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Rollin JA, Bomble YJ, St. John PC, Stark AK. Biochemical Production with Purified Cell-Free Systems. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2018.07.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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52
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Stamatis C, Farid SS. Process economics evaluation of cell-free synthesis for the commercial manufacture of antibody drug conjugates. Biotechnol J 2021; 16:e2000238. [PMID: 33231912 DOI: 10.1002/biot.202000238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 11/13/2020] [Indexed: 11/06/2022]
Abstract
Continuous improvements of cell-free synthesis (CFS) systems have generated interest in adopting the technology for the manufacture of biologics. This paper provides an evaluation of the manufacturing cost-effectiveness of CFS for the commercial production of antibody-drug conjugates (ADCs). The evaluation was performed using an advanced techno-economic engine (TEE) built in Python. The TEE is programmed in an object-oriented environment capable of simulating a plethora of process flowsheets and predicting size and cost metrics for the process and the facility. A case study was formulated to compare the economics of whole bioprocesses based on either a CFS system or a mammalian cell system (CHO) for the manufacture of an ADC at a range of product demands. The analysis demonstrated the potential of CFS for the commercial manufacture of biologics and identified key cost drivers related to the system. The CFS system showed an approximately 80% increase in the cost of goods compared to CHO with a significant cost attributed to the in-house manufacture of the bacterial cell extract, necessary for the CFS reaction step in the process. A sensitivity and target analysis highlighted the need for further process improvements especially in the titer for the CFS process to become more competitive against well-established systems.
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Affiliation(s)
- Christos Stamatis
- The Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering, University College London, London, UK
| | - Suzanne S Farid
- The Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering, University College London, London, UK
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53
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Development of a Cofactor Balanced, Multi Enzymatic Cascade Reaction for the Simultaneous Production of L-Alanine and L-Serine from 2-Keto-3-deoxy-gluconate. Catalysts 2020. [DOI: 10.3390/catal11010031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Enzymatic reaction cascades represent a powerful tool to convert biogenic resources into valuable chemicals for fuel and commodity markets. Sugars and their breakdown products constitute a significant group of possible substrates for such biocatalytic conversion strategies to value-added products. However, one major drawback of sugar cascades is the need for cofactor recycling without using additional enzymes and/or creating unwanted by-products. Here, we describe a novel, multi-enzymatic reaction cascade for the one-pot simultaneous synthesis of L-alanine and L-serine, using the sugar degradation product 2-keto-3-deoxygluconate and ammonium as precursors. To pursue this aim, we used four different, thermostable enzymes, while the necessary cofactor NADH is recycled entirely self-sufficiently. Buffer and pH optimisation in combination with an enzyme titration study yielded an optimised production of 21.3 +/− 1.0 mM L-alanine and 8.9 +/− 0.4 mM L-serine in one pot after 21 h.
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54
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Valliere MA, Korman TP, Arbing MA, Bowie JU. A bio-inspired cell-free system for cannabinoid production from inexpensive inputs. Nat Chem Biol 2020; 16:1427-1433. [PMID: 32839605 DOI: 10.1038/s41589-020-0631-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 07/22/2020] [Indexed: 11/09/2022]
Abstract
Moving cannabinoid production away from the vagaries of plant extraction and into engineered microbes could provide a consistent, purer, cheaper and environmentally benign source of these important therapeutic molecules, but microbial production faces notable challenges. An alternative to microbes and plants is to remove the complexity of cellular systems by employing enzymatic biosynthesis. Here we design and implement a new cell-free system for cannabinoid production with the following features: (1) only low-cost inputs are needed; (2) only 12 enzymes are employed; (3) the system does not require oxygen and (4) we use a nonnatural enzyme system to reduce ATP requirements that is generally applicable to malonyl-CoA-dependent pathways such as polyketide biosynthesis. The system produces ~0.5 g l-1 cannabigerolic acid (CBGA) or cannabigerovarinic acid (CBGVA) from low-cost inputs, nearly two orders of magnitude higher than yeast-based production. Cell-free systems such as this may provide a new route to reliable cannabinoid production.
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Affiliation(s)
- Meaghan A Valliere
- Department of Chemistry and Biochemistry, Molecular Biology Institute, UCLA-DOE Institute, University of California, Los Angeles, CA, USA
- Conagen, Inc., Bedford, MA, USA
| | - Tyler P Korman
- Department of Chemistry and Biochemistry, Molecular Biology Institute, UCLA-DOE Institute, University of California, Los Angeles, CA, USA
- Invizyne Technologies, Inc., Monrovia, CA, USA
| | - Mark A Arbing
- Department of Chemistry and Biochemistry, Molecular Biology Institute, UCLA-DOE Institute, University of California, Los Angeles, CA, USA
| | - James U Bowie
- Department of Chemistry and Biochemistry, Molecular Biology Institute, UCLA-DOE Institute, University of California, Los Angeles, CA, USA.
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55
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Mohr B, Giannone RJ, Hettich RL, Doktycz MJ. Targeted Growth Medium Dropouts Promote Aromatic Compound Synthesis in Crude E. coli Cell-Free Systems. ACS Synth Biol 2020; 9:2986-2997. [PMID: 33044063 DOI: 10.1021/acssynbio.9b00524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Progress in cell-free protein synthesis (CFPS) has spurred resurgent interest in engineering complex biological metabolism outside of the cell. Unlike purified enzyme systems, crude cell-free systems can be prepared for a fraction of the cost and contain endogenous cellular pathways that can be activated for biosynthesis. Endogenous activity performs essential functions in cell-free systems including substrate biosynthesis and energy regeneration; however, use of crude cell-free systems for bioproduction has been hampered by the under-described complexity of the metabolic networks inherent to a crude lysate. Physical and chemical cultivation parameters influence the endogenous activity of the resulting lysate, but targeted efforts to engineer this activity by manipulation of these nongenetic factors has been limited. Here growth medium composition was manipulated to improve the one-pot in vitro biosynthesis of phenol from glucose via the expression of Pasteurella multocida phenol-tyrosine lyase in crude E. coli lysates. Crude cell lysate metabolic activity was focused toward the limiting precursor tyrosine by targeted growth medium dropouts guided by proteomics. The result is the activation of a 25-step enzymatic reaction cascade involving at least three endogenous E. coli metabolic pathways. Additional modification of this system, through CFPS of feedback intolerant AroG improves yield. This effort demonstrates the ability to activate a long, complex pathway in vitro and provides a framework for harnessing the metabolic potential of diverse organisms for cell-free metabolic engineering. The more than 6-fold increase in phenol yield with limited genetic manipulation demonstrates the benefits of optimizing growth medium for crude cell-free extract production and illustrates the advantages of a systems approach to cell-free metabolic engineering.
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Affiliation(s)
- Benjamin Mohr
- Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Richard J. Giannone
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Robert L. Hettich
- Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, Tennessee 37996, United States
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Mitchel J. Doktycz
- Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
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56
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Lawson CE, Martí JM, Radivojevic T, Jonnalagadda SVR, Gentz R, Hillson NJ, Peisert S, Kim J, Simmons BA, Petzold CJ, Singer SW, Mukhopadhyay A, Tanjore D, Dunn JG, Garcia Martin H. Machine learning for metabolic engineering: A review. Metab Eng 2020; 63:34-60. [PMID: 33221420 DOI: 10.1016/j.ymben.2020.10.005] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/22/2020] [Accepted: 10/31/2020] [Indexed: 12/14/2022]
Abstract
Machine learning provides researchers a unique opportunity to make metabolic engineering more predictable. In this review, we offer an introduction to this discipline in terms that are relatable to metabolic engineers, as well as providing in-depth illustrative examples leveraging omics data and improving production. We also include practical advice for the practitioner in terms of data management, algorithm libraries, computational resources, and important non-technical issues. A variety of applications ranging from pathway construction and optimization, to genetic editing optimization, cell factory testing, and production scale-up are discussed. Moreover, the promising relationship between machine learning and mechanistic models is thoroughly reviewed. Finally, the future perspectives and most promising directions for this combination of disciplines are examined.
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Affiliation(s)
- Christopher E Lawson
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA
| | - Jose Manuel Martí
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Tijana Radivojevic
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Sai Vamshi R Jonnalagadda
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Reinhard Gentz
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Nathan J Hillson
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Sean Peisert
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; University of California Davis, Davis, CA, 95616, USA
| | - Joonhoon Kim
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA; Pacific Northwest National Laboratory, Richland, 99354, WA, USA
| | - Blake A Simmons
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Christopher J Petzold
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Steven W Singer
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, USA
| | - Deepti Tanjore
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Advanced Biofuels and Bioproducts Process Development Unit, Emeryville, CA, 94608, USA
| | | | - Hector Garcia Martin
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA; Basque Center for Applied Mathematics, 48009, Bilbao, Spain; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, USA.
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57
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58
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Hershewe J, Kightlinger W, Jewett MC. Cell-free systems for accelerating glycoprotein expression and biomanufacturing. J Ind Microbiol Biotechnol 2020; 47:977-991. [PMID: 33090335 PMCID: PMC7578589 DOI: 10.1007/s10295-020-02321-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/03/2020] [Indexed: 12/17/2022]
Abstract
Protein glycosylation, the enzymatic modification of amino acid sidechains with sugar moieties, plays critical roles in cellular function, human health, and biotechnology. However, studying and producing defined glycoproteins remains challenging. Cell-free glycoprotein synthesis systems, in which protein synthesis and glycosylation are performed in crude cell extracts, offer new approaches to address these challenges. Here, we review versatile, state-of-the-art systems for biomanufacturing glycoproteins in prokaryotic and eukaryotic cell-free systems with natural and synthetic N-linked glycosylation pathways. We discuss existing challenges and future opportunities in the use of cell-free systems for the design, manufacture, and study of glycoprotein biomedicines.
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Affiliation(s)
- Jasmine Hershewe
- Department of Chemical and Biological Engineering, Northwestern University, Technological Institute E136, 2145 Sheridan Road, Evanston, IL, 60208-3120, USA.,Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208-3120, USA.,Center for Synthetic Biology, Northwestern University, Technological Institute E136, 2145 Sheridan Road, Evanston, IL, 60208-3120, USA
| | - Weston Kightlinger
- Department of Chemical and Biological Engineering, Northwestern University, Technological Institute E136, 2145 Sheridan Road, Evanston, IL, 60208-3120, USA.,Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208-3120, USA.,Center for Synthetic Biology, Northwestern University, Technological Institute E136, 2145 Sheridan Road, Evanston, IL, 60208-3120, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Technological Institute E136, 2145 Sheridan Road, Evanston, IL, 60208-3120, USA. .,Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208-3120, USA. .,Center for Synthetic Biology, Northwestern University, Technological Institute E136, 2145 Sheridan Road, Evanston, IL, 60208-3120, USA. .,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, 676 North Saint Clair Street, Suite 1200, Chicago, IL, 60611-3068, USA. .,Simpson Querrey Institute, Northwestern University, 303 East Superior Street, Suite 11-131, Chicago, IL, 60611-2875, USA.
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59
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Ogawa A, Itoh Y. In Vitro Selection of RNA Aptamers Binding to Nanosized DNA for Constructing Artificial Riboswitches. ACS Synth Biol 2020; 9:2648-2655. [PMID: 33017145 DOI: 10.1021/acssynbio.0c00384] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We here designed an in vitro selection scheme for obtaining an aptamer with which to rationally construct an artificial riboswitch as its component part. In fact, a nanosized DNA-binding aptamer obtained through this scheme allowed us to easily and successfully create eukaryotic riboswitches that upregulate internal ribosome entry site-mediated translation in response to the ligand (nanosized DNA) in wheat germ extract, a eukaryotic cell-free expression system. The induction ratio of the best riboswitch ligand-dose-dependently increased to 21 at 300 μM ligand. This switching efficiency is much higher than that of the same type of riboswitch with a widely used theophylline-binding aptamer, which was in vitro selected without considering its utility for constructing riboswitches. The selection scheme described here would facilitate obtaining various ligand/aptamer pairs suitable for constructing artificial riboswitches, which could serve as elements of synthetic gene circuits in synthetic biology.
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Affiliation(s)
- Atsushi Ogawa
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Yu Itoh
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
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60
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Wei TY, Ruder WC. Engineering control circuits for molecular robots using synthetic biology. APL MATERIALS 2020; 8:101104. [PMID: 33101786 PMCID: PMC7560983 DOI: 10.1063/5.0020429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/24/2020] [Indexed: 06/11/2023]
Abstract
The integration of molecular robots and synthetic biology allows for the creation of sophisticated behaviors at the molecular level. Similar to the synergy between bioelectronics and soft robotics, synthetic biology provides control circuitry for molecular robots. By encoding perception-action modules within synthetic circuits, molecular machines can advance beyond repeating tasks to the incorporation of complex behaviors. In particular, cell-free synthetic biology provides biomolecular circuitry independent of living cells. This research update reviews the current progress in using synthetic biology as perception-action control modules in robots from molecular robots to macroscale robots. Additionally, it highlights recent developments in molecular robotics and cell-free synthetic biology and suggests their combined use as a necessity for future molecular robot development.
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Affiliation(s)
- Ting-Yen Wei
- Department of Bioengineering, University of
Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
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61
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Radivojević T, Costello Z, Workman K, Garcia Martin H. A machine learning Automated Recommendation Tool for synthetic biology. Nat Commun 2020; 11:4879. [PMID: 32978379 PMCID: PMC7519645 DOI: 10.1038/s41467-020-18008-4] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 07/27/2020] [Indexed: 01/07/2023] Open
Abstract
Synthetic biology allows us to bioengineer cells to synthesize novel valuable molecules such as renewable biofuels or anticancer drugs. However, traditional synthetic biology approaches involve ad-hoc engineering practices, which lead to long development times. Here, we present the Automated Recommendation Tool (ART), a tool that leverages machine learning and probabilistic modeling techniques to guide synthetic biology in a systematic fashion, without the need for a full mechanistic understanding of the biological system. Using sampling-based optimization, ART provides a set of recommended strains to be built in the next engineering cycle, alongside probabilistic predictions of their production levels. We demonstrate the capabilities of ART on simulated data sets, as well as experimental data from real metabolic engineering projects producing renewable biofuels, hoppy flavored beer without hops, fatty acids, and tryptophan. Finally, we discuss the limitations of this approach, and the practical consequences of the underlying assumptions failing.
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Affiliation(s)
- Tijana Radivojević
- DOE Agile BioFoundry, Emeryville, CA, 94608, USA
- Biofuels and Bioproducts Division, DOE Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Zak Costello
- DOE Agile BioFoundry, Emeryville, CA, 94608, USA
- Biofuels and Bioproducts Division, DOE Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kenneth Workman
- DOE Agile BioFoundry, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
| | - Hector Garcia Martin
- DOE Agile BioFoundry, Emeryville, CA, 94608, USA.
- Biofuels and Bioproducts Division, DOE Joint BioEnergy Institute, Emeryville, CA, 94608, USA.
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
- BCAM, Basque Center for Applied Mathematics, Bilbao, 48009, Spain.
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62
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Cell-free styrene biosynthesis at high titers. Metab Eng 2020; 61:89-95. [DOI: 10.1016/j.ymben.2020.05.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/13/2020] [Accepted: 05/25/2020] [Indexed: 11/18/2022]
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63
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Liu R, Zhang Y, Zhai G, Fu S, Xia Y, Hu B, Cai X, Zhang Y, Li Y, Deng Z, Liu T. A Cell-Free Platform Based on Nisin Biosynthesis for Discovering Novel Lanthipeptides and Guiding their Overproduction In Vivo. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2001616. [PMID: 32995136 PMCID: PMC7507342 DOI: 10.1002/advs.202001616] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/10/2020] [Indexed: 05/12/2023]
Abstract
Lanthipeptides have extensive therapeutic and industrial applications. However, because many are bactericidal, traditional in vivo platforms are limited in their capacity to discover and mass produce novel lanthipeptides as bacterial organisms are often critical components in these systems. Herein, the development of a cell-free protein synthesis (CFPS) platform that enables rapid genome mining, screening, and guided overproduction of lanthipeptides in vivo is described. For proof-of-concept studies, a type I lanthipeptide, nisin, is selected. Four novel lanthipeptides with antibacterial activity are identified among all nisin analogs in the National Center for Biotechnology Information (NCBI) database in a single day. Further, the CFPS platform is coupled with a screening assay for anti-gram-negative bacteria growth, resulting in the identification of a potent nisin mutant, M5. The titers of nisin and the nisin analog are found to be improved with CFPS platform guidance. Owing to the similarities in biosynthesis, the CFPS platform is broadly applicable to other lanthipeptides, thereby providing a universal method for lanthipeptide discovery and overproduction.
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Affiliation(s)
- Ran Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education and Wuhan University School of Pharmaceutical Sciences Wuhan 430071 China
| | - Yuchen Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education and Wuhan University School of Pharmaceutical Sciences Wuhan 430071 China
| | - Guoqing Zhai
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education and Wuhan University School of Pharmaceutical Sciences Wuhan 430071 China
| | - Shuai Fu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education and Wuhan University School of Pharmaceutical Sciences Wuhan 430071 China
| | - Yao Xia
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education and Wuhan University School of Pharmaceutical Sciences Wuhan 430071 China
| | - Ben Hu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education and Wuhan University School of Pharmaceutical Sciences Wuhan 430071 China
| | - Xuan Cai
- Department of Clinical Laboratory Renmin Hospital of Wuhan University Wuhan 430060 China
| | - Yan Zhang
- Department of Clinical Laboratory Renmin Hospital of Wuhan University Wuhan 430060 China
| | - Yan Li
- Department of Clinical Laboratory Renmin Hospital of Wuhan University Wuhan 430060 China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education and Wuhan University School of Pharmaceutical Sciences Wuhan 430071 China
- Hubei Engineering Laboratory for Synthetic Microbiology Wuhan Institute of Biotechnology Wuhan 430075 China
| | - Tiangang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education and Wuhan University School of Pharmaceutical Sciences Wuhan 430071 China
- Hubei Engineering Laboratory for Synthetic Microbiology Wuhan Institute of Biotechnology Wuhan 430075 China
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64
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Spice AJ, Aw R, Bracewell DG, Polizzi KM. Improving the reaction mix of a Pichia pastoris cell-free system using a design of experiments approach to minimise experimental effort. Synth Syst Biotechnol 2020; 5:137-144. [PMID: 32637667 PMCID: PMC7320237 DOI: 10.1016/j.synbio.2020.06.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 06/07/2020] [Accepted: 06/08/2020] [Indexed: 12/20/2022] Open
Abstract
A renaissance in cell-free protein synthesis (CFPS) is underway, enabled by the acceleration and adoption of synthetic biology methods. CFPS has emerged as a powerful platform technology for synthetic gene network design, biosensing and on-demand biomanufacturing. Whilst primarily of bacterial origin, cell-free extracts derived from a variety of host organisms have been explored, aiming to capitalise on cellular diversity and the advantageous properties associated with those organisms. However, cell-free extracts produced from eukaryotes are often overlooked due to their relatively low yields, despite the potential for improved protein folding and posttranslational modifications. Here we describe further development of a Pichia pastoris cell-free platform, a widely used expression host in both academia and the biopharmaceutical industry. Using a minimised Design of Experiments (DOE) approach, we were able to increase the productivity of the system by improving the composition of the complex reaction mixture. This was achieved in a minimal number of experimental runs, within the constraints of the design and without the need for liquid-handling robots. In doing so, we were able to estimate the main effects impacting productivity in the system and increased the protein synthesis of firefly luciferase and the biopharmaceutical HSA by 4.8-fold and 3.5-fold, respectively. This study highlights the P. pastoris-based cell-free system as a highly productive eukaryotic platform and displays the value of minimised DOE designs.
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Key Words
- AB, Albumin Blue
- CFPS, cell-free protein synthesis
- CHO, Chinese hamster ovary cells
- Cell-free protein synthesis
- DOE, design of Experiments
- DSD, definitive screening design
- Design of experiments (DOE)
- HSA, human serum albumin
- IRES, internal ribosome entry site
- Pichia pastoris
- RRL, rabbit reticulocyte lysate
- Synthetic biology
- VLP, virus-like particles
- WGE, wheat-germ etract
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Affiliation(s)
- Alex J. Spice
- Department of Chemical Engineering, Imperial College London, London, UK
- Imperial College Centre for Synthetic Biology, Imperial College London, UK
| | - Rochelle Aw
- Department of Chemical Engineering, Imperial College London, London, UK
- Imperial College Centre for Synthetic Biology, Imperial College London, UK
| | - Daniel G. Bracewell
- Department of Biochemical Engineering, University College London, London, UK
| | - Karen M. Polizzi
- Department of Chemical Engineering, Imperial College London, London, UK
- Imperial College Centre for Synthetic Biology, Imperial College London, UK
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65
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Takahashi H, Ogawa A. Preparation of a Millimeter-Sized Supergiant Liposome That Allows for Efficient, Eukaryotic Cell-Free Translation in the Interior by Spontaneous Emulsion Transfer. ACS Synth Biol 2020; 9:1608-1614. [PMID: 32559381 DOI: 10.1021/acssynbio.0c00173] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We sought to prepare millimeter-sized supergiant unilamellar vesicles (SGUVs) by spontaneous emulsion transfer for efficient, eukaryotic cell-free translation in the interior. Although the conventional protocols require that a considerably high concentration of sucrose be encapsulated into the SGUVs for their efficient formation, such high amounts of sucrose severely inhibited cell-free translation based on wheat germ extract (WGE). We thus optimized the preparation conditions to permit SGUV formation at a much lower concentration of sucrose that has almost no effect on WGE translation. Under the optimized conditions, we successfully prepared WGE translation system-encapsulating SGUVs that allow for protein synthesis with a high efficiency comparable to that outside a liposome. The optimization also resulted in a high rate of successful SGUV formation (>90%) and a decent stability of the formed SGUVs (>60 min). These SGUVs are expected to serve as research tools in cell-free synthetic biology and as foundations for artificial cell-based biosensors.
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Affiliation(s)
- Hajime Takahashi
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Atsushi Ogawa
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
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66
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Synthetic Biochemistry: The Bio-inspired Cell-Free Approach to Commodity Chemical Production. Trends Biotechnol 2020; 38:766-778. [DOI: 10.1016/j.tibtech.2019.12.024] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 12/19/2019] [Accepted: 12/20/2019] [Indexed: 01/26/2023]
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67
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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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68
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François JM, Jantti J, Daboussi F. Editorial: 4th Applied Synthetic Biology in Europe. Front Bioeng Biotechnol 2020; 8:431. [PMID: 32435639 PMCID: PMC7219059 DOI: 10.3389/fbioe.2020.00431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 04/15/2020] [Indexed: 11/25/2022] Open
Affiliation(s)
- Jean Marie François
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.,Toulouse White Biotechnology Center, UMS-INSA-INRA-CNRS, Ramonville St Agnes, France
| | - Jussi Jantti
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - Fayza Daboussi
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.,Toulouse White Biotechnology Center, UMS-INSA-INRA-CNRS, Ramonville St Agnes, France
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69
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Borkowski O, Koch M, Zettor A, Pandi A, Batista AC, Soudier P, Faulon JL. Large scale active-learning-guided exploration for in vitro protein production optimization. Nat Commun 2020; 11:1872. [PMID: 32312991 PMCID: PMC7170859 DOI: 10.1038/s41467-020-15798-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/24/2020] [Indexed: 12/21/2022] Open
Abstract
Lysate-based cell-free systems have become a major platform to study gene expression but batch-to-batch variation makes protein production difficult to predict. Here we describe an active learning approach to explore a combinatorial space of ~4,000,000 cell-free buffer compositions, maximizing protein production and identifying critical parameters involved in cell-free productivity. We also provide a one-step-method to achieve high quality predictions for protein production using minimal experimental effort regardless of the lysate quality.
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Affiliation(s)
- Olivier Borkowski
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Mathilde Koch
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Agnès Zettor
- Chemogenomic and Biological Screening Core Facility, Institut Pasteur, Department of Structural Biology and Chemistry, Center for Technological Resources and Research (C2RT), 25/28 rue du Dr Roux, 75724, Paris Cedex 15, France
| | - Amir Pandi
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | | | - Paul Soudier
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Jean-Loup Faulon
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France. .,Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France. .,SYNBIOCHEM Center, Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK.
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70
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Kyrilis FL, Meister A, Kastritis PL. Integrative biology of native cell extracts: a new era for structural characterization of life processes. Biol Chem 2020; 400:831-846. [PMID: 31091193 DOI: 10.1515/hsz-2018-0445] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 03/29/2019] [Indexed: 01/04/2023]
Abstract
Advances in electron microscopy have provided unprecedented access to the structural characterization of large, flexible and heterogeneous complexes. Until recently, cryo-electron microscopy (cryo-EM) has been applied to understand molecular organization in either highly purified, isolated biomolecules or in situ. An emerging field is developing, bridging the gap between the two approaches, and focuses on studying molecular organization in native cell extracts. This field has demonstrated its potential by resolving the structure of fungal fatty acid synthase (FAS) at 4.7 Å [Fourier shell correlation (FSC) = 0.143]; FAS was not only less than 50% enriched, but also retained higher-order binders, previously unknown. Although controversial in the sense that the lysis step might introduce artifacts, cell extracts preserve aspects of cellular function. In addition, cell extracts are accessible, besides cryo-EM, to modern proteomic methods, chemical cross-linking, network biology and biophysical modeling. We expect that automation in imaging cell extracts, along with the integration of molecular/cell biology approaches, will provide remarkable achievements in the study of closer-to-life biomolecular states of pronounced biotechnological and medical importance. Such steps will, eventually, bring us a step closer to the biophysical description of cellular processes in an integrative, holistic approach.
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Affiliation(s)
- Fotis L Kyrilis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, D-06120 Halle/Saale, Germany
| | - Annette Meister
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, D-06120 Halle/Saale, Germany.,Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, D-06120 Halle/Saale, Germany
| | - Panagiotis L Kastritis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, D-06120 Halle/Saale, Germany.,Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, D-06120 Halle/Saale, Germany.,Biozentrum, Martin Luther University Halle-Wittenberg, Weinbergweg 22, D-06120 Halle/Saale, Germany
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71
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Spice AJ, Aw R, Bracewell DG, Polizzi KM. Synthesis and Assembly of Hepatitis B Virus-Like Particles in a Pichia pastoris Cell-Free System. Front Bioeng Biotechnol 2020; 8:72. [PMID: 32117947 PMCID: PMC7033515 DOI: 10.3389/fbioe.2020.00072] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 01/28/2020] [Indexed: 12/13/2022] Open
Abstract
Virus-like particles (VLPs) are supramolecular protein assemblies with the potential for unique and exciting applications in synthetic biology and medicine. Despite the attention VLPs have gained thus far, considerable limitations still persist in their production. Poorly scalable manufacturing technologies and inconsistent product architectures continue to restrict the full potential of VLPs. Cell-free protein synthesis (CFPS) offers an alternative approach to VLP production and has already proven to be successful, albeit using extracts from a limited number of organisms. Using a recently developed Pichia pastoris-based CFPS system, we have demonstrated the production of the model Hepatitis B core antigen VLP as a proof-of-concept. The VLPs produced in the CFPS system were found to have comparable characteristics to those previously produced in vivo and in vitro. Additionally, we have developed a facile and rapid synthesis, assembly and purification methodology that could be applied as a rapid prototyping platform for vaccine development or synthetic biology applications. Overall the CFPS methodology allows far greater throughput, which will expedite the screening of optimal assembly conditions for more robust and stable VLPs. This approach could therefore support the characterization of larger sample sets to improve vaccine development efficiency.
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Affiliation(s)
- Alex J. Spice
- Department of Chemical Engineering, Imperial College London, London, United Kingdom
- The Imperial College Centre for Synthetic Biology Imperial College London, London, United Kingdom
| | - Rochelle Aw
- Department of Chemical Engineering, Imperial College London, London, United Kingdom
- The Imperial College Centre for Synthetic Biology Imperial College London, London, United Kingdom
| | - Daniel G. Bracewell
- Department of Biochemical Engineering, University College London, London, United Kingdom
| | - Karen M. Polizzi
- Department of Chemical Engineering, Imperial College London, London, United Kingdom
- The Imperial College Centre for Synthetic Biology Imperial College London, London, United Kingdom
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72
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Alissandratos A. In vitro multi-enzymatic cascades using recombinant lysates of E. coli: an emerging biocatalysis platform. Biophys Rev 2020; 12:175-182. [PMID: 31960346 PMCID: PMC7040066 DOI: 10.1007/s12551-020-00618-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 01/07/2020] [Indexed: 11/26/2022] Open
Abstract
In recent years, cell-free extracts (or lysates) have (re-)emerged as a third route to the traditional options of isolated or whole-cell biocatalysts. Advances in molecular biology and genetic engineering enable facile production of recombinant cell-free extracts, where endogenous enzymes are enriched with heterologous activities. These inexpensive preparations may be used to catalyse multistep enzymatic reactions without the constraints of cell toxicity and the cell membrane or the cost and complexity associated with production of isolated biocatalysts. Herein, we present an overview of the key advancements in cell-free synthetic biology that have led to the emergence of cell-free extracts as a promising biocatalysis platform.
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Affiliation(s)
- Apostolos Alissandratos
- Research School of Chemistry, The Australian National University, ACT, Canberra, 2601, Australia.
- CSIRO Synthetic Biology Future Science Platform, The Australian National University, ACT, Canberra, 2601, Australia.
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73
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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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74
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Woodley JM. Advances in biological conversion technologies: new opportunities for reaction engineering. REACT CHEM ENG 2020. [DOI: 10.1039/c9re00422j] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reaction engineering needs to embrace biological conversion technologies, on the road to identify more sustainable routes for chemical manufacture.
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Affiliation(s)
- John M. Woodley
- Department of Chemical and Biochemical Engineering
- Technical University of Denmark (DTU)
- DK-2800 Kgs. Lyngby
- Denmark
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75
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Whitfield CJ, Banks AM, Dura G, Love J, Fieldsend JE, Goodchild SA, Fulton DA, Howard TP. Cell-free protein synthesis in hydrogel materials. Chem Commun (Camb) 2020; 56:7108-7111. [DOI: 10.1039/d0cc02582h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Fabrication of macro-scale polysaccharide, proteinaceous, micellular and covalently crosslinked hydrogels for housing cell-free protein synthesis reactions.
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Affiliation(s)
- Colette J. Whitfield
- School of Natural and Environmental Sciences
- Faculty of Science, Agriculture and Engineering
- Newcastle University
- Newcastle
- UK
| | - Alice M. Banks
- School of Natural and Environmental Sciences
- Faculty of Science, Agriculture and Engineering
- Newcastle University
- Newcastle
- UK
| | - Gema Dura
- School of Natural and Environmental Sciences
- Faculty of Science, Agriculture and Engineering
- Newcastle University
- Newcastle
- UK
| | - John Love
- Biosciences, College of Life and Environmental Sciences
- University of Exeter
- Exeter
- UK
| | - Jonathan E. Fieldsend
- Computer Science, College of Engineering, Mathematics and Physical Sciences
- University of Exeter
- UK
| | | | - David A. Fulton
- School of Natural and Environmental Sciences
- Faculty of Science, Agriculture and Engineering
- Newcastle University
- Newcastle
- UK
| | - Thomas P. Howard
- School of Natural and Environmental Sciences
- Faculty of Science, Agriculture and Engineering
- Newcastle University
- Newcastle
- UK
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76
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Cui Z, Mao Y, Zhao Y, Zheng M, Wang Z, Ma H, Chen T. One-pot efficient biosynthesis of (3 R)-acetoin from pyruvate by a two-enzyme cascade. Catal Sci Technol 2020. [DOI: 10.1039/d0cy01332c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Opening the possibility of sustainable industrial (3R)-acetoin biomanufacturing in vitro.
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Affiliation(s)
- Zhenzhen Cui
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education)
- SynBio Research Platform
- Collaborative Innovation Center of Chemical Science and Engineering
- School of Chemical Engineering and Technology
- Tianjin University
| | - Yufeng Mao
- Biodesign Center
- Key Laboratory of Systems Microbial Biotechnology
- Tianjin Institute of Industrial Biotechnology
- Chinese Academy of Sciences
- Tianjin 300308
| | - Yujiao Zhao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education)
- SynBio Research Platform
- Collaborative Innovation Center of Chemical Science and Engineering
- School of Chemical Engineering and Technology
- Tianjin University
| | - Meiyu Zheng
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education)
- SynBio Research Platform
- Collaborative Innovation Center of Chemical Science and Engineering
- School of Chemical Engineering and Technology
- Tianjin University
| | - Zhiwen Wang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education)
- SynBio Research Platform
- Collaborative Innovation Center of Chemical Science and Engineering
- School of Chemical Engineering and Technology
- Tianjin University
| | - Hongwu Ma
- Biodesign Center
- Key Laboratory of Systems Microbial Biotechnology
- Tianjin Institute of Industrial Biotechnology
- Chinese Academy of Sciences
- Tianjin 300308
| | - Tao Chen
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education)
- SynBio Research Platform
- Collaborative Innovation Center of Chemical Science and Engineering
- School of Chemical Engineering and Technology
- Tianjin University
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77
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Interfacing electronic and genetic circuits. Nat Chem 2019; 12:14-16. [PMID: 31827273 DOI: 10.1038/s41557-019-0403-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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78
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Zang Y, Zha J, Wu X, Zheng Z, Ouyang J, Koffas MAG. In Vitro Naringenin Biosynthesis from p-Coumaric Acid Using Recombinant Enzymes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:13430-13436. [PMID: 30919618 DOI: 10.1021/acs.jafc.9b00413] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Naringenin is an important precursor for the production of a wide spectrum of flavonoids, and its production is of great interest in metabolic engineering. However, in cellular systems, identification of rate-limiting factors is often difficult because of complex regulatory networks. Cell-free catalytic systems emerge as a promising method to address this issue. Here, we explored the cell-free biosystem for naringenin production by combining different sources of 4-coumaroyl-CoA ligase (4CL), chalcone synthase (CHS), and chalcone isomerase (CHI). After systematic analysis of enzyme levels, substrate concentrations, and cofactors, 4CL and CHS were found to be crucial to the reaction. The best loading ratio of 4CL/CHS/CHI was 10:10:1, and malonyl-CoA was the limiting factor, as identified previously in fermentation. For the first time, we successfully constructed the system for naringenin production in vitro. Our study will deepen our understanding of the key factors in naringenin production and guide further engineering.
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79
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Horvath N, Vilkhovoy M, Wayman JA, Calhoun K, Swartz J, Varner JD. Toward a genome scale sequence specific dynamic model of cell-free protein synthesis in Escherichia coli. Metab Eng Commun 2019; 10:e00113. [PMID: 32280586 PMCID: PMC7136494 DOI: 10.1016/j.mec.2019.e00113] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 10/15/2019] [Accepted: 11/19/2019] [Indexed: 11/09/2022] Open
Abstract
In this study, we developed a dynamic mathematical model of E. coli cell-free protein synthesis (CFPS). Model parameters were estimated from a dataset consisting of glucose, organic acids, energy species, amino acids, and protein product, chloramphenicol acetyltransferase (CAT) measurements. The model was successfully trained to simulate these measurements, especially those of the central carbon metabolism. We then used the trained model to evaluate the performance, e.g., the yield and rates of protein production. CAT was produced with an energy efficiency of 12%, suggesting that the process could be further optimized. Reaction group knockouts showed that protein productivity was most sensitive to the oxidative phosphorylation and glycolysis/gluconeogenesis pathways. Amino acid biosynthesis was also important for productivity, while overflow metabolism and TCA cycle affected the overall system state. In addition, translation was more important to productivity than transcription. Finally, CAT production was robust to allosteric control, as were most of the predicted metabolite concentrations; the exceptions to this were the concentrations of succinate and malate, and to a lesser extent pyruvate and acetate, which varied from the measured values when allosteric control was removed. This study is the first to use kinetic modeling to predict dynamic protein production in a cell-free E. coli system, and could provide a foundation for genome scale, dynamic modeling of cell-free E. coli protein synthesis. Protein production is biphasic, powered initially by glucose and later by pyruvate. Protein is produced with an energy efficiency of only 12%. Protein productivity is most sensitive to oxidative phosphorylation and glycolysis. Protein production is robust to allosteric control.
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Affiliation(s)
- Nicholas Horvath
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Michael Vilkhovoy
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Joseph A Wayman
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, 14853, USA
| | - Kara Calhoun
- School of Chemical Engineering, Stanford University, Stanford, CA, 94395, USA
| | - James Swartz
- School of Chemical Engineering, Stanford University, Stanford, CA, 94395, USA
| | - Jeffrey D Varner
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
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80
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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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81
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Jones K, Kentala K, Beck MW, An W, Lippert AR, Lewis JC, Dickinson BC. Development of a Split Esterase for Protein-Protein Interaction-Dependent Small-Molecule Activation. ACS CENTRAL SCIENCE 2019; 5:1768-1776. [PMID: 31807678 PMCID: PMC6891849 DOI: 10.1021/acscentsci.9b00567] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Indexed: 05/21/2023]
Abstract
Split reporters based on fluorescent proteins and luciferases have emerged as valuable tools for measuring interactions in biological systems. Relatedly, biosensors that transduce measured input signals into outputs that influence the host system are key components of engineered gene circuits for synthetic biology applications. While small-molecule-based imaging agents are widely used in biological studies, and small-molecule-based drugs and chemical probes can target a range of biological processes, a general method for generating a target small molecule in a biological system based on a measured input signal is lacking. Here, we develop a proximity-dependent split esterase that selectively unmasks ester-protected small molecules in an interaction-dependent manner. Exploiting the versatility of an ester-protected small-molecule output, we demonstrate fluorescent, chemiluminescent, and pharmacological probe generation, each created by masking key alcohol functional groups on a target small molecule. We show that the split esterase system can be used in combination with ester-masked fluorescent or luminescent probes to measure protein-protein interactions and protein-protein interaction inhibitor engagement. We demonstrate that the esterase-based reporter system is compatible with other commonly used split reporter imaging systems for the simultaneous detection of multiple protein-protein interactions. Finally, we develop a system for selective small-molecule-dependent cell killing by unmasking a cytotoxic molecule using an inducible split esterase. Presaging utility in future synthetic biology-based therapeutic applications, we also show that the system can be used for intercellular cell killing via a bystander effect, where one activated cell unmasks a cytotoxic molecule and kills cells physically adjacent to the activated cells. Collectively, this work illustrates that the split esterase system is a valuable new addition to the split protein toolbox, with particularly exciting potential in synthetic biology applications.
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Affiliation(s)
- Krysten
A. Jones
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Kaitlin Kentala
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Michael W. Beck
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Weiwei An
- Department
of Chemistry, Center for Drug Discovery, Design, and Delivery (CD4),
Center for Global Health Impact (CGHI), Southern Methodist University, Dallas, Texas 75275-0314, United States
| | - Alexander R. Lippert
- Department
of Chemistry, Center for Drug Discovery, Design, and Delivery (CD4),
Center for Global Health Impact (CGHI), Southern Methodist University, Dallas, Texas 75275-0314, United States
| | - Jared C. Lewis
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Bryan C. Dickinson
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
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82
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Enzyme alchemy: cell-free synthetic biochemistry for natural products. Emerg Top Life Sci 2019; 3:529-535. [PMID: 33523168 DOI: 10.1042/etls20190083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/09/2019] [Accepted: 08/12/2019] [Indexed: 12/19/2022]
Abstract
Cell-free synthetic biochemistry aims to engineer chemical biology by exploiting biosynthetic dexterity outside of the constraints of a living cell. One particular use is for making natural products, where cell-free systems have initially demonstrated feasibility in the biosynthesis of a range of complex natural products classes. This has shown key advantages over total synthesis, such as increased yield, enhanced regioselectivity, use of reduced temperatures and less reaction steps. Uniquely, cell-free synthetic biochemistry represents a new area that seeks to advance upon these efforts and is particularly useful for defining novel synthetic pathways to replace natural routes and optimising the production of complex natural product targets from low-cost precursors. Key challenges and opportunities will include finding solutions to scaled-up cell-free biosynthesis, as well as the targeting of high value and toxic natural products that remain challenging to make either through whole-cell biotransformation platforms or total synthesis routes. Although underexplored, cell-free synthetic biochemistry could also be used to develop 'non-natural' natural products or so-called xenobiotics for novel antibiotics and drugs, which can be difficult to engineer directly within a living cell.
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83
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Des Soye BJ, Gerbasi VR, Thomas PM, Kelleher NL, Jewett MC. A Highly Productive, One-Pot Cell-Free Protein Synthesis Platform Based on Genomically Recoded Escherichia coli. Cell Chem Biol 2019; 26:1743-1754.e9. [PMID: 31706984 DOI: 10.1016/j.chembiol.2019.10.008] [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] [Received: 07/19/2018] [Revised: 06/05/2019] [Accepted: 10/18/2019] [Indexed: 12/26/2022]
Abstract
The site-specific incorporation of non-canonical amino acids (ncAAs) into proteins via amber suppression provides access to novel protein properties, structures, and functions. Historically, poor protein expression yields resulting from release factor 1 (RF1) competition has limited this technology. To address this limitation, we develop a high-yield, one-pot cell-free platform for synthesizing proteins bearing ncAAs based on genomically recoded Escherichia coli lacking RF1. A key feature of this platform is the independence on the addition of purified T7 DNA-directed RNA polymerase (T7RNAP) to catalyze transcription. Extracts derived from our final strain demonstrate high productivity, synthesizing 2.67 ± 0.06 g/L superfolder GFP in batch mode without supplementation of purified T7RNAP. Using an optimized one-pot platform, we demonstrate multi-site incorporation of the ncAA p-acetyl-L-phenylalanine into an elastin-like polypeptide with high accuracy of incorporation and yield. Our work has implications for chemical and synthetic biology.
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Affiliation(s)
- Benjamin J Des Soye
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Vincent R Gerbasi
- Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208, USA
| | - Paul M Thomas
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA; Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208, USA; Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Neil L Kelleher
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA; Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208, USA; Department of Chemistry, Northwestern University, Evanston, IL 60208, USA; Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Michael C Jewett
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA; Department of Chemical and Biological Engineering, 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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84
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Schmuck B, Gudmundsson M, Härd T, Sandgren M. Coupled chemistry kinetics demonstrate the utility of functionalized Sup35 amyloid nanofibrils in biocatalytic cascades. J Biol Chem 2019; 294:14966-14977. [PMID: 31416835 PMCID: PMC6791322 DOI: 10.1074/jbc.ra119.008455] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 08/14/2019] [Indexed: 01/06/2023] Open
Abstract
Concerns over the environment are a central driver for designing cell-free enzymatic cascade reactions that synthesize non-petrol-based commodity compounds. An often-suggested strategy that would demonstrate the economic competitiveness of this technology is recycling of valuable enzymes through their immobilization. For this purpose, amyloid nanofibrils are an ideal scaffold to realize chemistry-free covalent enzyme immobilization on a material that offers a large surface area. However, in most instances, only single enzyme-functionalized amyloid fibrils have so far been studied. To embark on the next stage, here we displayed xylanase A, β-xylosidase, and an aldose sugar dehydrogenase on Sup35(1-61) nanofibrils to convert beechwood xylan to xylonolactone. We characterized this enzymatic cascade by measuring the time-dependent accumulation of xylose, xylooligomers, and xylonolactone. Furthermore, we studied the effects of relative enzyme concentrations, pH, temperature, and agitation on product formation. Our investigations revealed that a modular cascade with a mixture of xylanase and β-xylosidase, followed by product removal and separate oxidation of xylose with the aldose sugar dehydrogenase, is more productive than an enzyme mix containing all of these enzymes together. Moreover, we found that the nanofibril-coupled enzymes do not lose activity compared with their native state. These findings provide proof of concept of the feasibility of functionalized Sup35(1-61) fibrils as a molecular scaffold for biocatalytic cascades consisting of reusable enzymes that can be used in biotechnology.
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Affiliation(s)
- Benjamin Schmuck
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, 750 07 Uppsala, Sweden
| | - Mikael Gudmundsson
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, 750 07 Uppsala, Sweden
| | - Torleif Härd
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, 750 07 Uppsala, Sweden
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, 750 07 Uppsala, Sweden
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85
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Khambhati K, Bhattacharjee G, Gohil N, Braddick D, Kulkarni V, Singh V. Exploring the Potential of Cell-Free Protein Synthesis for Extending the Abilities of Biological Systems. Front Bioeng Biotechnol 2019; 7:248. [PMID: 31681738 PMCID: PMC6797904 DOI: 10.3389/fbioe.2019.00248] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 09/16/2019] [Indexed: 12/19/2022] Open
Abstract
Cell-free protein synthesis (CFPS) system is a simple, rapid, and sensitive tool that is devoid of membrane-bound barriers, yet contains all the mandatory substrates, biomolecules, and machineries required for the synthesis of the desired proteins. It has the potential to overcome loopholes in the current in vivo production systems and is a promising tool in both basic and applied scientific research. It facilitates a simplified organization of desired experiments with a variety of reaction conditions, making CFPS a powerful tool in biological research. It has been used for the expansion of genetic code, assembly of viruses, and in metabolic engineering for production of toxic and complex proteins. Subsequently, CFPS systems have emerged as potent technology for high-throughput production of membrane proteins, enzymes, and therapeutics. The present review highlights the recent advances and uses of CFPS systems in biomedical, therapeutic, and biotechnological applications. Additionally, we highlight possible solutions to the potential biosafety issues that may be encountered while using CFPS technology.
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Affiliation(s)
- Khushal Khambhati
- Department of Biological Sciences and Biotechnology, Institute of Advanced Research, Gandhinagar, India
| | - Gargi Bhattacharjee
- Department of Biological Sciences and Biotechnology, Institute of Advanced Research, Gandhinagar, India
| | - Nisarg Gohil
- Department of Biological Sciences and Biotechnology, Institute of Advanced Research, Gandhinagar, India
| | | | - Vishwesh Kulkarni
- School of Engineering, University of Warwick, Coventry, United Kingdom
| | - Vijai Singh
- Department of Biological Sciences and Biotechnology, Institute of Advanced Research, Gandhinagar, India
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86
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Gabant P, Borrero J. PARAGEN 1.0: A Standardized Synthetic Gene Library for Fast Cell-Free Bacteriocin Synthesis. Front Bioeng Biotechnol 2019; 7:213. [PMID: 31552239 PMCID: PMC6743375 DOI: 10.3389/fbioe.2019.00213] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 08/22/2019] [Indexed: 02/06/2023] Open
Abstract
The continuous emergence of microbial resistance to our antibiotic arsenal is widely becoming recognized as an imminent threat to global human health. Bacteriocins are antimicrobial peptides currently under consideration as real alternatives or complements to common antibiotics. These peptides have been much studied, novel bacteriocins are regularly reported and several genomic databases on these peptides are currently updated. Despite this, to our knowledge, a physical collection of bacteriocins that would allow testing and comparing them for different applications does not exist. Rapid advances in synthetic biology in combination with cell-free protein synthesis technologies offer great potential for fast protein production. Based on the amino acid sequences of the mature peptide available in different databases, we have built a bacteriocin gene library, called PARAGEN 1.0, containing all the genetic elements required for in vitro cell-free peptide synthesis. Using PARAGEN 1.0 and a commercial kit for cell-free protein synthesis we have produced 164 different bacteriocins. Of the bacteriocins synthesized, 54% have shown antimicrobial activity against at least one of the indicator strains tested, including Gram-positive and Gram-negative bacteria representing commonly used lab strains, industrially relevant microorganisms, and known pathogens. This bacteriocin collection represents a streamlined pipeline for selection, production, and screening of bacteriocins as well as a reservoir of ready-to-use antimicrobials against virtually any class of relevant bacteria.
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87
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Marshall R, Noireaux V. Quantitative modeling of transcription and translation of an all-E. coli cell-free system. Sci Rep 2019; 9:11980. [PMID: 31427623 PMCID: PMC6700315 DOI: 10.1038/s41598-019-48468-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 08/06/2019] [Indexed: 11/09/2022] Open
Abstract
Cell-free transcription-translation (TXTL) is expanding as a polyvalent experimental platform to engineer biological systems outside living organisms. As the number of TXTL applications and users is rapidly growing, some aspects of this technology could be better characterized to provide a broader description of its basic working mechanisms. In particular, developing simple quantitative biophysical models that grasp the different regimes of in vitro gene expression, using relevant kinetic constants and concentrations of molecular components, remains insufficiently examined. In this work, we present an ODE (Ordinary Differential Equation)-based model of the expression of a reporter gene in an all E. coli TXTL that we apply to a set of regulatory elements spanning several orders of magnitude in strengths, far beyond the T7 standard system used in most of the TXTL platforms. Several key biochemical constants are experimentally determined through fluorescence assays. The robustness of the model is tested against the experimental parameters, and limitations of TXTL resources are described. We establish quantitative references between the performance of E. coli and synthetic promoters and ribosome binding sites. The model and the data should be useful for the TXTL community interested either in gene network engineering or in biomanufacturing beyond the conventional platforms relying on phage transcription.
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Affiliation(s)
- Ryan Marshall
- School of Physics and Astronomy, University of Minnesota, 115 Union Street SE, Minneapolis, MN, 55455, USA.
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, 115 Union Street SE, Minneapolis, MN, 55455, USA.
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88
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Nora LC, Westmann CA, Guazzaroni ME, Siddaiah C, Gupta VK, Silva-Rocha R. Recent advances in plasmid-based tools for establishing novel microbial chassis. Biotechnol Adv 2019; 37:107433. [PMID: 31437573 DOI: 10.1016/j.biotechadv.2019.107433] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 07/11/2019] [Accepted: 08/16/2019] [Indexed: 12/28/2022]
Abstract
A key challenge for domesticating alternative cultivable microorganisms with biotechnological potential lies in the development of innovative technologies. Within this framework, a myriad of genetic tools has flourished, allowing the design and manipulation of complex synthetic circuits and genomes to become the general rule in many laboratories rather than the exception. More recently, with the development of novel technologies such as DNA automated synthesis/sequencing and powerful computational tools, molecular biology has entered the synthetic biology era. In the beginning, most of these technologies were established in traditional microbial models (known as chassis in the synthetic biology framework) such as Escherichia coli and Saccharomyces cerevisiae, enabling fast advances in the field and the validation of fundamental proofs of concept. However, it soon became clear that these organisms, although extremely useful for prototyping many genetic tools, were not ideal for a wide range of biotechnological tasks due to intrinsic limitations in their molecular/physiological properties. Over the last decade, researchers have been facing the great challenge of shifting from these model systems to non-conventional chassis with endogenous capacities for dealing with specific tasks. The key to address these issues includes the generation of narrow and broad host plasmid-based molecular tools and the development of novel methods for engineering genomes through homologous recombination systems, CRISPR/Cas9 and other alternative methods. Here, we address the most recent advances in plasmid-based tools for the construction of novel cell factories, including a guide for helping with "build-your-own" microbial host.
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Affiliation(s)
- Luísa Czamanski Nora
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
| | - Cauã Antunes Westmann
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
| | - María-Eugenia Guazzaroni
- Faculty of Philosophy, Science and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
| | | | - Vijai Kumar Gupta
- ERA Chair of Green Chemistry, Department of Chemistry and Biotechnology, School of Science, Tallinn University of Technology, 12618 Tallinn, Estonia
| | - Rafael Silva-Rocha
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil.
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89
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Gmelch TJ, Sperl JM, Sieber V. Optimization of a reduced enzymatic reaction cascade for the production of L-alanine. Sci Rep 2019; 9:11754. [PMID: 31409820 PMCID: PMC6692406 DOI: 10.1038/s41598-019-48151-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 07/25/2019] [Indexed: 11/09/2022] Open
Abstract
Cell-free enzymatic reaction cascades combine the advantages of well-established in vitro biocatalysis with the power of multi-step in vivo pathways. The absence of a regulatory cell environment enables direct process control including methods for facile bottleneck identification and process optimization. Within this work, we developed a reduced, enzymatic reaction cascade for the direct production of L-alanine from D-glucose and ammonium sulfate. An efficient, activity based enzyme selection is demonstrated for the two branches of the cascade. The resulting redox neutral cascade is composed of a glucose dehydrogenase, two dihydroxyacid dehydratases, a keto-deoxy-aldolase, an aldehyde dehydrogenase and an L-alanine dehydrogenase. This artificial combination of purified biocatalysts eliminates the need for phosphorylation and only requires NAD as cofactor. We provide insight into in detail optimization of the process parameters applying a fluorescamine based L-alanine quantification assay. An optimized enzyme ratio and the necessary enzyme load were identified and together with the optimal concentrations of cofactor (NAD), ammonium and buffer yields of >95% for the main branch and of 8% for the side branch were achieved.
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Affiliation(s)
- Tobias J Gmelch
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, 94315, Straubing, Germany
| | - Josef M Sperl
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, 94315, Straubing, Germany
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, 94315, Straubing, Germany. .,Catalysis Research Center, Technical University of Munich, Garching, Germany. .,Fraunhofer Institute of Interfacial Biotechnology (IGB), Bio-, Electro- and Chemo Catalysis (BioCat) Branch, Straubing, Germany. .,School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia.
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90
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Yim SS, Johns NI, Park J, Gomes ALC, McBee RM, Richardson M, Ronda C, Chen SP, Garenne D, Noireaux V, Wang HH. Multiplex transcriptional characterizations across diverse bacterial species using cell-free systems. Mol Syst Biol 2019; 15:e8875. [PMID: 31464371 PMCID: PMC6692573 DOI: 10.15252/msb.20198875] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 07/01/2019] [Accepted: 07/03/2019] [Indexed: 12/14/2022] Open
Abstract
Cell-free expression systems enable rapid prototyping of genetic programs in vitro. However, current throughput of cell-free measurements is limited by the use of channel-limited fluorescent readouts. Here, we describe DNA Regulatory element Analysis by cell-Free Transcription and Sequencing (DRAFTS), a rapid and robust in vitro approach for multiplexed measurement of transcriptional activities from thousands of regulatory sequences in a single reaction. We employ this method in active cell lysates developed from ten diverse bacterial species. Interspecies analysis of transcriptional profiles from > 1,000 diverse regulatory sequences reveals functional differences in promoter activity that can be quantitatively modeled, providing a rich resource for tuning gene expression in diverse bacterial species. Finally, we examine the transcriptional capacities of dual-species hybrid lysates that can simultaneously harness gene expression properties of multiple organisms. We expect that this cell-free multiplex transcriptional measurement approach will improve genetic part prototyping in new bacterial chassis for synthetic biology.
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Affiliation(s)
- Sung Sun Yim
- Department of Systems BiologyColumbia UniversityNew YorkNYUSA
| | - Nathan I Johns
- Department of Systems BiologyColumbia UniversityNew YorkNYUSA
- Integrated Program in Cellular, Molecular, and Biomedical StudiesColumbia UniversityNew YorkNYUSA
- Present address:
Department of BioengineeringStanford UniversityStanfordCAUSA
| | - Jimin Park
- Department of Systems BiologyColumbia UniversityNew YorkNYUSA
- Integrated Program in Cellular, Molecular, and Biomedical StudiesColumbia UniversityNew YorkNYUSA
| | - Antonio LC Gomes
- Department of ImmunologyMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Ross M McBee
- Department of Systems BiologyColumbia UniversityNew YorkNYUSA
- Department of Biological SciencesColumbia UniversityNew YorkNYUSA
| | - Miles Richardson
- Department of Systems BiologyColumbia UniversityNew YorkNYUSA
- Integrated Program in Cellular, Molecular, and Biomedical StudiesColumbia UniversityNew YorkNYUSA
| | - Carlotta Ronda
- Department of Systems BiologyColumbia UniversityNew YorkNYUSA
| | - Sway P Chen
- Department of Systems BiologyColumbia UniversityNew YorkNYUSA
- Integrated Program in Cellular, Molecular, and Biomedical StudiesColumbia UniversityNew YorkNYUSA
| | - David Garenne
- School of Physics and AstronomyUniversity of MinnesotaMinneapolisMNUSA
| | - Vincent Noireaux
- School of Physics and AstronomyUniversity of MinnesotaMinneapolisMNUSA
| | - Harris H Wang
- Department of Systems BiologyColumbia UniversityNew YorkNYUSA
- Department of Pathology and Cell BiologyColumbia UniversityNew YorkNYUSA
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91
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Aiguo Z, Ruiwen D, Meizhi Z. Multi-enzymatic recycling of ATP and NADPH for the synthesis of 5-aminolevulinic acid using a semipermeable reaction system. Biosci Biotechnol Biochem 2019; 83:2213-2219. [PMID: 31362590 DOI: 10.1080/09168451.2019.1648204] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
5-Aminolevulinic acid (ALA) is an important cellular metabolic intermediate that has broad agricultural and medical applications. Previously, attempts have been made to synthesize ALA by multiple enzymes in cell free systems. Here we report the development of a semi-permeable system for ALA production using stable enzymes. Glucose, sodium polyphosphate, ATP, tRNA, glutamate and NADPH were used as substrates for ALA synthesis by a total of nine enzymes: adenylate kinase, polyphosphate kinase, glucose-6-phosphate dehydrogenase, phosphogluconolactonase, 6-phosphogluconate dehydrogenase, glutamyl-tRNA synthetase and glutamate-1-semialdehyde aminotransferase from E. coli, hexokinase from yeast, as well as glutamyl-tRNA reductase and its stimulator protein glutamyl-tRNA reductase binding protein (GBP) from Arabidopsis in a semi-permeable system. After reaction for 48 h, the glutamate conversion reached about 95%. This semi-permeable system facilitated the reuse of enzymes, and was helpful for the separation and purification of the product. The ALA production could be further improved by process optimization and enzyme engineering.Abbreviations: PPK: polyphosphate kinase; ADK: adenylate kinase; ALA: 5-Aminolevulinic acid; HK: hexokinase; ZWF: glucose-6-phosphatedehydrogenase; PGL: phosphogluconolactonase; GND: 6-phosphogluconate dehydrogenase; GTS: glutamyl-tRNA synthetase; GTR: glutamyl-tRNA reductase; GBP: GTR binding protein; GSAAT: glutamate-1-semialdehyde aminotransferase.
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Affiliation(s)
- Zhao Aiguo
- Walnut Research Center, College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Ding Ruiwen
- Walnut Research Center, College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhai Meizhi
- Walnut Research Center, College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
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92
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Carbonell P, Radivojevic T, García Martín H. Opportunities at the Intersection of Synthetic Biology, Machine Learning, and Automation. ACS Synth Biol 2019; 8:1474-1477. [PMID: 31319671 DOI: 10.1021/acssynbio.8b00540] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Our inability to predict the behavior of biological systems severely hampers progress in bioengineering and biomedical applications. We cannot predict the effect of genotype changes on phenotype, nor extrapolate the large-scale behavior from small-scale experiments. Machine learning techniques recently reached a new level of maturity, and are capable of providing the needed predictive power without a detailed mechanistic understanding. However, they require large amounts of data to be trained. The amount and quality of data required can only be produced through a combination of synthetic biology and automation, so as to generate a large diversity of biological systems with high reproducibility. A sustained investment in the intersection of synthetic biology, machine learning, and automation will drive forward predictive biology, and produce improved machine learning algorithms.
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Affiliation(s)
- Pablo Carbonell
- Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Tijana Radivojevic
- DOE Agile BioFoundry, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Héctor García Martín
- DOE Agile BioFoundry, Emeryville, California 94608, United States
- DOE Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- BCAM, Basque Center for Applied Mathematics, 48009 Bilbao, Spain
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93
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Bai X, Meng D, Wei X, Zhou X, Lu F, You C. Facile synthesis of (-)-vibo-quercitol from maltodextrin via an in vitro synthetic enzymatic biosystem. Biotechnol Bioeng 2019; 116:2710-2719. [PMID: 31237686 DOI: 10.1002/bit.27096] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 06/17/2019] [Accepted: 06/19/2019] [Indexed: 11/09/2022]
Abstract
(-)-vibo-Quercitol (VQ: 1L-1,2,4/3,5-cyclohexanepentol), a form of deoxyinositol, is an alternative chiral building block in the synthesis of bioactive compounds to control diabetes. In this study, an adenosine triphosphate-free in vitro synthetic enzymatic biosystem composed of five enzymes (including one enzyme for NADH regeneration) was constructed to produce VQ from maltodextrin in one-pot. After optimization of reaction conditions, 7.6 g/L VQ was produced from 10 g/L maltodextrin with a product yield (mol/mol) of 77%, and 25.3 g/L VQ with a purity of 87% was produced from 50 g/L maltodextrin through simple scaling up of this nonfermentative enzymatic biosystem. Therefore, this study provides an economical and environmentally friendly method for the envisioned quercitol biosynthesis.
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Affiliation(s)
- Xue Bai
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Bioengineering, Tianjin University of Science and Technology, Tianjin, People's Republic of China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China
| | - Dongdong Meng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China
| | - Xinlei Wei
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China
| | - Xigui Zhou
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Bioengineering, Tianjin University of Science and Technology, Tianjin, People's Republic of China
| | - Chun You
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China
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94
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Opgenorth P, Costello Z, Okada T, Goyal G, Chen Y, Gin J, Benites V, de Raad M, Northen TR, Deng K, Deutsch S, Baidoo EEK, Petzold CJ, Hillson NJ, Garcia Martin H, Beller HR. Lessons from Two Design-Build-Test-Learn Cycles of Dodecanol Production in Escherichia coli Aided by Machine Learning. ACS Synth Biol 2019; 8:1337-1351. [PMID: 31072100 DOI: 10.1021/acssynbio.9b00020] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The Design-Build-Test-Learn (DBTL) cycle, facilitated by exponentially improving capabilities in synthetic biology, is an increasingly adopted metabolic engineering framework that represents a more systematic and efficient approach to strain development than historical efforts in biofuels and biobased products. Here, we report on implementation of two DBTL cycles to optimize 1-dodecanol production from glucose using 60 engineered Escherichia coli MG1655 strains. The first DBTL cycle employed a simple strategy to learn efficiently from a relatively small number of strains (36), wherein only the choice of ribosome-binding sites and an acyl-ACP/acyl-CoA reductase were modulated in a single pathway operon including genes encoding a thioesterase (UcFatB1), an acyl-ACP/acyl-CoA reductase (Maqu_2507, Maqu_2220, or Acr1), and an acyl-CoA synthetase (FadD). Measured variables included concentrations of dodecanol and all proteins in the engineered pathway. We used the data produced in the first DBTL cycle to train several machine-learning algorithms and to suggest protein profiles for the second DBTL cycle that would increase production. These strategies resulted in a 21% increase in dodecanol titer in Cycle 2 (up to 0.83 g/L, which is more than 6-fold greater than previously reported batch values for minimal medium). Beyond specific lessons learned about optimizing dodecanol titer in E. coli, this study had findings of broader relevance across synthetic biology applications, such as the importance of sequencing checks on plasmids in production strains as well as in cloning strains, and the critical need for more accurate protein expression predictive tools.
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Affiliation(s)
- Paul Opgenorth
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Zak Costello
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
| | - Takuya Okada
- Research Institute for Bioscience Product & Fine Chemicals, Ajinomoto Co., Inc., Kawasaki 210-8680, Japan
| | - Garima Goyal
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
| | - Yan Chen
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
| | - Jennifer Gin
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
| | - Veronica Benites
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
| | - Markus de Raad
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Joint Genome Institute, Walnut Creek, California 94598, United States
| | - Trent R. Northen
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Joint Genome Institute, Walnut Creek, California 94598, United States
| | - Kai Deng
- Sandia National Laboratories, Livermore, California 94550, United States
| | - Samuel Deutsch
- DOE Joint Genome Institute, Walnut Creek, California 94598, United States
| | - Edward E. K. Baidoo
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
| | - Christopher J. Petzold
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
| | - Nathan J. Hillson
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
- DOE Joint Genome Institute, Walnut Creek, California 94598, United States
| | - Hector Garcia Martin
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
- BCAM, Basque Center for Applied Mathematics, 48009 Bilbao, Spain
| | - Harry R. Beller
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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95
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Hallinan JS, Wipat A, Kitney R, Woods S, Taylor K, Goñi‐Moreno A. Future‐proofing synthetic biology: educating the next generation. ENGINEERING BIOLOGY 2019. [DOI: 10.1049/enb.2019.0001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Affiliation(s)
| | - Anil Wipat
- School of ComputingNewcastle UniversityNewcastle upon TyneUK
| | - Richard Kitney
- Department of BioengineeringImperial College LondonLondonUK
| | - Simon Woods
- Policy, Ethics and Life Sciences (PEALS) Research CentreNewcastle UniversityNewcastle upon TyneUK
| | - Ken Taylor
- Policy, Ethics and Life Sciences (PEALS) Research CentreNewcastle UniversityNewcastle upon TyneUK
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96
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O’Kane PT, Dudley QM, McMillan AK, Jewett MC, Mrksich M. High-throughput mapping of CoA metabolites by SAMDI-MS to optimize the cell-free biosynthesis of HMG-CoA. SCIENCE ADVANCES 2019; 5:eaaw9180. [PMID: 31183410 PMCID: PMC6551189 DOI: 10.1126/sciadv.aaw9180] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/02/2019] [Indexed: 05/30/2023]
Abstract
Metabolic engineering uses enzymes to produce small molecules with industrial, pharmaceutical, and energy applications. However, efforts to optimize enzymatic pathways for commercial production are limited by the throughput of assays for quantifying metabolic intermediates and end products. We developed a multiplexed method for profiling CoA-dependent pathways that uses a cysteine-terminated peptide to covalently capture CoA-bound metabolites. Captured metabolites are then rapidly separated from the complex mixture by immobilization onto arrays of self-assembled monolayers and directly quantified by SAMDI mass spectrometry. We demonstrate the throughput of the assay by characterizing the cell-free synthesis of HMG-CoA, a key intermediate in the biosynthesis of isoprenoids, collecting over 10,000 individual spectra to map more than 800 unique reaction conditions. We anticipate that our rapid and robust analytical method will accelerate efforts to engineer metabolic pathways.
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Affiliation(s)
- Patrick T. O’Kane
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Quentin M. Dudley
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Aislinn K. McMillan
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Michael C. Jewett
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Milan Mrksich
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Department of Chemistry, Northwestern University, Evanston, IL, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
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97
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Choi SY, Cho IJ, Lee Y, Park S, Lee SY. Biocatalytic synthesis of polylactate and its copolymers by engineered microorganisms. Methods Enzymol 2019; 627:125-162. [PMID: 31630738 DOI: 10.1016/bs.mie.2019.04.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Poly(lactate), also called poly(lactic acid) or poly(lactide) [PLA], has been one of the most attractive bio-based polymers since it possesses desirable material properties for its use in general performance plastics in addition to biodegradability and biocompatibility. PLA has been produced by biological and chemical hybrid process comprising microbial fermentation for lactate (LA) production followed by purification and chemical polymerization process of LA. Recently, the direct one-step fermentative processes for production of PLA and several LA-containing polyesters have been developed by employing metabolically engineered microorganisms. Since natural microorganisms cannot produce the LA-containing polymers, several engineering strategies have been employed together based on the polyhydroxyalkanoate (PHA) biosynthesis system. In this chapter, we summarize strategies and procedures on developing the engineered microorganisms producing PLA and its copolymers, cultivating the cells, and extracting the polymers from the cells. Focuses were given on construction of enzymatic polymerization process of LA: design of metabolic pathway for PLA by mimicking PHA biosynthetic pathway, examination of possible enzymes, and engineering of the enzymes for better performances. This synthetic pathway has been established in a microorganism producing LA that enabled one-step fermentative production of LA-containing polyesters from carbohydrates derived from renewable biomass. Polymer production has been further enhanced by implementing strain engineering to concentrate the metabolic fluxes toward PLA formation. In addition, various monomers such as glycolate, 2-hydroxybutyrate, and phenyllactate have been copolymerized with LA by the microbial system. These fermentative production systems developed by using the engineered microorganisms can be versatile and sustainable platforms for the production of LA-containing polyesters and other non-natural polymers.
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Affiliation(s)
- So Young Choi
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea; Metabolic and Biomolecular Engineering National Research Laboratory and Institute for the BioCentury, KAIST, Daejeon, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon, Republic of Korea; Applied Science Research Institute, KAIST, Daejeon, Republic of Korea
| | - In Jin Cho
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea; Metabolic and Biomolecular Engineering National Research Laboratory and Institute for the BioCentury, KAIST, Daejeon, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon, Republic of Korea
| | - Youngjoon Lee
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea; Metabolic and Biomolecular Engineering National Research Laboratory and Institute for the BioCentury, KAIST, Daejeon, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon, Republic of Korea
| | - Seongjin Park
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea; Metabolic and Biomolecular Engineering National Research Laboratory and Institute for the BioCentury, KAIST, Daejeon, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon, Republic of Korea
| | - Sang Yup Lee
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea; Metabolic and Biomolecular Engineering National Research Laboratory and Institute for the BioCentury, KAIST, Daejeon, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon, Republic of Korea; Applied Science Research Institute, KAIST, Daejeon, Republic of Korea.
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98
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Garenne D, Beisel CL, Noireaux V. Characterization of the all-E. coli transcription-translation system myTXTL by mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33:1036-1048. [PMID: 30900355 DOI: 10.1002/rcm.8438] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 03/05/2019] [Accepted: 03/13/2019] [Indexed: 06/09/2023]
Abstract
RATIONALE Cell-free transcription-translation (TXTL) is becoming a popular technology to prototype and engineer biological systems outside living organisms. TXTL relies commonly on a cytoplasmic extract that provides the molecular components necessary to recapitulate gene expression in vitro, where most of the available systems are derived from E. coli. The proteinic and enzymatic composition of lysates, however, is typically unknown. In this work, we analyzed by mass spectrometry the molecular constituents of the all-E. coli TXTL platform myTXTL prepared from the E. coli strain BL21 Rosetta2. METHODS Standard TXTL reactions were assembled and executed for 10-12 hours at 29°C. In addition to a no-DNA control, four DNA programs were executed in separate reactions to synthesize the reporter protein deGFP as well as the phages MS2, phix174 and T7. The reactions were treated according to standard procedures (trypsin treatment, cleaning) before performing liquid chromatography/mass spectrometry (LC/MS). Data analysis was performed using Sequest and protein identification using Scaffold. RESULTS A total of 500-800 proteins were identified by LC/MS in the blank reactions. We organized the most abundant protein sets into several categories pertaining, in particular, to transcription, translation and ATP regeneration. The synthesis of deGFP was easily measured. The major structural proteins that compose the three phages MS2, phix174 and T7 were also identified. CONCLUSIONS Mass spectrometry is a practical tool to characterize biochemical solutions as complex as a cell-free TXTL reaction and to determine the presence of synthesized proteins. The data presented demonstrate that the composition of TXTL based on lysates can be used to validate some underlying molecular mechanisms implicated in cell-free protein synthesis. The composition of the lysate shows significant differences with respect to similar studies on other E. coli strains.
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Affiliation(s)
- David Garenne
- School of Physics and Astronomy, University of Minnesota, 115 Union Street SE, Minneapolis, MN, 55455, USA
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection (HZI) Research, 97080, Würzburg, Germany
- Medical Faculty, University of Würzburg, Würzburg, Germany
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, 115 Union Street SE, Minneapolis, MN, 55455, USA
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99
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Supramaniam P, Ces O, Salehi-Reyhani A. Microfluidics for Artificial Life: Techniques for Bottom-Up Synthetic Biology. MICROMACHINES 2019; 10:E299. [PMID: 31052344 PMCID: PMC6562628 DOI: 10.3390/mi10050299] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/24/2019] [Accepted: 04/26/2019] [Indexed: 01/08/2023]
Abstract
Synthetic biology is a rapidly growing multidisciplinary branch of science that exploits the advancement of molecular and cellular biology. Conventional modification of pre-existing cells is referred to as the top-down approach. Bottom-up synthetic biology is an emerging complementary branch that seeks to construct artificial cells from natural or synthetic components. One of the aims in bottom-up synthetic biology is to construct or mimic the complex pathways present in living cells. The recent, and rapidly growing, application of microfluidics in the field is driven by the central tenet of the bottom-up approach-the pursuit of controllably generating artificial cells with precisely defined parameters, in terms of molecular and geometrical composition. In this review we survey conventional methods of artificial cell synthesis and their limitations. We proceed to show how microfluidic approaches have been pivotal in overcoming these limitations and ushering in a new generation of complexity that may be imbued in artificial cells and the milieu of applications that result.
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Affiliation(s)
- Pashiini Supramaniam
- Department of Chemistry, White City Campus, Imperial College London, London SW7 2AZ, UK.
| | - Oscar Ces
- Department of Chemistry, White City Campus, Imperial College London, London SW7 2AZ, UK.
- FabriCELL, Imperial College London, London SW7 2AZ, UK.
| | - Ali Salehi-Reyhani
- FabriCELL, Imperial College London, London SW7 2AZ, UK.
- Department of Chemistry, King's College London, Britannia House, London SE1 1DB, UK.
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100
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Zuo R, Ding Y. Direct Aromatic Nitration System for Synthesis of Nitrotryptophans in Escherichia coli. ACS Synth Biol 2019; 8:857-865. [PMID: 30865826 DOI: 10.1021/acssynbio.8b00534] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Nitrotryptophan and its analogues are useful building blocks for synthesizing bioactive and biotechnologically relevant chemicals, materials, and proteins. However, synthetic routes to enantiopure nitro-containing tryptophan derivatives are either complex and polluting or even unestablished yet. Herein, we describe microbial production of 4-NO2-l-tryptophan (Nitrotrp) and its analogues by designing and expressing the biosynthetic pathway in Escherichia coli. The biosynthetic pathway comprised one engineered self-sufficient P450 TB14 of Streptomyces origin for direct nitration of the C-4 of l-Trp indole and one nitric oxide synthase from Bacillus subtilis (BsNOS) for the production of nitric oxide (NO) from l-Arg to support the direct aromatic nitration. As both TB14 and BsNOS require reducing agent NADPH for their reactions, we also included one glucose dehydrogenase (GDH) from B. subtilis for in situ NADPH regeneration. The initially designed pathway led to 16.2 ± 2.3 mg/L of Nitrotrp by the engineered E. coli fermented in the M9 minimal medium for 3 days. A combination of the design and screening of three additional pathways, fermentation optimization and the knockout of competitive metabolic pathways together improved the Nitrotrp titer to around 192 mg/L within 20 h. Finally, the whole-cell biotransformation system produced eight Nitrotrp analogues with their titers varying from 2.5 to 61.5 mg/L. This work provides the first microbial direct aromatic nitration processes and sets the stage for the development of biocatalytic routes to other useful nitroaromatics in the future.
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Affiliation(s)
- Ran Zuo
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
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