focused on generating high yields of proteins. Furthermore, these systems represent an attractive alternative for producing difficult-to-express proteins, such as membrane proteins. In this review, we highlight the recent improvements of these cell-free expression systems and their direct applications in the fields of membrane proteins production, protein therapy and modern proteomics.
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Affiliation(s)
- Lavinia Liguori
- University Joseph Fourier, HumProTher Laboratory, GREPI, CHU-Grenoble, 38043 Grenoble, France.
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40
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Rosenblum G, Cooperman BS. Engine out of the chassis: cell-free protein synthesis and its uses. FEBS Lett 2013; 588:261-8. [PMID: 24161673 DOI: 10.1016/j.febslet.2013.10.016] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 10/14/2013] [Accepted: 10/15/2013] [Indexed: 12/15/2022]
Abstract
The translation machinery is the engine of life. Extracting the cytoplasmic milieu from a cell affords a lysate capable of producing proteins in concentrations reaching to tens of micromolar. Such lysates, derivable from a variety of cells, allow the facile addition and subtraction of components that are directly or indirectly related to the translation machinery and/or the over-expressed protein. The flexible nature of such cell-free expression systems, when coupled with high throughput monitoring, can be especially suitable for protein engineering studies, allowing one to bypass multiple steps typically required using conventional in vivo protein expression.
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Affiliation(s)
- Gabriel Rosenblum
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, United States.
| | - Barry S Cooperman
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, United States
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41
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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: 3.1] [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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42
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Welsh JP, Lu Y, He XS, Greenberg HB, Swartz JR. Cell-free production of trimeric influenza hemagglutinin head domain proteins as vaccine antigens. Biotechnol Bioeng 2012; 109:2962-9. [PMID: 22729608 DOI: 10.1002/bit.24581] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 06/10/2012] [Accepted: 06/13/2012] [Indexed: 12/11/2022]
Abstract
In order to effectively combat pandemic influenza threats, there is a need for more rapid and robust vaccine production methods. In this article, we demonstrate E. coli-based cell-free protein synthesis (CFPS) as a method to rapidly produce domains from the protein hemagglutinin (HA), which is present on the surface of the influenza virus. The portion of the HA coding sequence for the "head" domain from the 2009 pandemic H1N1 strain was first optimized for E. coli expression. The protein domain was then produced in CFPS reactions and purified in soluble form first as a monomer and then as a trimer by a C-terminal addition of the T4 bacteriophage foldon domain. Production of soluble trimeric HA head domain was enhanced by introducing stabilizing amino acid mutations to the construct in order to avoid aggregation. Trimerization was verified using size exclusion HPLC, and the stabilized HA head domain trimer was more effectively recognized by antibodies from pandemic H1N1 influenza vaccine recipients than was the monomer and also bound to sialic acids more strongly, indicating that the trimers are correctly formed and could be potentially effective as vaccines.
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Affiliation(s)
- John P Welsh
- Department of Chemical Engineering, Stanford University, 381 North-South Mall, Stanford, California 94305-5025, USA
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43
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Abstract
Crude cell-free extracts are useful tools for investigating biochemical phenomena and exploiting complex enzymatic processes such as protein synthesis. Extracts derived from E. coli have been used for over 50 years to study the mechanism of protein synthesis. In addition, these S30 extracts are commonly used as a laboratory tool for protein production. The preparation of S30 extract has been streamlined over the years and now it is a relatively simple process. The procedure described here includes some suggestions for extracts to be used for ribosome display.
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44
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Hodgman CE, Jewett MC. Cell-free synthetic biology: thinking outside the cell. Metab Eng 2011; 14:261-9. [PMID: 21946161 DOI: 10.1016/j.ymben.2011.09.002] [Citation(s) in RCA: 284] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 08/19/2011] [Accepted: 09/09/2011] [Indexed: 01/19/2023]
Abstract
Cell-free synthetic biology is emerging as a powerful approach aimed to understand, harness, and expand the capabilities of natural biological systems without using intact cells. Cell-free systems bypass cell walls and remove genetic regulation to enable direct access to the inner workings of the cell. The unprecedented level of control and freedom of design, relative to in vivo systems, has inspired the rapid development of engineering foundations for cell-free systems in recent years. These efforts have led to programmed circuits, spatially organized pathways, co-activated catalytic ensembles, rational optimization of synthetic multi-enzyme pathways, and linear scalability from the micro-liter to the 100-liter scale. It is now clear that cell-free systems offer a versatile test-bed for understanding why nature's designs work the way they do and also for enabling biosynthetic routes to novel chemicals, sustainable fuels, and new classes of tunable materials. While challenges remain, the emergence of cell-free systems is poised to open the way to novel products that until now have been impractical, if not impossible, to produce by other means.
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Affiliation(s)
- C Eric Hodgman
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
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45
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Welsh JP, Bonomo J, Swartz JR. Localization of BiP to translating ribosomes increases soluble accumulation of secreted eukaryotic proteins in an Escherichia coli cell-free system. Biotechnol Bioeng 2011; 108:1739-48. [PMID: 21351069 PMCID: PMC3120890 DOI: 10.1002/bit.23111] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Revised: 01/04/2011] [Accepted: 02/14/2011] [Indexed: 01/30/2023]
Abstract
The endoplasmic reticulum (ER) resident Hsp70 chaperone, BiP, docks to the Sec translocon and interacts co-translationally with polypeptides entering the ER to encourage proper folding. In order to recreate this interaction in Escherichia coli cell-free protein synthesis (CFPS) reactions, a fusion protein was formed between the ribosome-binding portion of the E. coli protein trigger factor (TF) and BiP. The biophysical affinity to ribosomes as well as the characteristic Hsp70 ATPase activity were both verified for the fusion protein. When added to E. coli-based CFPS reactions, the TF-BiP fusion chaperone increased soluble yields of several protein fragments that are normally secreted through the ER and have poor solubility in typical CFPS reactions. For comparison, a fusion between TF and the native E. coli Hsp70, DnaK, was also constructed. This fusion was also biologically active and increased soluble yields of certain protein targets in CFPS. The TF-BiP fusion described in this study can be seen as a first step in reconstituting and better understanding ER folding pathways in the prokaryotic environment of E. coli CFPS.
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Affiliation(s)
- John P. Welsh
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305
| | - Jeanne Bonomo
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305
| | - James R. Swartz
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305
- Department of Bioengineering, Stanford University, Stanford, CA 94305
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46
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Kovtun O, Mureev S, Jung W, Kubala MH, Johnston W, Alexandrov K. Leishmania cell-free protein expression system. Methods 2011; 55:58-64. [PMID: 21704167 DOI: 10.1016/j.ymeth.2011.06.006] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Revised: 06/02/2011] [Accepted: 06/03/2011] [Indexed: 10/18/2022] Open
Abstract
Cell-free protein expression is an important tool for a rapid production, engineering and labeling of recombinant proteins. However the complex protocols for preparation of eukaryotic cell-free protein expression systems result in high manufacturing costs and limit their utility. Recently we reported a novel cell-free expression system based on the lysate of a fermentable protozoan Leishmania tarentolae. Herein we describe a protocol for high throughput protein expression using Leishmania cell-free lysate. The protocol combines PCR-based synthesis and engineering of translation templates with a combined transcription-translation system. The protocol is adapted to multiwell plate format and allows translation of large protein libraries. In the presented example we translate in vitro and isolate a nearly complete complement of mammalian Rab GTPases. Further applications and developments of the system are discussed.
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Affiliation(s)
- Oleksiy Kovtun
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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47
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Zawada JF, Yin G, Steiner AR, Yang J, Naresh A, Roy SM, Gold DS, Heinsohn HG, Murray CJ. Microscale to manufacturing scale-up of cell-free cytokine production--a new approach for shortening protein production development timelines. Biotechnol Bioeng 2011; 108:1570-8. [PMID: 21337337 PMCID: PMC3128707 DOI: 10.1002/bit.23103] [Citation(s) in RCA: 262] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2010] [Revised: 01/29/2011] [Accepted: 02/07/2011] [Indexed: 11/12/2022]
Abstract
Engineering robust protein production and purification of correctly folded biotherapeutic proteins in cell-based systems is often challenging due to the requirements for maintaining complex cellular networks for cell viability and the need to develop associated downstream processes that reproducibly yield biopharmaceutical products with high product quality. Here, we present an alternative Escherichia coli-based open cell-free synthesis (OCFS) system that is optimized for predictable high-yield protein synthesis and folding at any scale with straightforward downstream purification processes. We describe how the linear scalability of OCFS allows rapid process optimization of parameters affecting extract activation, gene sequence optimization, and redox folding conditions for disulfide bond formation at microliter scales. Efficient and predictable high-level protein production can then be achieved using batch processes in standard bioreactors. We show how a fully bioactive protein produced by OCFS from optimized frozen extract can be purified directly using a streamlined purification process that yields a biologically active cytokine, human granulocyte-macrophage colony-stimulating factor, produced at titers of 700 mg/L in 10 h. These results represent a milestone for in vitro protein synthesis, with potential for the cGMP production of disulfide-bonded biotherapeutic proteins. Biotechnol. Bioeng. 2011; 108:1570–1578. © 2011 Wiley Periodicals, Inc.
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Affiliation(s)
- James F Zawada
- Sutro Biopharma, Inc. 310 Utah Ave. Suite 150, South San Francisco, California 94080, USA
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48
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Schmidt M, Pei L. Synthetic toxicology: where engineering meets biology and toxicology. Toxicol Sci 2011; 120 Suppl 1:S204-24. [PMID: 21068213 DOI: 10.1093/toxsci/kfq339] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
This article examines the implications of synthetic biology (SB) for toxicological sciences. Starting with a working definition of SB, we describe its current subfields, namely, DNA synthesis, the engineering of DNA-based biological circuits, minimal genome research, attempts to construct protocells and synthetic cells, and efforts to diversify the biochemistry of life through xenobiology. Based on the most important techniques, tools, and expected applications in SB, we describe the ramifications of SB for toxicology under the label of synthetic toxicology. We differentiate between cases where SB offers opportunities for toxicology and where SB poses challenges for toxicology. Among the opportunities, we identified the assistance of SB to construct novel toxicity testing platforms, define new toxicity-pathway assays, explore the potential of SB to improve in vivo biotransformation of toxins, present novel biosensors developed by SB for environmental toxicology, discuss cell-free protein synthesis of toxins, reflect on the contribution to toxic use reduction, and the democratization of toxicology through do-it-yourself biology. Among the identified challenges for toxicology, we identify synthetic toxins and novel xenobiotics, biosecurity and dual-use considerations, the potential bridging of toxic substances and infectious agents, and do-it-yourself toxin production.
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Affiliation(s)
- Markus Schmidt
- Organization for International Dialogue and Conflict Management, Biosafety Working Group, 1070 Vienna, Austria.
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49
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Pedersen A, Hellberg K, Enberg J, Karlsson BG. Rational improvement of cell-free protein synthesis. N Biotechnol 2010; 28:218-24. [PMID: 20603235 DOI: 10.1016/j.nbt.2010.06.015] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Accepted: 06/26/2010] [Indexed: 11/25/2022]
Abstract
Experimental design principles were applied on cell-free protein synthesis to optimize performance with regard to the expression yield and the incorporation efficiency of amino acid precursors. A versatile screening platform based on batch-mode cell-free expression and central composite design was used. The performance of different extracts (S12 and S30), the concentration dependence of key components and the effect of different additives were investigated. We find that the initial expression yield can be enhanced twofold to threefold in this manner. The improved conditions comprise a modified S12 extract, optimized concentrations of creatine phosphate and key amino acids, as well as introduction of ketoacid additives. Our results show that current cell-free expression technology is far from optimal and that higher yields and increased utilization of the provided precursors are attainable with further optimization.
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Affiliation(s)
- Anders Pedersen
- Swedish NMR Centre, University of Gothenburg, PO Box 465, SE-40530 Gothenburg, Sweden
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50
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Bonomo J, Welsh JP, Manthiram K, Swartz JR. Comparing the functional properties of the Hsp70 chaperones, DnaK and BiP. Biophys Chem 2010; 149:58-66. [PMID: 20435400 PMCID: PMC3175487 DOI: 10.1016/j.bpc.2010.04.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Revised: 04/05/2010] [Accepted: 04/05/2010] [Indexed: 11/23/2022]
Abstract
The Hsp70 family of molecular chaperones is an essential class of chaperones that is present in many different cell types and cellular compartments. We have compared the bioactivities of the prokaryotic cytosolic Hsp70, DnaK, to that of the eukaryotic Hsp70, BiP, located in the endoplasmic reticulum (ER). Both chaperones helped to prevent protein aggregation. However, only DnaK provided enhanced refolding of denatured proteins. We also tested chaperone folding assistance during translation in the context of cell-free protein synthesis reactions for several protein targets and show that both DnaK and BiP can provide folding assistance under these conditions. Our results support previous reports suggesting that DnaK provides both post-translational and co-translational folding assistance while BiP predominantly provides folding assistance that is contemporaneous with translation.
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Affiliation(s)
- Jeanne Bonomo
- Department of Chemical Engineering, Stanford University, 381 North-South Mall, Stanford, CA 94305-5025, USA.
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