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Yue K, Chen J, Li Y, Kai L. Advancing synthetic biology through cell-free protein synthesis. Comput Struct Biotechnol J 2023; 21:2899-2908. [PMID: 37216017 PMCID: PMC10196276 DOI: 10.1016/j.csbj.2023.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/03/2023] [Accepted: 05/03/2023] [Indexed: 05/24/2023] Open
Abstract
The rapid development of synthetic biology has enabled the production of compounds with revolutionary improvements in biotechnology. DNA manipulation tools have expedited the engineering of cellular systems for this purpose. Nonetheless, the inherent constraints of cellular systems persist, imposing an upper limit on mass and energy conversion efficiencies. Cell-free protein synthesis (CFPS) has demonstrated its potential to overcome these inherent constraints and has been instrumental in the further advancement of synthetic biology. Via the removal of the cell membranes and redundant parts of cells, CFPS has provided flexibility in directly dissecting and manipulating the Central Dogma with rapid feedback. This mini-review summarizes recent achievements of the CFPS technique and its application to a wide range of synthetic biology projects, such as minimal cell assembly, metabolic engineering, and recombinant protein production for therapeutics, as well as biosensor development for in vitro diagnostics. In addition, current challenges and future perspectives in developing a generalized cell-free synthetic biology are outlined.
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Affiliation(s)
- Ke Yue
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
| | - Junyu Chen
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
| | - Yingqiu Li
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
| | - Lei Kai
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
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2
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Yue K, Li Y, Cao M, Shen L, Gu J, Kai L. Bottom-Up Synthetic Biology Using Cell-Free Protein Synthesis. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 185:1-20. [PMID: 37526707 DOI: 10.1007/10_2023_232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Technical advances in biotechnology have greatly accelerated the development of bottom-up synthetic biology. Unlike top-down approaches, bottom-up synthetic biology focuses on the construction of a minimal cell from scratch and the application of these principles to solve challenges. Cell-free protein synthesis (CFPS) systems provide minimal machinery for transcription and translation, from either a fractionated cell lysate or individual purified protein elements, thus speeding up the development of synthetic cell projects. In this review, we trace the history of the cell-free technique back to the first in vitro fermentation experiment using yeast cell lysate. Furthermore, we summarized progresses of individual cell mimicry modules, such as compartmentalization, gene expression regulation, energy regeneration and metabolism, growth and division, communication, and motility. Finally, current challenges and future perspectives on the field are outlined.
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Affiliation(s)
- Ke Yue
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Yingqiu Li
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Mengjiao Cao
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Lulu Shen
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Jingsheng Gu
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Lei Kai
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China.
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3
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Seo K, Hagino K, Ichihashi N. Progresses in Cell-Free In Vitro Evolution. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 186:121-140. [PMID: 37306699 DOI: 10.1007/10_2023_219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Biopolymers, such as proteins and RNA, are integral components of living organisms and have evolved through a process of repeated mutation and selection. The technique of "cell-free in vitro evolution" is a powerful experimental approach for developing biopolymers with desired functions and structural properties. Since Spiegelman's pioneering work over 50 years ago, biopolymers with a wide range of functions have been developed using in vitro evolution in cell-free systems. The use of cell-free systems offers several advantages, including the ability to synthesize a wider range of proteins without the limitations imposed by cytotoxicity, and the capacity for higher throughput and larger library sizes than cell-based evolutionary experiments. In this chapter, we provide a comprehensive overview of the progress made in the field of cell-free in vitro evolution by categorizing evolution into directed and undirected. The biopolymers produced by these methods are valuable assets in medicine and industry, and as a means of exploring the potential of biopolymers.
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Affiliation(s)
- Kaito Seo
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo, Tokyo, Japan
| | - Katsumi Hagino
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo, Tokyo, Japan
| | - Norikazu Ichihashi
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo, Tokyo, Japan.
- Komaba Institute for Science, The University of Tokyo, Tokyo, Japan.
- Universal Biology Institute, The University of Tokyo, Tokyo, Japan.
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4
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Nakai H, Isshiki K, Hattori M, Maehira H, Yamaguchi T, Masuda K, Shimizu Y, Watanabe T, Hohsaka T, Shihoya W, Nureki O, Kato Y, Watanabe H, Matsuura T. Cell-Free Synthesis of Human Endothelin Receptors and Its Application to Ribosome Display. Anal Chem 2022; 94:3831-3839. [PMID: 35188389 DOI: 10.1021/acs.analchem.1c04714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Engineering G-protein-coupled receptors (GPCRs) for improved stability or altered function is of great interest, as GPCRs consist of the largest protein family, are involved in many important signaling pathways, and thus, are one of the major drug targets. Here, we report the development of a high-throughput screening method for GPCRs using a reconstituted in vitro transcription-translation (IVTT) system. Human endothelin receptor type-B (ETBR), a class A GPCR that binds endothelin-1 (ET-1), a 21-residue peptide hormone, was synthesized in the presence of nanodisc (ND) composed of a phospholipid, 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (POPG). The ET-1 binding of ETBR was significantly reduced or was undetectable when other phospholipids were used for ND preparation. However, when functional ETBR purified from Sf9 cells was reconstituted into NDs, ET-1 binding was observed with two different phospholipids tested, including POPG. These results suggest that POPG likely supports the folding of ETBR into its functional form in the IVTT system. Using the same conditions as ETBR, whose three-dimensional structure has been solved, human endothelin receptor type-A (ETAR), whose three-dimensional structure remains unsolved, was also synthesized in its functional form. By adding POPG-ND to the IVTT system, both ETAR and ETBR were successfully subjected to ribosome display, a method of in vitro directed evolution that facilitates the screening of up to 1012 mutants. Finally, using a mock library, we showed that ribosome display can be applied for gene screening of ETBR, suggesting that high-throughput screening and directed evolution of GPCRs is possible in vitro.
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Affiliation(s)
- Hiroki Nakai
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kinuka Isshiki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masato Hattori
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hiromasa Maehira
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tatsumi Yamaguchi
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.,Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama 2-12-1-i7E-307, Meguro-Ku, Tokyo 152-8550, Japan
| | - Keiko Masuda
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystem Dynamics Research (BDR), 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan
| | - Yoshihiro Shimizu
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystem Dynamics Research (BDR), 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan
| | - Takayoshi Watanabe
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Takahiro Hohsaka
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Wataru Shihoya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Yasuhiko Kato
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hajime Watanabe
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tomoaki Matsuura
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.,Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama 2-12-1-i7E-307, Meguro-Ku, Tokyo 152-8550, Japan
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5
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Reyes SG, Kuruma Y, Fujimi M, Yamazaki M, Eto S, Nishikawa S, Tamaki S, Kobayashi A, Mizuuchi R, Rothschild L, Ditzler M, Fujishima K. PURE mRNA display and cDNA display provide rapid detection of core epitope motif via high-throughput sequencing. Biotechnol Bioeng 2021; 118:1736-1749. [PMID: 33501662 DOI: 10.1002/bit.27696] [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] [Received: 06/03/2020] [Revised: 01/02/2021] [Accepted: 01/17/2021] [Indexed: 12/17/2022]
Abstract
The reconstructed in vitro translation system known as the PURE system has been used in a variety of cell-free experiments such as the expression of native and de novo proteins as well as various display methods to select for functional polypeptides. We developed a refined PURE-based display method for the preparation of stable messenger RNA (mRNA) and complementary DNA (cDNA)-peptide conjugates and validated its utility for in vitro selection. Our conjugate formation efficiency exceeded 40%, followed by gel purification to allow minimum carry-over of components from the translation system to the downstream assay enabling clean and efficient random peptide sequence screening. We chose the commercially available anti-FLAG M2 antibody as a target molecule for validation. Starting from approximately 1.7 × 1012 random sequences, a round-by-round high-throughput sequencing showed clear enrichment of the FLAG epitope DYKDDD as well as revealing consensus FLAG epitope motif DYK(D/L/N)(L/Y/D/N/F)D. Enrichment of core FLAG motifs lacking one of the four key residues (DYKxxD) indicates that Tyr (Y) and Lys (K) appear as the two key residues essential for binding. Furthermore, the comparison between mRNA display and cDNA display method resulted in overall similar performance with slightly higher enrichment for mRNA display. We also show that gel purification steps in the refined PURE-based display method improve conjugate formation efficiency and enhance the enrichment rate of FLAG epitope motifs in later rounds of selection especially for mRNA display. Overall, the generalized procedure and consistent performance of two different display methods achieved by the commercially available PURE system will be useful for future studies to explore the sequence and functional space of diverse polypeptides.
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Affiliation(s)
- Sabrina Galiñanes Reyes
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan.,Extra-cutting-edge Science and Technology Avant-garde Research Program, Japan Agency for Marine-Earth Science and Technology, Kanagawa, Japan.,James Watt School of Engineering, The University of Glasgow, Glasgow, UK
| | - Yutetsu Kuruma
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan.,Extra-cutting-edge Science and Technology Avant-garde Research Program, Japan Agency for Marine-Earth Science and Technology, Kanagawa, Japan.,JST, PRESTO, Saitama, Japan
| | - Mai Fujimi
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
| | | | - Sumie Eto
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan.,MOLCURE Inc., Shinagawa, Tokyo, Japan
| | - Shota Nishikawa
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan.,School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | | | - Asaki Kobayashi
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, Evry, France
| | - Ryo Mizuuchi
- JST, PRESTO, Saitama, Japan.,Komaba Institute for Science, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Lynn Rothschild
- Center for the Emergence of Life, NASA Ames Research Center, Moffett Field, California, USA
| | - Mark Ditzler
- Center for the Emergence of Life, NASA Ames Research Center, Moffett Field, California, USA
| | - Kosuke Fujishima
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan.,Graduate School of Media and Governance, Keio University, Fujisawa, Japan
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6
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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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7
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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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8
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Natural selection in compartmentalized environment with reshuffling. J Math Biol 2019; 79:1401-1454. [PMID: 31302727 DOI: 10.1007/s00285-019-01399-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 07/04/2019] [Indexed: 10/26/2022]
Abstract
The emerging field of high-throughput compartmentalized in vitro evolution is a promising new approach to protein engineering. In these experiments, libraries of mutant genotypes are randomly distributed and expressed in microscopic compartments-droplets of an emulsion. The selection of desirable variants is performed according to the phenotype of each compartment. The random partitioning leads to a fraction of compartments receiving more than one genotype making the whole process a lab implementation of the group selection. From a practical point of view (where efficient selection is typically sought), it is important to know the impact of the increase in the mean occupancy of compartments on the selection efficiency. We carried out a theoretical investigation of this problem in the context of selection dynamics for an infinite non-mutating subdivided population that randomly colonizes an infinite number of patches (compartments) at each reproduction cycle. We derive here an update equation for any distribution of phenotypes and any value of the mean occupancy. Using this result, we demonstrate that, for the linear additive fitness, the best genotype is still selected regardless of the mean occupancy. Furthermore, the selection process is remarkably resilient to the presence of multiple genotypes per compartments, and slows down approximately inversely proportional to the mean occupancy at high values. We extend out results to more general expressions that cover nonadditive and non-linear fitnesses, as well non-Poissonian distribution among compartments. Our conclusions may also apply to natural genetic compartmentalized replicators, such as viruses or early trans-acting RNA replicators.
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9
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Room Temperature X-Ray Crystallography Reveals Conformational Heterogeneity of Engineered Proteins. Structure 2019; 25:691-692. [PMID: 28467914 DOI: 10.1016/j.str.2017.04.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In this issue of Structure, Biel et al. (2017) present multi-conformer analyses from room temperature X-ray data of two ubiquitin phage display variants binding deubiquitinase USP7. The first contains core mutations. The second matured variant contains additional surface mutations. Alternate conformations detected in the core mutant were removed by maturation.
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10
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Kai L, Schwille P. Cell-Free Protein Synthesis and Its Perspectives for Assembling Cells from the Bottom-Up. ACTA ACUST UNITED AC 2019; 3:e1800322. [PMID: 32648712 DOI: 10.1002/adbi.201800322] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/14/2019] [Indexed: 12/20/2022]
Abstract
The underlying idea of synthetic biology is that biological reactions/modules/systems can be precisely engineered and controlled toward desired products. Numerous efforts in the past decades in deciphering the complexity of biological systems in vivo have led to a variety of tools for synthetic biology, especially based on recombinant DNA. However, one generic limitation of all living systems is that the vast majority of energy input is dedicated to maintain the system as a whole, rather than the small part of interest. Cell-free synthetic biology is aiming at exactly this fundamental limitation, providing the next level of flexibility for engineering and designing biological systems in vitro. New technology has continuously inspired cell-free biology and extended its applications, including gene circuits, spatiotemporally controlled pathways, coactivated catalysts systems, and rationally designed multienzyme pathways, in particular, minimal cell construction. In the context of this special issue, discussing work being carried out in the "MaxSynBio" consortium, the advances in characterizing stochasticity and dynamics of cell-free protein synthesis within cell-sized compartments, as well as the molecular crowding effect, are discussed. The organization of spatial heterogeneity is the key prerequisite for achieving hierarchy and stepwise assembly of minimal cells from the bottom-up.
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Affiliation(s)
- Lei Kai
- School of Life Sciences, Jiangsu Normal University, Shanghai Road 101, 221116, Xuzhou, P. R. China.,Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, D-82152, Martinsried, Germany
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, D-82152, Martinsried, Germany
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11
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Expanding biological applications using cell-free metabolic engineering: An overview. Metab Eng 2018; 50:156-172. [PMID: 30367967 DOI: 10.1016/j.ymben.2018.09.011] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 09/21/2018] [Accepted: 09/22/2018] [Indexed: 11/21/2022]
Abstract
Expanding the concept of cell-free biology, implemented both with purified components and crude extracts, is continuing to deepen our appreciation of biological fundamentals while enlarging the range of applications. We are no longer intimidated by the complexity of crude extracts and complicated reaction systems with hundreds of active components, and, instead, coordinately activate and inactivate metabolic processes to focus and expand the capabilities of natural biological processes. This, in turn, dramatically increases the range of benefits offered by new products, both natural and supernatural, that were previously infeasible and/or unimaginable. This overview of cell-free metabolic engineering provides a broad range of examples and insights to guide and motivate continued research that will further expand fundamental understanding and beneficial applications. However, this survey also reveals how far we are from fully unlocking the potential offered by natural and engineered biological components and systems. This is an exciting conclusion, but metabolic engineering by itself is not sufficient. Going forward, innovative metabolic engineering must be intimately combined with creative process engineering to fully realize potential contributions toward a sustainable global civilization.
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12
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Abstract
Directed evolution (DE) is a powerful tool for optimizing an enzyme's properties toward a particular objective, such as broader substrate scope, greater thermostability, or increased kcat. A successful DE project requires the generation of genetic diversity and subsequent screening or selection to identify variants with improved fitness. In contrast to random methods (error-prone PCR or DNA shuffling), site-directed mutagenesis enables the rational design of variant libraries and provides control over the nature and frequency of the encoded mutations. Knowledge of protein structure, dynamics, enzyme mechanisms, and natural evolution demonstrates that multiple (combinatorial) mutations are required to discover the most improved variants. To this end, we describe an experimentally straightforward and low-cost method for the preparation of combinatorial variant libraries. Our approach employs a two-step PCR protocol, first producing mutagenic megaprimers, which can then be combined in a "mix-and-match" fashion to generate diverse sets of combinatorial variant libraries both quickly and accurately.
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13
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Yang X, Feng Y, Chong H, Wang D, Hu X, Pu J, Zhan CG, Liao F. High-throughput estimation of specific activities of enzyme/mutants in cell lysates through immunoturbidimetric assay of proteins. Anal Biochem 2017; 534:91-98. [DOI: 10.1016/j.ab.2017.05.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 05/14/2017] [Indexed: 01/02/2023]
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14
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Pohorille A, Wilson MA, Shannon G. Flexible Proteins at the Origin of Life. Life (Basel) 2017; 7:E23. [PMID: 28587235 PMCID: PMC5492145 DOI: 10.3390/life7020023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 05/10/2017] [Accepted: 05/24/2017] [Indexed: 11/17/2022] Open
Abstract
Almost all modern proteins possess well-defined, relatively rigid scaffolds that provide structural preorganization for desired functions. Such scaffolds require the sufficient length of a polypeptide chain and extensive evolutionary optimization. How ancestral proteins attained functionality, even though they were most likely markedly smaller than their contemporary descendants, remains a major, unresolved question in the origin of life. On the basis of evidence from experiments and computer simulations, we argue that at least some of the earliest water-soluble and membrane proteins were markedly more flexible than their modern counterparts. As an example, we consider a small, evolved in vitro ligase, based on a novel architecture that may be the archetype of primordial enzymes. The protein does not contain a hydrophobic core or conventional elements of the secondary structure characteristic of modern water-soluble proteins, but instead is built of a flexible, catalytic loop supported by a small hydrophilic core containing zinc atoms. It appears that disorder in the polypeptide chain imparts robustness to mutations in the protein core. Simple ion channels, likely the earliest membrane protein assemblies, could also be quite flexible, but still retain their functionality, again in contrast to their modern descendants. This is demonstrated in the example of antiamoebin, which can serve as a useful model of small peptides forming ancestral ion channels. Common features of the earliest, functional protein architectures discussed here include not only their flexibility, but also a low level of evolutionary optimization and heterogeneity in amino acid composition and, possibly, the type of peptide bonds in the protein backbone.
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Affiliation(s)
- Andrew Pohorille
- Exobiology Branch, MS 239-4, NASA Ames Research Center, Moffett Field, CA 94035, USA.
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94132, USA.
| | - Michael A Wilson
- Exobiology Branch, MS 239-4, NASA Ames Research Center, Moffett Field, CA 94035, USA.
- SETI Institute, 189 N Bernardo Ave #200, Mountain View, CA 94043, USA.
| | - Gareth Shannon
- Exobiology Branch, MS 239-4, NASA Ames Research Center, Moffett Field, CA 94035, USA.
- NASA Postdoctoral Program Fellow, NASA Ames Research Center, Moffett Field, CA 94035, USA.
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15
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Caschera F. Bacterial cell-free expression technology to in vitro systems engineering and optimization. Synth Syst Biotechnol 2017; 2:97-104. [PMID: 29062966 PMCID: PMC5637228 DOI: 10.1016/j.synbio.2017.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 07/25/2017] [Accepted: 07/25/2017] [Indexed: 12/26/2022] Open
Abstract
Cell-free expression system is a technology for the synthesis of proteins in vitro. The system is a platform for several bioengineering projects, e.g. cell-free metabolic engineering, evolutionary design of experiments, and synthetic minimal cell construction. Bacterial cell-free protein synthesis system (CFPS) is a robust tool for synthetic biology. The bacteria lysate, the DNA, and the energy module, which are the three optimized sub-systems for in vitro protein synthesis, compose the integrated system. Currently, an optimized E. coli cell-free expression system can produce up to ∼2.3 mg/mL of a fluorescent reporter protein. Herein, I will describe the features of ATP-regeneration systems for in vitro protein synthesis, and I will present a machine-learning experiment for optimizing the protein yield of E. coli cell-free protein synthesis systems. Moreover, I will introduce experiments on the synthesis of a minimal cell using liposomes as dynamic containers, and E. coli cell-free expression system as biochemical platform for metabolism and gene expression. CFPS can be further integrated with other technologies for novel applications in environmental, medical and material science.
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16
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17
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Interactions of in vitro selected fluorogenic peptide aptamers with calmodulin. Biotechnol Lett 2016; 39:375-382. [DOI: 10.1007/s10529-016-2257-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 11/10/2016] [Indexed: 10/20/2022]
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18
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Mankowska SA, Gatti-Lafranconi P, Chodorge M, Sridharan S, Minter RR, Hollfelder F. A Shorter Route to Antibody Binders via Quantitative in vitro Bead-Display Screening and Consensus Analysis. Sci Rep 2016; 6:36391. [PMID: 27819305 PMCID: PMC5098251 DOI: 10.1038/srep36391] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 10/11/2016] [Indexed: 12/13/2022] Open
Abstract
Affinity panning of large libraries is a powerful tool to identify protein binders. However, panning rounds are followed by the tedious re-screening of the clones obtained to evaluate binders precisely. In a first application of Bead Surface Display (BeSD) we show successful in vitro affinity selections based on flow cytometric analysis that allows fine quantitative discrimination between binders. Subsequent consensus analysis of the resulting sequences enables identification of clones that bind tighter than those arising directly from the experimental selection output. This is demonstrated by evolution of an anti-Fas receptor single-chain variable fragment (scFv) that was improved 98-fold vs the parental clone. Four rounds of quantitative screening by fluorescence-activated cell sorting of an error-prone library based on fine discrimination between binders in BeSD were followed by analysis of 200 full-length output sequences that suggested a new consensus design with a Kd ∼140 pM. This approach shortens the time and effort to obtain high affinity reagents and its cell-free nature transcends limitations inherent in previous in vivo display systems.
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Affiliation(s)
- Sylwia A Mankowska
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.,Antibody Discovery and Protein Engineering, MedImmune Ltd, Milstein Building, Granta Park, Cambridge, CB21 6GH, UK
| | - Pietro Gatti-Lafranconi
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Matthieu Chodorge
- Antibody Discovery and Protein Engineering, MedImmune Ltd, Milstein Building, Granta Park, Cambridge, CB21 6GH, UK
| | - Sudharsan Sridharan
- Antibody Discovery and Protein Engineering, MedImmune Ltd, Milstein Building, Granta Park, Cambridge, CB21 6GH, UK
| | - Ralph R Minter
- Antibody Discovery and Protein Engineering, MedImmune Ltd, Milstein Building, Granta Park, Cambridge, CB21 6GH, UK
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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Karim AS, Jewett MC. A cell-free framework for rapid biosynthetic pathway prototyping and enzyme discovery. Metab Eng 2016; 36:116-126. [PMID: 26996382 DOI: 10.1016/j.ymben.2016.03.002] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 02/12/2016] [Accepted: 03/10/2016] [Indexed: 10/22/2022]
Abstract
Speeding up design-build-test (DBT) cycles is a fundamental challenge facing biochemical engineering. To address this challenge, we report a new cell-free protein synthesis driven metabolic engineering (CFPS-ME) framework for rapid biosynthetic pathway prototyping. In our framework, cell-free cocktails for synthesizing target small molecules are assembled in a mix-and-match fashion from crude cell lysates either containing selectively enriched pathway enzymes from heterologous overexpression or directly producing pathway enzymes in lysates by CFPS. As a model, we apply our approach to n-butanol biosynthesis showing that Escherichia coli lysates support a highly active 17-step CoA-dependent n-butanol pathway in vitro. The elevated degree of flexibility in the cell-free environment allows us to manipulate physiochemical conditions, access enzymatic nodes, discover new enzymes, and prototype enzyme sets with linear DNA templates to study pathway performance. We anticipate that CFPS-ME will facilitate efforts to define, manipulate, and understand metabolic pathways for accelerated DBT cycles without the need to reengineer organisms.
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Affiliation(s)
- Ashty S Karim
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Tech E-136, Evanston, IL 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Tech E-136, Evanston, IL 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA; Simpson Querrey Institute, Northwestern University, Chicago, IL 60611, USA.
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High-Throughput Screening in Protein Engineering: Recent Advances and Future Perspectives. Int J Mol Sci 2015; 16:24918-45. [PMID: 26492240 PMCID: PMC4632782 DOI: 10.3390/ijms161024918] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 10/13/2015] [Accepted: 10/13/2015] [Indexed: 11/17/2022] Open
Abstract
Over the last three decades, protein engineering has established itself as an important tool for the development of enzymes and (therapeutic) proteins with improved characteristics. New mutagenesis techniques and computational design tools have greatly aided in the advancement of protein engineering. Yet, one of the pivotal components to further advance protein engineering strategies is the high-throughput screening of variants. Compartmentalization is one of the key features allowing miniaturization and acceleration of screening. This review focuses on novel screening technologies applied in protein engineering, highlighting flow cytometry- and microfluidics-based platforms.
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Ravikumar Y, Nadarajan SP, Hyeon Yoo T, Lee CS, Yun H. Incorporating unnatural amino acids to engineer biocatalysts for industrial bioprocess applications. Biotechnol J 2015; 10:1862-76. [DOI: 10.1002/biot.201500153] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 08/13/2015] [Accepted: 09/02/2015] [Indexed: 12/22/2022]
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