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Schulze C, Hädrich M, Borger J, Rühmann B, Döring M, Sieber V, Thoma F, Blombach B. Investigation of exopolysaccharide formation and its impact on anaerobic succinate production with Vibrio natriegens. Microb Biotechnol 2024; 17:e14277. [PMID: 37256270 PMCID: PMC10832516 DOI: 10.1111/1751-7915.14277] [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: 03/08/2023] [Accepted: 05/16/2023] [Indexed: 06/01/2023] Open
Abstract
Vibrio natriegens is an emerging host for biotechnology due to its high growth and substrate consumption rates. In industrial processes typically fed-batch processes are applied to obtain high space-time yields. In this study, we established an aerobic glucose-limited fed-batch fermentation with the wild type (wt) of V. natriegens which yielded biomass concentrations of up to 28.4 gX L-1 . However, we observed that the viscosity of the culture broth increased by a factor of 800 at the end of the cultivation due to the formation of 157 ± 20 mg exopolysaccharides (EPS) L-1 . Analysis of the genomic repertoire revealed several genes and gene clusters associated with EPS formation. Deletion of the transcriptional regulator cpsR in V. natriegens wt did not reduce EPS formation, however, it resulted in a constantly low viscosity of the culture broth and altered the carbohydrate content of the EPS. A mutant lacking the cps cluster secreted two-fold less EPS compared to the wt accompanied by an overall low viscosity and a changed EPS composition. When we cultivated the succinate producer V. natriegens Δlldh Δdldh Δpfl Δald Δdns::pycCg (Succ1) under anaerobic conditions on glucose, we also observed an increased viscosity at the end of the cultivation. Deletion of cpsR and the cps cluster in V. natriegens Succ1 reduced the viscosity five- to six-fold which remained at the same level observed at the start of the cultivation. V. natriegens Succ1 ΔcpsR and V. natriegens Succ1 Δcps achieved final succinate concentrations of 51 and 46 g L-1 with a volumetric productivity of 8.5 and 7.7 gSuc L-1 h-1 , respectively. Both strains showed a product yield of about 1.4 molSuc molGlc -1 , which is 27% higher compared with that of V. natriegens Succ1 and corresponds to 81% of the theoretical maximum.
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Affiliation(s)
- Clarissa Schulze
- Microbial Biotechnology, Campus Straubing for Biotechnology and SustainabilityTechnical University of MunichStraubingGermany
| | - Maurice Hädrich
- Microbial Biotechnology, Campus Straubing for Biotechnology and SustainabilityTechnical University of MunichStraubingGermany
| | - Jennifer Borger
- Microbial Biotechnology, Campus Straubing for Biotechnology and SustainabilityTechnical University of MunichStraubingGermany
| | - Broder Rühmann
- Chemistry of Biogenic Resources, Campus Straubing for Biotechnology and SustainabilityTechnical University of MunichStraubingGermany
| | - Manuel Döring
- Chemistry of Biogenic Resources, Campus Straubing for Biotechnology and SustainabilityTechnical University of MunichStraubingGermany
| | - Volker Sieber
- Chemistry of Biogenic Resources, Campus Straubing for Biotechnology and SustainabilityTechnical University of MunichStraubingGermany
- SynBiofoundry@TUMTechnical University of MunichStraubingGermany
| | - Felix Thoma
- Microbial Biotechnology, Campus Straubing for Biotechnology and SustainabilityTechnical University of MunichStraubingGermany
- SynBiofoundry@TUMTechnical University of MunichStraubingGermany
| | - Bastian Blombach
- Microbial Biotechnology, Campus Straubing for Biotechnology and SustainabilityTechnical University of MunichStraubingGermany
- SynBiofoundry@TUMTechnical University of MunichStraubingGermany
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2
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Rolf J, Handke J, Burzinski F, Lütz S, Rosenthal K. Amino acid balancing for the prediction and evaluation of protein concentrations in cell-free protein synthesis systems. Biotechnol Prog 2023; 39:e3373. [PMID: 37408088 DOI: 10.1002/btpr.3373] [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: 03/12/2023] [Revised: 05/31/2023] [Accepted: 06/19/2023] [Indexed: 07/07/2023]
Abstract
Cell-free protein synthesis (CFPS) systems are an attractive method to complement the usual cell-based synthesis of proteins, especially for screening approaches. The literature describes a wide variety of CFPS systems, but their performance is difficult to compare since the reaction components are often used at different concentrations. Therefore, we have developed a calculation tool based on amino acid balancing to evaluate the performance of CFPS by determining the fractional yield as the ratio between theoretically achievable and experimentally achieved protein molar concentration. This tool was applied to a series of experiments from our lab and to various systems described in the literature to identify systems that synthesize proteins very efficiently and those that still have potential for higher yields. The well-established Escherichia coli system showed a high efficiency in the utilization of amino acids, but interestingly, less considered systems, such as those based on Vibrio natriegens or Leishmania tarentolae, also showed exceptional fractional yields of over 70% and 90%, respectively, implying very efficient conversions of amino acids. The methods and tools described here can quickly identify when a system has reached its maximum or has limitations. We believe that this approach will facilitate the evaluation and optimization of existing CFPS systems and provides the basis for the systematic development of new CFPS systems.
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Affiliation(s)
- Jascha Rolf
- Department of Biochemical and Chemical Engineering, Chair for Bioprocess Engineering, TU Dortmund University, Dortmund, Germany
| | - Julian Handke
- Department of Biochemical and Chemical Engineering, Chair for Bioprocess Engineering, TU Dortmund University, Dortmund, Germany
| | - Frank Burzinski
- Department of Biochemical and Chemical Engineering, Chair for Bioprocess Engineering, TU Dortmund University, Dortmund, Germany
| | - Stephan Lütz
- Department of Biochemical and Chemical Engineering, Chair for Bioprocess Engineering, TU Dortmund University, Dortmund, Germany
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3
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Smith AD, Tschirhart T, Compton J, Hennessa TM, VanArsdale E, Wang Z. Rapid, high-titer biosynthesis of melanin using the marine bacterium Vibrio natriegens. Front Bioeng Biotechnol 2023; 11:1239756. [PMID: 37781538 PMCID: PMC10534004 DOI: 10.3389/fbioe.2023.1239756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/25/2023] [Indexed: 10/03/2023] Open
Abstract
Melanin is one of the most abundant natural biomolecules on Earth. These macromolecular biopolymers display several unique physical and chemical properties and have garnered interest as biomaterials for various commercial and industrial applications. To this end, extensive research has gone into refining methods for the synthesis and extraction of melanin from natural and recombinant sources. In this study, we developed and refined a procedure using a recombinant microbial system for the biosynthesis of melanin using the tyrosinase enzyme Tyr1 and tyrosine as a substrate. Using the emergent microbial chassis organisms Vibrio natriegens, we achieved maximal yields of 7.57 g/L, and one of the highest reported volumetric productivities of 473 mg L-1 h-1 with 100% conversion rates in an optimized, minimally defined medium. Additionally, we identified and investigated the use of a native copper responsive promoter in V. natriegens for stringent regulation of heterologous protein expression as a cost effective alternative to traditional IPTG-based induction. This research represents a promising advancement towards a green, rapid, and economical alternative for the biomanufacture of melanin.
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Affiliation(s)
- Aaron D. Smith
- United States Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, Washington, DC, United States
- College of Science, George Mason University, Fairfax, VA, United States
| | - Tanya Tschirhart
- United States Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, Washington, DC, United States
| | - Jaimee Compton
- United States Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, Washington, DC, United States
| | - Tiffany M. Hennessa
- American Society for Engineering Education Postdoctoral Research Associate, United States Naval Research Laboratory, Washington, DC, United States
| | - Eric VanArsdale
- National Research Council Postdoctoral Research Associate, United States Naval Research Laboratory, Washington, DC, United States
| | - Zheng Wang
- United States Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, Washington, DC, United States
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4
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Liu J, Hu Y, Gu W, Lan H, Zhang Z, Jiang L, Xu X. Research progress on the application of cell-free synthesis systems for enzymatic processes. Crit Rev Biotechnol 2023; 43:938-955. [PMID: 35994247 DOI: 10.1080/07388551.2022.2090314] [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: 10/13/2021] [Revised: 02/24/2022] [Accepted: 04/09/2022] [Indexed: 11/03/2022]
Abstract
Cell-free synthesis systems can complete the transcription and translation process in vitro to produce complex proteins that are difficult to be expressed in traditional cell-based systems. Such systems also can be used for the assembly of efficient localized multienzyme cascades to synthesize products that are toxic to cells. Cell-free synthesis systems provide a simpler and faster engineering solution than living cells, allowing unprecedented design freedom. This paper reviews the latest progress on the application of cell-free synthesis systems in the field of enzymatic catalysis, including cell-free protein synthesis and cell-free metabolic engineering. In cell-free protein synthesis: complex proteins, toxic proteins, membrane proteins, and artificial proteins containing non-natural amino acids can be easily synthesized by directly controlling the reaction conditions in the cell-free system. In cell-free metabolic engineering, the synthesis of desired products can be made more specific and efficient by designing metabolic pathways and screening biocatalysts based on purified enzymes or crude extracts. Through the combination of cell-free synthesis systems and emerging technologies, such as: synthetic biology, microfluidic control, cofactor regeneration, and artificial scaffolds, we will be able to build increasingly complex biomolecule systems. In the next few years, these technologies are expected to mature and reach industrialization, providing innovative platforms for a wide range of biotechnological applications.
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Affiliation(s)
- Jie Liu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Yongqi Hu
- School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Wanyi Gu
- School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Haiquan Lan
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Zhidong Zhang
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Ling Jiang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Xian Xu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
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5
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Brück P, Wasser D, Soppa J. Ploidy in Vibrio natriegens: Very Dynamic and Rapidly Changing Copy Numbers of Both Chromosomes. Genes (Basel) 2023; 14:1437. [PMID: 37510340 PMCID: PMC10379091 DOI: 10.3390/genes14071437] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 07/05/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Vibrio natriegens is the fastest-growing bacterium, with a doubling time of approximately 12-14 min. It has a high potential for basic research and biotechnological applications, e.g., it can be used for the cell-free production of (labeled) heterologous proteins, for synthetic biological applications, and for the production of various compounds. However, the ploidy level in V. natriegens remains unknown. At nine time points throughout the growth curve, we analyzed the numbers of origins and termini of both chromosomes with qPCR and the relative abundances of all genomic sites with marker frequency analyses. During the lag phase until early exponential growth, the origin copy number and origin/terminus ratio of chromosome 1 increased severalfold, but the increase was lower for chromosome 2. This increase was paralleled by an increase in cell volume. During the exponential phase, the origin/terminus ratio and cell volume decreased again. This highly dynamic and fast regulation has not yet been described for any other species. In this study, the gene dosage increase in origin-adjacent genes during the lag phase is discussed together with the nonrandom distribution of genes on the chromosomes of V. natriegens. Taken together, the results of this study provide the first comprehensive overview of the chromosome dynamics in V. natriegens and will guide the optimization of molecular biological characterization and biotechnological applications.
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Affiliation(s)
- Patrik Brück
- Institute for Molecular Biosciences, Goethe University, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
| | - Daniel Wasser
- Institute for Molecular Biosciences, Goethe University, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
| | - Jörg Soppa
- Institute for Molecular Biosciences, Goethe University, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
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6
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João J, Prazeres DMF. Manufacturing of non-viral protein nanocages for biotechnological and biomedical applications. Front Bioeng Biotechnol 2023; 11:1200729. [PMID: 37520292 PMCID: PMC10374429 DOI: 10.3389/fbioe.2023.1200729] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/05/2023] [Indexed: 08/01/2023] Open
Abstract
Protein nanocages are highly ordered nanometer scale architectures, which are typically formed by homo- or hetero-self-assembly of multiple monomers into symmetric structures of different size and shape. The intrinsic characteristics of protein nanocages make them very attractive and promising as a biological nanomaterial. These include, among others, a high surface/volume ratio, multi-functionality, ease to modify or manipulate genetically or chemically, high stability, mono-dispersity, and biocompatibility. Since the beginning of the investigation into protein nanocages, several applications were conceived in a variety of areas such as drug delivery, vaccine development, bioimaging, biomineralization, nanomaterial synthesis and biocatalysis. The ability to generate large amounts of pure and well-folded protein assemblies is one of the keys to transform nanocages into clinically valuable products and move biomedical applications forward. This calls for the development of more efficient biomanufacturing processes and for the setting up of analytical techniques adequate for the quality control and characterization of the biological function and structure of nanocages. This review concisely covers and overviews the progress made since the emergence of protein nanocages as a new, next-generation class of biologics. A brief outline of non-viral protein nanocages is followed by a presentation of their main applications in the areas of bioengineering, biotechnology, and biomedicine. Afterwards, we focus on a description of the current processes used in the manufacturing of protein nanocages with particular emphasis on the most relevant aspects of production and purification. The state-of-the-art on current characterization techniques is then described and future alternative or complementary approaches in development are also discussed. Finally, a critical analysis of the limitations and drawbacks of the current manufacturing strategies is presented, alongside with the identification of the major challenges and bottlenecks.
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Affiliation(s)
- Jorge João
- iBB–Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB–Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Duarte Miguel F. Prazeres
- iBB–Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB–Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
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7
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Dinglasan JLN, Sword TT, Barker JW, Doktycz MJ, Bailey CB. Investigating and Optimizing the Lysate-Based Expression of Nonribosomal Peptide Synthetases Using a Reporter System. ACS Synth Biol 2023; 12:1447-1460. [PMID: 37039644 PMCID: PMC11236431 DOI: 10.1021/acssynbio.2c00658] [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: 04/12/2023]
Abstract
Lysate-based cell-free expression (CFE) systems are accessible platforms for expressing proteins that are difficult to synthesize in vivo, such as nonribosomal peptide synthetases (NRPSs). NRPSs are large (>100 kDa), modular enzyme complexes that synthesize bioactive peptide natural products. This synthetic process is analogous to transcription/translation (TX/TL) in lysates, resulting in potential resource competition between NRPS expression and NRPS activity in cell-free environments. Moreover, CFE conditions depend on the size and structure of the protein. Here, a reporter system for rapidly investigating and optimizing reaction environments for NRPS CFE is described. This strategy is demonstrated in E. coli lysate reactions using blue pigment synthetase A (BpsA), a model NRPS, carrying a C-terminal tetracysteine (TC) tag which forms a fluorescent complex with the biarsenical dye, FlAsH. A colorimetric assay was adapted for lysate reactions to detect the blue pigment product, indigoidine, of cell-free expressed BpsA-TC, confirming that the tagged enzyme is catalytically active. An optimized protocol for end point TC/FlAsH complex measurements in reactions enables quick comparisons of full-length BpsA-TC expressed under different reaction conditions, defining unique requirements for NRPS expression that are related to the protein's catalytic activity and size. Importantly, these protein-dependent CFE conditions enable higher indigoidine titer and improve the expression of other monomodular NRPSs. Notably, these conditions differ from those used for the expression of superfolder GFP (sfGFP), a common reporter for optimizing lysate-based CFE systems, indicating the necessity for tailored reporters to optimize expression for specific enzyme classes. The reporter system is anticipated to advance lysate-based CFE systems for complex enzyme synthesis, enabling natural product discovery.
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Affiliation(s)
- Jaime Lorenzo N Dinglasan
- Graduate School of Genome Science & Technology, University of Tennessee-Knoxville, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Tien T Sword
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, Tennessee 37996, United States
| | - J William Barker
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, Tennessee 37996, United States
| | - Mitchel J Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Constance B Bailey
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, Tennessee 37996, United States
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8
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Multiple Gene Expression in Cell-Free Protein Synthesis Systems for Reconstructing Bacteriophages and Metabolic Pathways. Microorganisms 2022; 10:microorganisms10122477. [PMID: 36557730 PMCID: PMC9786908 DOI: 10.3390/microorganisms10122477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/10/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
As a fast and reliable technology with applications in diverse biological studies, cell-free protein synthesis has become popular in recent decades. The cell-free protein synthesis system can be considered a complex chemical reaction system that is also open to exogenous manipulation, including that which could otherwise potentially harm the cell's viability. On the other hand, since the technology depends on the cell lysates by which genetic information is transformed into active proteins, the whole system resembles the cell to some extent. These features make cell-free protein synthesis a valuable addition to synthetic biology technologies, expediting the design-build-test-learn cycle of synthetic biology routines. While the system has traditionally been used to synthesize one protein product from one gene addition, recent studies have employed multiple gene products in order to, for example, develop novel bacteriophages, viral particles, or synthetic metabolisms. Thus, we would like to review recent advancements in applying cell-free protein synthesis technology to synthetic biology, with an emphasis on multiple gene expressions.
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9
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Mahler M, Costa AR, van Beljouw SPB, Fineran PC, Brouns SJJ. Approaches for bacteriophage genome engineering. Trends Biotechnol 2022; 41:669-685. [PMID: 36117025 DOI: 10.1016/j.tibtech.2022.08.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/08/2022] [Accepted: 08/22/2022] [Indexed: 12/26/2022]
Abstract
In recent years, bacteriophage research has been boosted by a rising interest in using phage therapy to treat antibiotic-resistant bacterial infections. In addition, there is a desire to use phages and their unique proteins for specific biocontrol applications and diagnostics. However, the ability to manipulate phage genomes to understand and control gene functions, or alter phage properties such as host range, has remained challenging due to a lack of universal selectable markers. Here, we discuss the state-of-the-art techniques to engineer and select desired phage genomes using advances in cell-free methodologies and clustered regularly interspaced short palindromic repeats-CRISPR associated protein (CRISPR-Cas) counter-selection approaches.
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Affiliation(s)
- Marina Mahler
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand; Department of Bionanoscience, Delft University of Technology, Delft, the Netherlands
| | - Ana Rita Costa
- Department of Bionanoscience, Delft University of Technology, Delft, the Netherlands; Kavli Institute of Nanoscience, Delft, the Netherlands
| | - Sam P B van Beljouw
- Department of Bionanoscience, Delft University of Technology, Delft, the Netherlands; Kavli Institute of Nanoscience, Delft, the Netherlands
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand; Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand; Genetics Otago, University of Otago, Dunedin, New Zealand
| | - Stan J J Brouns
- Department of Bionanoscience, Delft University of Technology, Delft, the Netherlands; Kavli Institute of Nanoscience, Delft, the Netherlands.
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10
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Stadler KA, Becker W, Darnhofer B, Birner-Gruenberger R, Zangger K. Overexpression of recombinant proteins containing non-canonical amino acids in Vibrio natriegens: p-azido-L-phenylalanine as coupling site for 19F-tags. Amino Acids 2022; 54:1041-1053. [PMID: 35419750 PMCID: PMC9217835 DOI: 10.1007/s00726-022-03148-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 02/27/2022] [Indexed: 11/26/2022]
Abstract
Vibrio natriegens is the fastest growing organism identified so far. The minimum doubling time of only 9.4 min, the ability to utilize over 60 different carbon sources and its non-pathogenic properties make it an interesting alternative to E. coli as a new production host for recombinant proteins. We investigated the ability of the engineered V. natriegens strain, Vmax™ Express, to incorporate the non-canonical amino acid (ncAA) p-azido-L-phenylalanine (AzF) into recombinant proteins for NMR applications. AzF was incorporated into enhanced yellow fluorescent protein (EYFP) and MlaC, an intermembrane transport protein, by stop codon suppression. AzF incorporation into EYFP resulted in an improved suppression efficiency (SE) of up to 35.5 ± 0.8% and a protein titer of 26.7 ± 0.7 mg/L. The expression levels of MlaC-AzF even exceeded those of E. coli BL21 cells. For the recording of 1H-15N and 19F NMR spectra, EYFP-AzF was expressed and isotopically labeled in minimal medium and the newly introduced azido-group was used as coupling site for NMR sensitive 19F-tags. Our findings show that Vmax is a flexible expression host, suitable for the incorporation of ncAAs in recombinant proteins with the potential to surpass protein yields of E. coli. The presented method suggests the implementation of V. natriegens for expression of isotopically labeled proteins containing ncAAs, which can be chemically modified for the application in protein-observed 19F-NMR.
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Affiliation(s)
- Karina A Stadler
- Institute of Chemistry, University of Graz, Heinrichstrasse 28, 8010, Graz, Austria
| | - Walter Becker
- Institute of Chemistry, University of Graz, Heinrichstrasse 28, 8010, Graz, Austria
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 9, 17177, Stockholm, Sweden
| | - Barbara Darnhofer
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Stiftingtalstrasse 6, 8010, Graz, Austria
- Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse 24, 8010, Graz, Austria
| | - Ruth Birner-Gruenberger
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Stiftingtalstrasse 6, 8010, Graz, Austria
- Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse 24, 8010, Graz, Austria
- Institute of Chemical Technologies and Analytics, Faculty of Technical Chemistry, Technische Universität Wien, Getreidemarkt 9/164, 1060, Vienna, Austria
| | - Klaus Zangger
- Institute of Chemistry, University of Graz, Heinrichstrasse 28, 8010, Graz, Austria.
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11
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Cell-Free Escherichia coli Synthesis System Based on Crude Cell Extracts: Acquisition of Crude Extracts and Energy Regeneration. Processes (Basel) 2022. [DOI: 10.3390/pr10061122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Cell-free synthetic biology is advancing with unprecedented control and design. The development of cell-free biosynthesis involves both pure enzyme and crude enzyme systems. The relatively cheap crude enzyme system is more suitable for the scientific research needs of ordinary laboratories. The key factor in giving full play to the advantages of the system is to obtain high-quality cell crude extract and its energy regeneration system, but there is no systematic report on the development history of these two aspects. Therefore, in this paper, the development history of the process of obtaining crude extract from cell-free biosynthesis was carried out based on Escherichia coli, which is widely used at present, and the energy regeneration system was briefly introduced. Finally, the challenges of current cell-free synthetic systems are discussed.
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12
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Sakai A, Deich CR, Nelissen FHT, Jonker AJ, Bittencourt DMDC, Kempes CP, Wise KS, Heus HA, Huck WTS, Adamala KP, Glass JI. Traditional Protocols and Optimization Methods Lead to Absent Expression in a Mycoplasma Cell-Free Gene Expression Platform. Synth Biol (Oxf) 2022; 7:ysac008. [PMID: 35774105 PMCID: PMC9239315 DOI: 10.1093/synbio/ysac008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 04/11/2022] [Accepted: 05/20/2022] [Indexed: 11/23/2022] Open
Abstract
Cell-free expression (CFE) systems are one of the main platforms for building synthetic cells. A major drawback is the orthogonality of cell-free systems across species. To generate a CFE system compatible with recently established minimal cell constructs, we attempted to optimize a Mycoplasma bacterium-based CFE system using lysates of the genome-minimized cell JCVI-syn3A (Syn3A) and its close phylogenetic relative Mycoplasma capricolum (Mcap). To produce mycoplasma-derived crude lysates, we systematically tested methods commonly used for bacteria, based on the S30 protocol of Escherichia coli. Unexpectedly, after numerous attempts to optimize lysate production methods or composition of feeding buffer, none of the Mcap or Syn3A lysates supported cell-free gene expression. Only modest levels of in vitro transcription of RNA aptamers were observed. While our experimental systems were intended to perform transcription and translation, our assays focused on RNA. Further investigations identified persistently high ribonuclease (RNase) activity in all lysates, despite removal of recognizable nucleases from the respective genomes and attempts to inhibit nuclease activities in assorted CFE preparations. An alternative method using digitonin to permeabilize the mycoplasma cell membrane produced a lysate with diminished RNase activity yet still was unable to support cell-free gene expression. We found that intact mycoplasma cells poisoned E. coli cell-free extracts by degrading ribosomal RNAs, indicating that the mycoplasma cells, even the minimal cell, have a surface-associated RNase activity. However, it is not clear which gene encodes the RNase. This work summarizes attempts to produce mycoplasma-based CFE and serves as a cautionary tale for researchers entering this field.
Graphical Abstract
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Affiliation(s)
- Andrei Sakai
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
| | - Christopher R Deich
- Department of Genetics, Cell Biology and Development, University of Minnesota, 420 Washington Avenue SE, Minneapolis, MN 55455, USA
| | - Frank H T Nelissen
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
| | - Aafke J Jonker
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
| | - Daniela M de C Bittencourt
- The J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USA
- Embrapa Genetic Resources and Biotechnology/National Institute of Science and Technology - Synthetic Biology, Parque Estação Biológica, PqEB, Av. W5 Norte (final), Brasília, DF, 70770-917, Brazil, Norte (final), Brasília, DF, 70770-917, Brazil
| | | | - Kim S Wise
- The J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USA
| | - Hans A Heus
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
| | - Katarzyna P Adamala
- Department of Genetics, Cell Biology and Development, University of Minnesota, 420 Washington Avenue SE, Minneapolis, MN 55455, USA
| | - John I Glass
- The J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USA
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13
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Yasin A, Begum MK, Eshik MME, Punom NJ, Ahmmed S, Rahman MS. Molecular identification and antibiotic resistance patterns of diverse bacteria associated with shrimp PL nurseries of Bangladesh: suspecting Acinetobacter venetianus as future threat. PeerJ 2022; 10:e12808. [PMID: 35223199 PMCID: PMC8868018 DOI: 10.7717/peerj.12808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 12/27/2021] [Indexed: 01/11/2023] Open
Abstract
Shrimp aquaculture has been accomplished with breeding and nursing of shrimp in an artificial environment to fulfill the increasing demand of shrimp consumption worldwide. However, the microbial diseases appear as a serious problem in this industry. The study was designed to identify the diverse bacteria from shrimp PL (post-larvae) nurseries and to profile antibiotic resistance patterns. The rearing water (raw seawater, treated and outlet water) and shrimp PL were collected from eight nurseries of south-west Bangladesh. Using selective agar plates, thirty representative isolates were selected for 16S rRNA gene sequencing, antibiotic susceptibility test and MAR index calculation. Representative isolates were identified as Aeromonas caviae, Pseudomonas monteilii, Shewanella algae, Vibrio alginolyticus, V. brasiliensis, V. natriegens, V. parahaemolyticus, V. shilonii, V. xuii, Zobellella denitrificans which are Gram-negative, and Bacillus licheniformis and B. pumilus which are Gram-positive. Notably, six strains identified as Acinetobacter venetianus might be a concern of risk for shrimp industry. The antibiotic resistance pattern reveals that the strain YWO8-97 (identified as P. monteilii) was resistant to all twelve antibiotics. Ceftazidime was the most powerful antibiotic since most of the studied strains were sensitive against it. The six strains of A. venetianus showed multiple antibiotic resistance patterns. MAR index were ranged from 0.08 to 1.0, and values of 26 isolates were more than 0.2 which means prior high exposure to the antibiotics. From the present study, it can be concluded that shrimp PL nurseries in southern part of Bangladesh are getting contaminated with antibiotic resistant pathogenic bacteria.
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Affiliation(s)
- Abdullah Yasin
- Aquatic Animal Health Group, Department of Fisheries, Faculty of Biological Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Mst. Khadiza Begum
- Aquatic Animal Health Group, Department of Fisheries, Faculty of Biological Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Md. Mostavi Enan Eshik
- Aquatic Animal Health Group, Department of Fisheries, Faculty of Biological Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Nusrat Jahan Punom
- Aquatic Animal Health Group, Department of Fisheries, Faculty of Biological Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Shawon Ahmmed
- Aquatic Animal Health Group, Department of Fisheries, Faculty of Biological Sciences, University of Dhaka, Dhaka, Bangladesh,Brackishwater Station, Bangladesh Fisheries Research Institute (BFRI), Khulna, Bangladesh
| | - Mohammad Shamsur Rahman
- Aquatic Animal Health Group, Department of Fisheries, Faculty of Biological Sciences, University of Dhaka, Dhaka, Bangladesh
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14
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Hiering F, Failmezger J, Siemann-Herzberg M. Preparation and Screening of Cell-Free Extract from Nongrowing Escherichia coli A19 Cells. Methods Mol Biol 2022; 2433:65-73. [PMID: 34985737 DOI: 10.1007/978-1-0716-1998-8_3] [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: 06/14/2023]
Abstract
Cell-free extracts have been researched and continuously streamlined for around 50 years. It is believed that these extracts work best when routinely obtained from exponentially growing cells to capture the most active translation system. Here we report on an active cell-free extract derived from E. coli A19 that was harvested under nongrowing, stressed conditions. Although this process is based on the conventional routine process for the production of S30-extracts, our process is less labor intensive and reduces variability between extracts.
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Affiliation(s)
- Florian Hiering
- Institute of Biochemical Engineering, Universität Stuttgart, Stuttgart, Germany
| | - Jurek Failmezger
- Institute of Biochemical Engineering, Universität Stuttgart, Stuttgart, Germany
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15
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Biosensor-based isolation of amino acid-producing Vibrio natriegens strains. Metab Eng Commun 2021; 13:e00187. [PMID: 34824977 PMCID: PMC8605253 DOI: 10.1016/j.mec.2021.e00187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 10/19/2021] [Accepted: 11/07/2021] [Indexed: 12/28/2022] Open
Abstract
The marine bacterium Vibrio natriegens has recently been demonstrated to be a promising new host for molecular biology and next generation bioprocesses. V. natriegens is a Gram-negative, non-pathogenic slight-halophilic bacterium, with a high nutrient versatility and a reported doubling time of under 10 min. However, V. natriegens is not an established model organism yet, and further research is required to promote its transformation into a microbial workhorse. In this work, the potential of V. natriegens as an amino acid producer was investigated. First, the transcription factor-based biosensor LysG, from Corynebacterium glutamicum, was adapted for expression in V. natriegens to facilitate the detection of positively charged amino acids. A set of different biosensor variants were constructed and characterized, using the expression of a fluorescent protein as sensor output. After random mutagenesis, one of the LysG-based sensors was used to screen for amino acid producer strains. Here, fluorescence-activated cell sorting enabled the selective sorting of highly fluorescent cells, i.e. potential producer cells. Using this approach, individual L-lysine, L-arginine and L-histidine producers could be obtained producing up to 1 mM of the effector amino acid, extracellularly. Genome sequencing of the producer strains provided insight into the amino acid production metabolism of V. natriegens. This work demonstrates the successful expression and application of transcription factor-based biosensors in V. natriegens and provides insight into the underlying physiology, forming a solid basis for further development of this promising microbe. Vibrio natriegens is a promising new host for biotechnology. Transcription factor-based biosensors were expressed in V. natriegens. Mutagenesis and screening using FACS provided amino acid producing mutants. Genome sequencing revealed several causal mutations leading to amino acid production. These results will support further efforts to develop V. natriegens as a production host.
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16
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Stukenberg D, Hensel T, Hoff J, Daniel B, Inckemann R, Tedeschi JN, Nousch F, Fritz G. The Marburg Collection: A Golden Gate DNA Assembly Framework for Synthetic Biology Applications in Vibrio natriegens. ACS Synth Biol 2021; 10:1904-1919. [PMID: 34255476 DOI: 10.1021/acssynbio.1c00126] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Vibrio natriegens is known as the world's fastest growing organism with a doubling time of less than 10 min. This incredible growth speed empowers V. natriegens as a chassis for synthetic and molecular biology, potentially replacing E. coli in many applications. While first genetic parts have been built and tested for V. natriegens, a comprehensive toolkit containing well-characterized and standardized parts did not exist. To close this gap, we created the Marburg Collection-a highly flexible Golden Gate cloning toolbox optimized for the emerging chassis organism V. natriegens, containing 191 genetic parts. The Marburg Collection overcomes the paradigm of plasmid construction-integrating inserts into a backbone-by enabling the de novo assembly of plasmids from basic genetic parts. This allows users to select the plasmid replication origin and resistance part independently, which is highly advantageous when limited knowledge about the behavior of those parts in the target organism is available. Additional design highlights of the Marburg Collection are novel connector parts, which facilitate modular circuit assembly and, optionally, the inversion of individual transcription units to reduce transcriptional crosstalk in multigene constructs. To quantitatively characterize the genetic parts contained in the Marburg Collection in V. natriegens, we developed a reliable microplate reader measurement workflow for reporter experiments and overcame organism-specific challenges. We think the Marburg Collection with its thoroughly characterized parts will provide a valuable resource for the growing V. natriegens community.
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Affiliation(s)
- Daniel Stukenberg
- Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg 35032, Germany
- Max-Planck Institute for Terrestrial Microbiology, Marburg 35043, Germany
| | - Tobias Hensel
- Faculty of Chemistry, Philipps-Universität Marburg, Marburg 35032, Germany
| | - Josef Hoff
- Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg 35032, Germany
- Max-Planck Institute for Terrestrial Microbiology, Marburg 35043, Germany
| | - Benjamin Daniel
- Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg 35032, Germany
- Institute of Microbiology, ETH Zurich, Zürich 8093, Switzerland
| | - René Inckemann
- Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg 35032, Germany
- Max-Planck Institute for Terrestrial Microbiology, Marburg 35043, Germany
| | - Jamie N. Tedeschi
- School of Molecular Sciences, The University of Western Australia, Perth 6009, Australia
| | - Franziska Nousch
- Faculty of Chemistry, Philipps-Universität Marburg, Marburg 35032, Germany
| | - Georg Fritz
- School of Molecular Sciences, The University of Western Australia, Perth 6009, Australia
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17
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Metabolic engineering of Vibrio natriegens. Essays Biochem 2021; 65:381-392. [PMID: 33835156 PMCID: PMC8314017 DOI: 10.1042/ebc20200135] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 12/13/2022]
Abstract
Vibrio natriegens is emerging as a promising host for biotechnology which is basically due to the remarkable intrinsic properties such as the exceptionally high growth and substrate consumption rates. The facultatively anaerobic marine bacterium possesses a versatile metabolism, is able to utilize a variety of substrates as carbon and energy sources and is easy to handle in the lab. These features initiated the rapid development of genetic tools and resulted in extensive engineering of production strains in the past years. Although recent examples illustrate the potential of V. natriegens for biotechnology, a comprehensive understanding of the metabolism and its regulation is still lacking but essential to exploit the full potential of this bacterium. In this review, we summarize the current knowledge on the physiological traits and the genomic organization, provide an overview of the available genetic engineering tools and recent advances in metabolic engineering of V. natriegens. Finally, we discuss the obstacles which have to be overcome in order to establish V. natriegens as industrial production host.
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18
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Norouzi M, Panfilov S, Pardee K. High-Efficiency Protection of Linear DNA in Cell-Free Extracts from Escherichia coli and Vibrio natriegens. ACS Synth Biol 2021; 10:1615-1624. [PMID: 34161082 DOI: 10.1021/acssynbio.1c00110] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The field of cell-free synthetic biology is an emerging branch of engineered biology that allows for rapid prototyping of biological designs and, in its own right, is becoming a venue for the in vitro operation of gene circuit-based sensors and biomanufacturing. To date, the related DNA encoded tools that operate in cell-free reactions have primarily relied on plasmid DNA inputs, as linear templates are highly susceptible to degradation by exonucleases present in cell-free extracts. This incompatibility has precluded significant throughput, time and cost benefits that could be gained with the use of linear DNA in the cell-free expression workflow. Here to tackle this limitation, we report that terminal incorporation of Ter binding sites for the DNA-binding protein Tus enables highly efficient protection of linear expression templates encoding mCherry and deGFP. In Escherichia coli extracts, our method compares favorably with the previously reported GamS-mediated protection scheme. Importantly, we extend the Tus-Ter system to Vibrio natriegens extracts, and demonstrate that this simple and easily implemented method can enable an unprecedented plasmid-level expression from linear templates in this emerging chassis organism.
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Affiliation(s)
- Masoud Norouzi
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Sabina Panfilov
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Keith Pardee
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario M5S 3G8, Canada
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19
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Zhang L, Lin X, Wang T, Guo W, Lu Y. Development and comparison of cell-free protein synthesis systems derived from typical bacterial chassis. BIORESOUR BIOPROCESS 2021; 8:58. [PMID: 34249606 PMCID: PMC8258279 DOI: 10.1186/s40643-021-00413-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 06/29/2021] [Indexed: 12/13/2022] Open
Abstract
Cell-free protein synthesis (CFPS) systems have become an ideal choice for pathway prototyping, protein production, and biosensing, due to their high controllability, tolerance, stability, and ability to produce proteins in a short time. At present, the widely used CFPS systems are mainly based on Escherichia coli strain. Bacillus subtilis, Corynebacterium glutamate, and Vibrio natriegens are potential chassis cells for many biotechnological applications with their respective characteristics. Therefore, to expand the platform of the CFPS systems and options for protein production, four prokaryotes, E. coli, B. subtilis, C. glutamate, and V. natriegens were selected as host organisms to construct the CFPS systems and be compared. Moreover, the process parameters of the CFPS system were optimized, including the codon usage, plasmid synthesis competent cell selection, plasmid concentration, ribosomal binding site (RBS), and CFPS system reagent components. By optimizing and comparing the main influencing factors of different CFPS systems, the systems can be optimized directly for the most influential factors to further improve the protein yield of the systems. In addition, to demonstrate the applicability of the CFPS systems, it was proved that the four CFPS systems all had the potential to produce therapeutic proteins, and they could produce the receptor-binding domain (RBD) protein of SARS-CoV-2 with functional activity. They not only could expand the potential options for in vitro protein production, but also could increase the application range of the system by expanding the cell-free protein synthesis platform. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1186/s40643-021-00413-2.
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Affiliation(s)
- Liyuan Zhang
- Department of Ecology, Shenyang Agricultural University, Shenyang, 110866 Liaoning Province China
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
| | - Xiaomei Lin
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
| | - Ting Wang
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
| | - Wei Guo
- Department of Ecology, Shenyang Agricultural University, Shenyang, 110866 Liaoning Province China
| | - Yuan Lu
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
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20
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Ozer E, Alfonta L. Genetic Code Expansion of Vibrio natriegens. Front Bioeng Biotechnol 2021; 9:594429. [PMID: 33718334 PMCID: PMC7953155 DOI: 10.3389/fbioe.2021.594429] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 01/26/2021] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli has been considered as the most used model bacteria in the majority of studies for several decades. However, a new, faster chassis for synthetic biology is emerging in the form of the fast-growing gram-negative bacterium Vibrio natriegens. Different methodologies, well established in E. coli, are currently being adapted for V. natriegens in the hope to enable a much faster platform for general molecular biology studies. Amongst the vast technologies available for E. coli, genetic code expansion, the incorporation of unnatural amino acids into proteins, serves as a robust tool for protein engineering and biorthogonal modifications. Here we designed and adapted the genetic code expansion methodology for V. natriegens and demonstrate an unnatural amino acid incorporation into a protein for the first time in this organism.
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Affiliation(s)
- Eden Ozer
- Department of Life Sciences, Department of Chemistry and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Lital Alfonta
- Department of Life Sciences, Department of Chemistry and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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21
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Xu J, Dong F, Wu M, Tao R, Yang J, Wu M, Jiang Y, Yang S, Yang L. Vibrio natriegens as a pET-Compatible Expression Host Complementary to Escherichia coli. Front Microbiol 2021; 12:627181. [PMID: 33679648 PMCID: PMC7933001 DOI: 10.3389/fmicb.2021.627181] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 01/18/2021] [Indexed: 12/20/2022] Open
Abstract
Efficient and novel recombinant protein expression systems can further reduce the production cost of enzymes. Vibrio natriegens is the fastest growing free-living bacterium with a doubling time of less than 10 min, which makes it highly attractive as a protein expression host. Here, 196 pET plasmids with different genes of interest (GOIs) were electroporated into the V. natriegens strain VnDX, which carries an integrated T7 RNA polymerase expression cassette. As a result, 65 and 75% of the tested GOIs obtained soluble expression in V. natriegens and Escherichia coli, respectively, 20 GOIs of which showed better expression in the former. Furthermore, we have adapted a consensus "what to try first" protocol for V. natriegens based on Terrific Broth medium. Six sampled GOIs encoding biocatalysts enzymes thus achieved 50-128% higher catalytic efficiency under the optimized expression conditions. Our study demonstrated V. natriegens as a pET-compatible expression host with a spectrum of highly expressed GOIs distinct from E. coli and an easy-to-use consensus protocol, solving the problem that some GOIs cannot be expressed well in E. coli.
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Affiliation(s)
- Jiaqi Xu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Feng Dong
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Huzhou, China
| | - Meixian Wu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Rongsheng Tao
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Huzhou, China.,Huzhou Yisheng Biotechnology Co., Ltd., Huzhou, China
| | - Junjie Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Mianbin Wu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Yu Jiang
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Huzhou, China.,Shanghai Taoyusheng Biotechnology Co., Ltd., Shanghai, China
| | - Sheng Yang
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Huzhou, China.,Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lirong Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
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22
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Cole SD, Miklos AE, Chiao AC, Sun ZZ, Lux MW. Methodologies for preparation of prokaryotic extracts for cell-free expression systems. Synth Syst Biotechnol 2020; 5:252-267. [PMID: 32775710 PMCID: PMC7398980 DOI: 10.1016/j.synbio.2020.07.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 07/22/2020] [Accepted: 07/23/2020] [Indexed: 12/19/2022] Open
Abstract
Cell-free systems that mimic essential cell functions, such as gene expression, have dramatically expanded in recent years, both in terms of applications and widespread adoption. Here we provide a review of cell-extract methods, with a specific focus on prokaryotic systems. Firstly, we describe the diversity of Escherichia coli genetic strains available and their corresponding utility. We then trace the history of cell-extract methodology over the past 20 years, showing key improvements that lower the entry level for new researchers. Next, we survey the rise of new prokaryotic cell-free systems, with associated methods, and the opportunities provided. Finally, we use this historical perspective to comment on the role of methodology improvements and highlight where further improvements may be possible.
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Affiliation(s)
- Stephanie D. Cole
- US Army Combat Capabilities Development Command Chemical Biological Center, 8567 Ricketts Point Road, Aberdeen Proving Ground, MD, 21010, USA
| | - Aleksandr E. Miklos
- US Army Combat Capabilities Development Command Chemical Biological Center, 8567 Ricketts Point Road, Aberdeen Proving Ground, MD, 21010, USA
| | - Abel C. Chiao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Synvitrobio Inc., San Francisco, CA, USA
| | - Zachary Z. Sun
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Synvitrobio Inc., San Francisco, CA, USA
| | - Matthew W. Lux
- US Army Combat Capabilities Development Command Chemical Biological Center, 8567 Ricketts Point Road, Aberdeen Proving Ground, MD, 21010, USA
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23
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Aw R, Spice AJ, Polizzi KM. Methods for Expression of Recombinant Proteins Using a
Pichia pastoris
Cell‐Free System. ACTA ACUST UNITED AC 2020; 102:e115. [DOI: 10.1002/cpps.115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Rochelle Aw
- Imperial College Centre for Synthetic Biology Imperial College London London United Kingdom
- Department of Chemical Engineering Imperial College London London United Kingdom
| | - Alex J. Spice
- Imperial College Centre for Synthetic Biology Imperial College London London United Kingdom
- Department of Chemical Engineering Imperial College London London United Kingdom
| | - Karen M. Polizzi
- Imperial College Centre for Synthetic Biology Imperial College London London United Kingdom
- Department of Chemical Engineering Imperial College London London United Kingdom
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24
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Zhu B, Gan R, Cabezas MD, Kojima T, Nicol R, Jewett MC, Nakano H. Increasing cell-free gene expression yields from linear templates in Escherichia coli and Vibrio natriegens extracts by using DNA-binding proteins. Biotechnol Bioeng 2020; 117:3849-3857. [PMID: 32816360 DOI: 10.1002/bit.27538] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 08/08/2020] [Accepted: 08/17/2020] [Indexed: 12/12/2022]
Abstract
In crude extract-based cell-free protein synthesis (CFPS), DNA templates are transcribed and translated into functional proteins. Although linear expression templates (LETs) are less laborious and expensive to generate, plasmid templates are often desired over polymerase chain reaction-generated LETs due to increased stability and protection against exonucleases present in the extract of the reaction. Here we demonstrate that addition of a double stranded DNA-binding protein to the CFPS reaction, termed single-chain Cro protein (scCro), achieves terminal protection of LETs. This CroP-LET (scCro-based protection of LET) method effectively increases superfolder green fluorescent protein (sfGFP) expression levels from LETs in Escherichia coli CFPS reactions by sixfold. Our yields are comparable to other strategies that provide chemical and enzymatic DNA stabilization in E. coli CFPS. Notably, we also report that the CroP-LET method successfully enhanced yields in CFPS platforms derived from nonmodel organisms. Our results show that CroP-LET increased sfGFP yields by 18-fold in the Vibrio natriegens CFPS platform. With the fast-expanding applications of CFPS platforms, this method provides a practical and generalizable solution to protect linear expression DNA templates.
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Affiliation(s)
- Bo Zhu
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Rui Gan
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois
| | - Maria D Cabezas
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois
| | - Takaaki Kojima
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Robert Nicol
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois.,Center for Synthetic Biology, Northwestern University, Evanston, Illinois.,Simpson Querrey Institute, Northwestern University, Evanston, Illinois.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, Illinois
| | - Hideo Nakano
- Laboratory of Molecular Biotechnology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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25
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Hoff J, Daniel B, Stukenberg D, Thuronyi BW, Waldminghaus T, Fritz G. Vibrio natriegens
: an ultrafast‐growing marine bacterium as emerging synthetic biology chassis. Environ Microbiol 2020; 22:4394-4408. [DOI: 10.1111/1462-2920.15128] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/11/2020] [Accepted: 06/12/2020] [Indexed: 12/28/2022]
Affiliation(s)
- Josef Hoff
- School of Molecular Sciences The University of Western Australia Perth Australia
- Center for Synthetic Microbiology Philipps‐Universität Marburg Marburg Germany
| | - Benjamin Daniel
- Center for Synthetic Microbiology Philipps‐Universität Marburg Marburg Germany
- Institute of Microbiology, ETH Zurich Zürich Switzerland
| | - Daniel Stukenberg
- Center for Synthetic Microbiology Philipps‐Universität Marburg Marburg Germany
| | | | - Torsten Waldminghaus
- Centre for Synthetic Biology Technische Universität Darmstadt Darmstadt Germany
- Department of Biology Technische Universität Darmstadt Darmstadt Germany
| | - Georg Fritz
- School of Molecular Sciences The University of Western Australia Perth Australia
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26
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Zhang L, Liu WQ, Li J. Establishing a Eukaryotic Pichia pastoris Cell-Free Protein Synthesis System. Front Bioeng Biotechnol 2020; 8:536. [PMID: 32626695 PMCID: PMC7314905 DOI: 10.3389/fbioe.2020.00536] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/04/2020] [Indexed: 12/13/2022] Open
Abstract
In recent years, cell-free protein synthesis (CFPS) systems have been used to synthesize proteins, prototype genetic elements, manufacture chemicals, and diagnose diseases. These exciting, novel applications lead to a new wave of interest in the development of new CFPS systems that are derived from prokaryotic and eukaryotic organisms. The eukaryotic Pichia pastoris is emerging as a robust chassis host for recombinant protein production. To expand the current CFPS repertoire, we report here the development and optimization of a eukaryotic CFPS system, which is derived from a protease-deficient strain P. pastoris SMD1163. By developing a simple crude extract preparation protocol and optimizing CFPS reaction conditions, we were able to achieve superfolder green fluorescent protein (sfGFP) yields of 50.16 ± 7.49 μg/ml in 5 h batch reactions. Our newly developed P. pastoris CFPS system fits to the range of the productivity achieved by other eukaryotic CFPS platforms, normally ranging from several to tens of micrograms protein per milliliter in batch mode reactions. Looking forward, we believe that our P. pastoris CFPS system will not only expand the CFPS toolbox for synthetic biology applications, but also provide a novel platform for cost-effective, high-yielding production of complex proteins that need post-translational modification and functionalization.
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Affiliation(s)
| | | | - Jian Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
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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: 24] [Impact Index Per Article: 6.0] [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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Abstract
Proteins are the main source of drug targets and some of them possess therapeutic potential themselves. Among them, membrane proteins constitute approximately 50% of the major drug targets. In the drug discovery pipeline, rapid methods for producing different classes of proteins in a simple manner with high quality are important for structural and functional analysis. Cell-free systems are emerging as an attractive alternative for the production of proteins due to their flexible nature without any cell membrane constraints. In a bioproduction context, open systems based on cell lysates derived from different sources, and with batch-to-batch consistency, have acted as a catalyst for cell-free synthesis of target proteins. Most importantly, proteins can be processed for downstream applications like purification and functional analysis without the necessity of transfection, selection, and expansion of clones. In the last 5 years, there has been an increased availability of new cell-free lysates derived from multiple organisms, and their use for the synthesis of a diverse range of proteins. Despite this progress, major challenges still exist in terms of scalability, cost effectiveness, protein folding, and functionality. In this review, we present an overview of different cell-free systems derived from diverse sources and their application in the production of a wide spectrum of proteins. Further, this article discusses some recent progress in cell-free systems derived from Chinese hamster ovary and Sf21 lysates containing endogenous translocationally active microsomes for the synthesis of membrane proteins. We particularly highlight the usage of internal ribosomal entry site sequences for more efficient protein production, and also the significance of site-specific incorporation of non-canonical amino acids for labeling applications and creation of antibody drug conjugates using cell-free systems. We also discuss strategies to overcome the major challenges involved in commercializing cell-free platforms from a laboratory level for future drug development.
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Affiliation(s)
- Srujan Kumar Dondapati
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Marlitt Stech
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany.
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus-Senftenberg, The Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany.
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Kelwick RJR, Webb AJ, Freemont PS. Biological Materials: The Next Frontier for Cell-Free Synthetic Biology. Front Bioeng Biotechnol 2020; 8:399. [PMID: 32478045 PMCID: PMC7235315 DOI: 10.3389/fbioe.2020.00399] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 04/08/2020] [Indexed: 12/13/2022] Open
Abstract
Advancements in cell-free synthetic biology are enabling innovations in sustainable biomanufacturing, that may ultimately shift the global manufacturing paradigm toward localized and ecologically harmonized production processes. Cell-free synthetic biology strategies have been developed for the bioproduction of fine chemicals, biofuels and biological materials. Cell-free workflows typically utilize combinations of purified enzymes, cell extracts for biotransformation or cell-free protein synthesis reactions, to assemble and characterize biosynthetic pathways. Importantly, cell-free reactions can combine the advantages of chemical engineering with metabolic engineering, through the direct addition of co-factors, substrates and chemicals -including those that are cytotoxic. Cell-free synthetic biology is also amenable to automatable design cycles through which an array of biological materials and their underpinning biosynthetic pathways can be tested and optimized in parallel. Whilst challenges still remain, recent convergences between the materials sciences and these advancements in cell-free synthetic biology enable new frontiers for materials research.
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Affiliation(s)
- Richard J. R. Kelwick
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Alexander J. Webb
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Paul S. Freemont
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
- The London Biofoundry, Imperial College Translation & Innovation Hub, London, United Kingdom
- UK Dementia Research Institute Care Research and Technology Centre, Imperial College London, London, United Kingdom
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Ayoubi-Joshaghani MH, Dianat-Moghadam H, Seidi K, Jahanban-Esfahalan A, Zare P, Jahanban-Esfahlan R. Cell-free protein synthesis: The transition from batch reactions to minimal cells and microfluidic devices. Biotechnol Bioeng 2020; 117:1204-1229. [PMID: 31840797 DOI: 10.1002/bit.27248] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 11/23/2019] [Accepted: 12/09/2019] [Indexed: 12/13/2022]
Abstract
Thanks to the synthetic biology, the laborious and restrictive procedure for producing a target protein in living microorganisms by biotechnological approaches can now experience a robust, pliant yet efficient alternative. The new system combined with lab-on-chip microfluidic devices and nanotechnology offers a tremendous potential envisioning novel cell-free formats such as DNA brushes, hydrogels, vesicular particles, droplets, as well as solid surfaces. Acting as robust microreactors/microcompartments/minimal cells, the new platforms can be tuned to perform various tasks in a parallel and integrated manner encompassing gene expression, protein synthesis, purification, detection, and finally enabling cell-cell signaling to bring a collective cell behavior, such as directing differentiation process, characteristics of higher order entities, and beyond. In this review, we issue an update on recent cell-free protein synthesis (CFPS) formats. Furthermore, the latest advances and applications of CFPS for synthetic biology and biotechnology are highlighted. In the end, contemporary challenges and future opportunities of CFPS systems are discussed.
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Affiliation(s)
| | | | - Khaled Seidi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Peyman Zare
- Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland
| | - Rana Jahanban-Esfahlan
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.,Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
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Schuh LK, Weyler C, Heinzle E. In‐depth characterization of genome‐scale network reconstructions for the in vitro synthesis in cell‐free systems. Biotechnol Bioeng 2020; 117:1137-1147. [DOI: 10.1002/bit.27249] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/25/2019] [Accepted: 12/06/2019] [Indexed: 01/15/2023]
Affiliation(s)
- Lisa Katharina Schuh
- Biochemical Engineering Institute Saarland University Campus A1.5 Saarbrücken Germany
| | - Christian Weyler
- Biochemical Engineering Institute Saarland University Campus A1.5 Saarbrücken Germany
| | - Elmar Heinzle
- Biochemical Engineering Institute Saarland University Campus A1.5 Saarbrücken Germany
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Ellis GA, Tschirhart T, Spangler J, Walper SA, Medintz IL, Vora GJ. Exploiting the Feedstock Flexibility of the Emergent Synthetic Biology Chassis Vibrio natriegens for Engineered Natural Product Production. Mar Drugs 2019; 17:E679. [PMID: 31801279 PMCID: PMC6950413 DOI: 10.3390/md17120679] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/26/2019] [Accepted: 11/28/2019] [Indexed: 12/21/2022] Open
Abstract
A recent goal of synthetic biology has been to identify new chassis that provide benefits lacking in model organisms. Vibrio natriegens is a marine Gram-negative bacterium which is an emergent synthetic biology chassis with inherent benefits: An extremely fast growth rate, genetic tractability, and the ability to grow on a variety of carbon sources ("feedstock flexibility"). Given these inherent benefits, we sought to determine its potential to heterologously produce natural products, and chose beta-carotene and violacein as test cases. For beta-carotene production, we expressed the beta-carotene biosynthetic pathway from the sister marine bacterium Vibrio campbellii, as well as the mevalonate biosynthetic pathway from the Gram-positive bacterium Lactobacillus acidophilus to improve precursor abundance. Violacein was produced by expressing a biosynthetic gene cluster derived from Chromobacterium violaceum. Not only was V. natriegens able to heterologously produce these compounds in rich media, illustrating its promise as a new chassis for small molecule drug production, but it also did so in minimal media using a variety of feedstocks. The ability for V. natriegens to produce natural products with multiple industrially-relevant feedstocks argues for continued investigations into the production of more complex natural products in this chassis.
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Affiliation(s)
- Gregory A. Ellis
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Washington, DC 20375, USA; (G.A.E.); (S.A.W.); (I.L.M.)
| | - Tanya Tschirhart
- American Society for Engineering Education, Postdoctoral Research Associate, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Joseph Spangler
- National Academy of Sciences, National Research Council, Postdoctoral Research Associate, U.S. Naval Research Laboratory, Washington, DC 20375, USA;
| | - Scott A. Walper
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Washington, DC 20375, USA; (G.A.E.); (S.A.W.); (I.L.M.)
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Washington, DC 20375, USA; (G.A.E.); (S.A.W.); (I.L.M.)
| | - Gary J. Vora
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Washington, DC 20375, USA; (G.A.E.); (S.A.W.); (I.L.M.)
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Silverman AD, Karim AS, Jewett MC. Cell-free gene expression: an expanded repertoire of applications. Nat Rev Genet 2019; 21:151-170. [DOI: 10.1038/s41576-019-0186-3] [Citation(s) in RCA: 246] [Impact Index Per Article: 49.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2019] [Indexed: 12/24/2022]
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Tschirhart T, Shukla V, Kelly EE, Schultzhaus Z, NewRingeisen E, Erickson JS, Wang Z, Garcia W, Curl E, Egbert RG, Yeung E, Vora GJ. Synthetic Biology Tools for the Fast-Growing Marine Bacterium Vibrio natriegens. ACS Synth Biol 2019; 8:2069-2079. [PMID: 31419124 DOI: 10.1021/acssynbio.9b00176] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The fast-growing nonmodel marine bacterium Vibrio natriegens has recently garnered attention as a host for molecular biology and biotechnology applications. In order to further its capabilities as a synthetic biology chassis, we have characterized a wide range of genetic parts and tools for use in V. natriegens. These parts include many commonly used resistance markers, promoters, ribosomal binding sites, reporters, terminators, degradation tags, origin of replication sequences, and plasmid backbones. We have characterized the behavior of these parts in different combinations and have compared their functionality in V. natriegens and Escherichia coli. Plasmid stability over time, plasmid copy numbers, and production load on the cells were also evaluated. Additionally, we tested constructs for chemical and optogenetic induction and characterized basic engineered circuit behavior in V. natriegens. The results indicate that, while most parts and constructs work similarly in the two organisms, some deviate significantly. Overall, these results will serve as a primer for anyone interested in engineering V. natriegens and will aid in developing more robust synthetic biology principles and approaches for this nonmodel chassis.
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Affiliation(s)
- Tanya Tschirhart
- American Society for Engineering Education, Postdoctoral Fellowship Program, US Naval Research Laboratory, Washington, DC 20375, United States of America
| | - Vrinda Shukla
- Center for Bio/Molecular Science and Engineering, US Naval Research Laboratory, Washington, DC 20375, United States of America
| | - Erin E. Kelly
- National Research Council, Postdoctoral Fellowship Program, US Naval Research Laboratory, Washington, DC 20375, United States of America
| | - Zachary Schultzhaus
- National Research Council, Postdoctoral Fellowship Program, US Naval Research Laboratory, Washington, DC 20375, United States of America
| | - Erin NewRingeisen
- Center for Bio/Molecular Science and Engineering, US Naval Research Laboratory, Washington, DC 20375, United States of America
| | - Jeffrey S. Erickson
- Center for Bio/Molecular Science and Engineering, US Naval Research Laboratory, Washington, DC 20375, United States of America
| | - Zheng Wang
- Center for Bio/Molecular Science and Engineering, US Naval Research Laboratory, Washington, DC 20375, United States of America
| | - Whitney Garcia
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States of America
| | - Emaleigh Curl
- Biomolecular Science and Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States of America
| | - Robert G. Egbert
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States of America
| | - Enoch Yeung
- Department of Mechanical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States of America
| | - Gary J. Vora
- Center for Bio/Molecular Science and Engineering, US Naval Research Laboratory, Washington, DC 20375, United States of America
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Cole SD, Beabout K, Turner KB, Smith ZK, Funk VL, Harbaugh SV, Liem AT, Roth PA, Geier BA, Emanuel PA, Walper SA, Chávez JL, Lux MW. Quantification of Interlaboratory Cell-Free Protein Synthesis Variability. ACS Synth Biol 2019; 8:2080-2091. [PMID: 31386355 DOI: 10.1021/acssynbio.9b00178] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Cell-free protein synthesis (CFPS) platforms, once primarily a research tool to produce difficult to express proteins, are increasingly being pursued by the synthetic biology community for applications including biomanufacturing, rapid screening systems, and field-ready sensors. While consistency within individual studies is apparent in the literature, challenges with reproducing results between laboratories, or even between individuals within a laboratory, are discussed openly by practitioners. As the field continues to grow and move toward applications, a quantitative understanding of expected variability for CFPS and the relative contribution of underlying sources will become increasingly important. Here we offer the first quantitative assessment of interlaboratory variability in CFPS. Three laboratories implemented a single CFPS protocol and performed a series of exchanges, both of material and personnel, designed to quantify relative contributions to variability associated with the site, operator, cell extract preparation, and supplemental reagent preparation. We found that materials prepared at each laboratory, exchanged pairwise, and tested at each site resulted in 40.3% coefficient of variation compared to 7.64% for a single operator across days using a single set of materials. Reagent preparations contributed significantly to observed variability; extract preparations, however, surprisingly did not explain any of the observed variability, even when prepared in different laboratories by different operators. Subsequent exchanges showed that both the site and the operator each contributed to observed interlaboratory variability. In addition to providing the first quantitative assessment of interlaboratory variability in CFPS, these results establish a baseline for individual operator variability across days that can be used as an initial benchmark for community-driven standardization efforts. We anticipate that our results will narrow future avenues of investigation to develop best practices that will ultimately drive down interlaboratory variability, accelerating research progress and informing the suitability of CFPS for real-world applications.
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Affiliation(s)
- Stephanie D. Cole
- US Army Combat Capabilities Development Command Chemical Biological Center. 8198 Blackhawk Road, APG, Maryland 21010, United States
- Excet, Inc., 6225 Brandon Avenue #360, Springfield, Virginia 22150, United States
| | - Kathryn Beabout
- UES, Inc., Dayton, Ohio 45432, United States
- Air Force Research Laboratory, 711th Human Performance Wing, Wright-Patterson Air Force Base, Ohio 45433, United States
| | - Kendrick B. Turner
- Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, D.C. 20375, United States
| | - Zachary K. Smith
- UES, Inc., Dayton, Ohio 45432, United States
- Air Force Research Laboratory, 711th Human Performance Wing, Wright-Patterson Air Force Base, Ohio 45433, United States
| | - Vanessa L. Funk
- US Army Combat Capabilities Development Command Chemical Biological Center. 8198 Blackhawk Road, APG, Maryland 21010, United States
| | - Svetlana V. Harbaugh
- Air Force Research Laboratory, 711th Human Performance Wing, Wright-Patterson Air Force Base, Ohio 45433, United States
| | - Alvin T. Liem
- DCS Corporation, 100 Walter Ward Blvd, Suite 100, Abingdon, Maryland 21009, United States
| | - Pierce A. Roth
- DCS Corporation, 100 Walter Ward Blvd, Suite 100, Abingdon, Maryland 21009, United States
| | - Brian A. Geier
- Air Force Research Laboratory, 711th Human Performance Wing, Wright-Patterson Air Force Base, Ohio 45433, United States
| | - Peter A. Emanuel
- US Army Combat Capabilities Development Command Chemical Biological Center. 8198 Blackhawk Road, APG, Maryland 21010, United States
| | - Scott A. Walper
- Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, D.C. 20375, United States
| | - Jorge L. Chávez
- Air Force Research Laboratory, 711th Human Performance Wing, Wright-Patterson Air Force Base, Ohio 45433, United States
| | - Matthew W. Lux
- US Army Combat Capabilities Development Command Chemical Biological Center. 8198 Blackhawk Road, APG, Maryland 21010, United States
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Generation of a Prophage-Free Variant of the Fast-Growing Bacterium Vibrio natriegens. Appl Environ Microbiol 2019; 85:AEM.00853-19. [PMID: 31253674 PMCID: PMC6696956 DOI: 10.1128/aem.00853-19] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/19/2019] [Indexed: 12/16/2022] Open
Abstract
The fast-growing marine bacterium Vibrio natriegens represents an emerging strain for molecular biology and biotechnology. Genome sequencing and quantitative PCR analysis revealed that the first chromosome of V. natriegens ATCC 14048 contains two prophage regions (VNP1 and VNP2) that are both inducible by the DNA-damaging agent mitomycin C and exhibit spontaneous activation under standard cultivation conditions. Their activation was also confirmed by live cell imaging of an mCherry fusion to the major capsid proteins of VNP1 and VNP2. Transmission electron microscopy visualized the release of phage particles belonging to the Siphoviridae family into the culture supernatant. Freeing V. natriegens from its proviral load, followed by phenotypic characterization, revealed an improved robustness of the prophage-free variant toward DNA-damaging conditions, reduced cell lysis under hypo-osmotic conditions, and an increased pyruvate production compared to wild-type levels. Remarkably, the prophage-free strain outcompeted the wild type in a competitive growth experiment, emphasizing that this strain is a promising platform for future metabolic engineering approaches.IMPORTANCE The fast-growing marine bacterium Vibrio natriegens represents an emerging model host for molecular biology and biotechnology, featuring a reported doubling time of less than 10 minutes. In many bacterial species, viral DNA (prophage elements) may constitute a considerable fraction of the whole genome and may have detrimental effects on the growth and fitness of industrial strains. Genome analysis revealed the presence of two prophage regions in the V. natriegens genome that were shown to undergo spontaneous induction under standard cultivation conditions. In this study, we generated a prophage-free variant of V. natriegens Remarkably, the prophage-free strain exhibited a higher tolerance toward DNA damage and hypo-osmotic stress. Moreover, it was shown to outcompete the wild-type strain in a competitive growth experiment. In conclusion, our study presents the prophage-free variant of V. natriegens as a promising platform strain for future biotechnological applications.
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Abstract
Cell-free systems (CFS) have recently evolved into key platforms for synthetic biology applications. Many synthetic biology tools have traditionally relied on cell-based systems, and while their adoption has shown great progress, the constraints inherent to the use of cellular hosts have limited their reach and scope. Cell-free systems, which can be thought of as programmable liquids, have removed many of these complexities and have brought about exciting opportunities for rational design and manipulation of biological systems. Here we review how these simple and accessible enzymatic systems are poised to accelerate the rate of advancement in synthetic biology and, more broadly, biotechnology.
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Affiliation(s)
- Aidan Tinafar
- Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College St., Toronto, ON, M5S 3M2, Canada
| | - Katariina Jaenes
- Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College St., Toronto, ON, M5S 3M2, Canada
| | - Keith Pardee
- Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College St., Toronto, ON, M5S 3M2, Canada.
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Garenne D, Noireaux V. Cell-free transcription–translation: engineering biology from the nanometer to the millimeter scale. Curr Opin Biotechnol 2019; 58:19-27. [DOI: 10.1016/j.copbio.2018.10.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 10/14/2018] [Indexed: 01/01/2023]
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Wiegand DJ, Lee HH, Ostrov N, Church GM. Cell-free Protein Expression Using the Rapidly Growing Bacterium Vibrio natriegens. J Vis Exp 2019:10.3791/59495. [PMID: 30933074 PMCID: PMC6512795 DOI: 10.3791/59495] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The marine bacterium Vibrio natriegens has garnered considerable attention as an emerging microbial host for biotechnology due to its fast growth rate. A general protocol is described for the preparation of V. natriegens crude cell extracts using common laboratory equipment. This high yielding protocol has been specifically optimized for user accessibility and reduced cost. Cell-free protein synthesis (CFPS) can be carried out in small scale 10 μL batch reactions in either a 96- or 384-well format and reproducibly yields concentrations of > 260 μg/mL super folder GFP (sfGFP) within 3 h. Overall, crude cell extract preparation and CFPS can be achieved in 1-2 full days by a single user. This protocol can be easily integrated into existing protein synthesis pipelines to facilitate advances in bio-production and synthetic biology applications.
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Affiliation(s)
- Daniel J Wiegand
- Department of Genetics, Harvard Medical School; Wyss Institute for Biologically Inspired Engineering;
| | - Henry H Lee
- Department of Genetics, Harvard Medical School
| | - Nili Ostrov
- Department of Genetics, Harvard Medical School;
| | - George M Church
- Department of Genetics, Harvard Medical School; Wyss Institute for Biologically Inspired Engineering;
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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: 126] [Impact Index Per Article: 25.2] [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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Liu WQ, Zhang L, Chen M, Li J. Cell-free protein synthesis: Recent advances in bacterial extract sources and expanded applications. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2018.10.023] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Dubuc E, Pieters PA, van der Linden AJ, van Hest JC, Huck WT, de Greef TF. Cell-free microcompartmentalised transcription-translation for the prototyping of synthetic communication networks. Curr Opin Biotechnol 2018; 58:72-80. [PMID: 30594098 PMCID: PMC6723619 DOI: 10.1016/j.copbio.2018.10.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 10/14/2018] [Indexed: 12/21/2022]
Abstract
Recent efforts in synthetic biology have shown the possibility of engineering distributed functions in populations of living cells, which requires the development of highly orthogonal, genetically encoded communication pathways. Cell-free transcription-translation (TXTL) reactions encapsulated in microcompartments enable prototyping of molecular communication channels and their integration into engineered genetic circuits by mimicking critical cell features, such as gene expression, cell size, and cell individuality within a community. In this review, we discuss the uses of cell-free transcription-translation reactions for the development of synthetic genetic circuits, with a special focus on the use of microcompartments supporting this reaction. We highlight several studies where molecular communication between non-living microcompartments and living cells have been successfully engineered.
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Affiliation(s)
- Emilien Dubuc
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands; Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands; Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Pascal A Pieters
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands; Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands; Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Ardjan J van der Linden
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands; Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands; Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Jan Cm van Hest
- Department of Biomedical Engineering & Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Wilhelm Ts Huck
- Department of Physical Organic Chemistry, Institute for Molecules and Materials, Radboud University, Nijmegen 6525 HP, The Netherlands
| | - Tom Fa de Greef
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands; Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands; Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands; Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
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Schleicher L, Muras V, Claussen B, Pfannstiel J, Blombach B, Dibrov P, Fritz G, Steuber J. Vibrio natriegens as Host for Expression of Multisubunit Membrane Protein Complexes. Front Microbiol 2018; 9:2537. [PMID: 30410475 PMCID: PMC6209661 DOI: 10.3389/fmicb.2018.02537] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 10/04/2018] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli is a convenient host for the expression of proteins, but the heterologous production of large membrane protein complexes often is hampered by the lack of specific accessory genes required for membrane insertion or cofactor assembly. In this study we introduce the non-pathogenic and fast-growing Vibrio natriegens as a suitable expression host for membrane-bound proteins from Vibrio cholerae. We achieved production of the primary Na+ pump, the NADH:quinone oxidoreductase (NQR), from V. cholerae in an active state, as indicated by increased overall NADH:quinone oxidoreduction activity of membranes from the transformed V. natriegens, and the sensitivity toward Ag+, a specific inhibitor of the NQR. Complete assembly of V. cholerae NQR expressed in V. natriegens was demonstrated by BN PAGE followed by activity staining. The secondary transport system Mrp from V. cholerae, another membrane-bound multisubunit complex, was also produced in V. natriegens in a functional state, as demonstrated by in vivo Li+ transport. V. natriegens is a promising expression host for the production of membrane protein complexes from Gram-negative pathogens.
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Affiliation(s)
- Lena Schleicher
- Institute of Microbiology, University of Hohenheim, Stuttgart, Germany
| | - Valentin Muras
- Institute of Microbiology, University of Hohenheim, Stuttgart, Germany
| | - Björn Claussen
- Institute of Microbiology, University of Hohenheim, Stuttgart, Germany
| | - Jens Pfannstiel
- Mass Spectrometry Core Facility, University of Hohenheim, Stuttgart, Germany
| | - Bastian Blombach
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Pavel Dibrov
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Günter Fritz
- Institute of Microbiology, University of Hohenheim, Stuttgart, Germany.,Institute for Neuropathology, University of Freiburg, Freiburg im Breisgau, Germany
| | - Julia Steuber
- Institute of Microbiology, University of Hohenheim, Stuttgart, Germany
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Wiegand DJ, Lee HH, Ostrov N, Church GM. Establishing a Cell-Free Vibrio natriegens Expression System. ACS Synth Biol 2018; 7:2475-2479. [PMID: 30160938 DOI: 10.1021/acssynbio.8b00222] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The fast growing bacterium Vibrio natriegens is an emerging microbial host for biotechnology. Harnessing its productive cellular components may offer a compelling platform for rapid protein production and prototyping of metabolic pathways or genetic circuits. Here, we report the development of a V. natriegens cell-free expression system. We devised a simplified crude extract preparation protocol and achieved >260 μg/mL of superfolder GFP in a small-scale batch reaction after 3 h. Culturing conditions, including growth media and cell density, significantly affect translation kinetics and protein yield of extracts. We observed maximal protein yield at incubation temperatures of 26 or 30 °C, and show improved yield by tuning ions crucial for ribosomal stability. This work establishes an initial V. natriegens cell-free expression system, enables probing of V. natriegens biology, and will serve as a platform to accelerate metabolic engineering and synthetic biology applications.
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Affiliation(s)
- Daniel J. Wiegand
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, United States
| | - Henry H. Lee
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Nili Ostrov
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, United States
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Pardee K. Perspective: Solidifying the impact of cell-free synthetic biology through lyophilization. Biochem Eng J 2018; 138:91-97. [PMID: 30740032 PMCID: PMC6358126 DOI: 10.1016/j.bej.2018.07.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/03/2018] [Accepted: 07/09/2018] [Indexed: 12/20/2022]
Abstract
Cell-free synthetic biology is an exciting and new branch in the field of synthetic biology. Based on in vitro transcription and translation systems, this application-focused domain builds on decades of cell-free biochemistry and protein expression to operate synthetic gene networks outside of cellular environments. This has brought new and perhaps even unexpected advantages. Chief among these is the ability to operate genetically encoded tools in a sterile and abiotic format. Recent work has extended this advantage by freeze-drying these cell-free systems into dried pellets or embedded paper-based reactions. Taken together, these new ideas have solved the longstanding challenge of how to deploy poised synthetic gene networks in a biosafe mode outside of the laboratory. There is significant excitement in the potential of this newfound venue and the community has begun to extend proof-of-concept demonstrations in important and creative ways. Here I explore these new efforts and provide my thoughts on the challenges and opportunities ahead for freeze-dried, cell-free synthetic biology.
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Des Soye BJ, Davidson SR, Weinstock MT, Gibson DG, Jewett MC. Establishing a High-Yielding Cell-Free Protein Synthesis Platform Derived from Vibrio natriegens. ACS Synth Biol 2018; 7:2245-2255. [PMID: 30107122 DOI: 10.1021/acssynbio.8b00252] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A new wave of interest in cell-free protein synthesis (CFPS) systems has shown their utility for producing proteins at high titers, establishing genetic regulatory element libraries ( e.g., promoters, ribosome binding sites) in nonmodel organisms, optimizing biosynthetic pathways before implementation in cells, and sensing biomarkers for diagnostic applications. Unfortunately, most previous efforts have focused on a select few model systems, such as Escherichia coli. Broadening the spectrum of organisms used for CFPS promises to better mimic host cell processes in prototyping applications and open up new areas of research. Here, we describe the development and characterization of a facile CFPS platform based on lysates derived from the fast-growing bacterium Vibrio natriegens, which is an emerging host organism for biotechnology. We demonstrate robust preparation of highly active extracts using sonication, without specialized and costly equipment. After optimizing the extract preparation procedure and cell-free reaction conditions, we show synthesis of 1.6 ± 0.05 g/L of superfolder green fluorescent protein in batch mode CFPS, making it competitive with existing E. coli CFPS platforms. To showcase the flexibility of the system, we demonstrate that it can be lyophilized and retain biosynthesis capability, that it is capable of producing antimicrobial peptides, and that our extract preparation procedure can be coupled with the recently described Vmax Express strain in a one-pot system. Finally, to further increase system productivity, we explore a knockout library in which putative negative effectors of CFPS are genetically removed from the source strain. Our V. natriegens-derived CFPS platform is versatile and simple to prepare and use. We expect it will facilitate expansion of CFPS systems into new laboratories and fields for compelling applications in synthetic biology.
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Affiliation(s)
| | | | | | - Daniel G. Gibson
- Synthetic Genomics, Inc., La Jolla, California 92037, United States
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