1
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Lee SJ, Kim DM. Cell-Free Synthesis: Expediting Biomanufacturing of Chemical and Biological Molecules. Molecules 2024; 29:1878. [PMID: 38675698 PMCID: PMC11054211 DOI: 10.3390/molecules29081878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 04/14/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
The increasing demand for sustainable alternatives underscores the critical need for a shift away from traditional hydrocarbon-dependent processes. In this landscape, biomanufacturing emerges as a compelling solution, offering a pathway to produce essential chemical materials with significantly reduced environmental impacts. By utilizing engineered microorganisms and biomass as raw materials, biomanufacturing seeks to achieve a carbon-neutral footprint, effectively counteracting the carbon dioxide emissions associated with fossil fuel use. The efficiency and specificity of biocatalysts further contribute to lowering energy consumption and enhancing the sustainability of the production process. Within this context, cell-free synthesis emerges as a promising approach to accelerate the shift towards biomanufacturing. Operating with cellular machinery in a controlled environment, cell-free synthesis offers multiple advantages: it enables the rapid evaluation of biosynthetic pathways and optimization of the conditions for the synthesis of specific chemicals. It also holds potential as an on-demand platform for the production of personalized and specialized products. This review explores recent progress in cell-free synthesis, highlighting its potential to expedite the transformation of chemical processes into more sustainable biomanufacturing practices. We discuss how cell-free techniques not only accelerate the development of new bioproducts but also broaden the horizons for sustainable chemical production. Additionally, we address the challenges of scaling these technologies for commercial use and ensuring their affordability, which are critical for cell-free systems to meet the future demands of industries and fully realize their potential.
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Affiliation(s)
| | - Dong-Myung Kim
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, 99 Daehak-Ro, Daejeon 34134, Republic of Korea;
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2
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Wang S, Meng D, Feng M, Li C, Wang Y. Efficient Plant Triterpenoids Synthesis in Saccharomyces cerevisiae: from Mechanisms to Engineering Strategies. ACS Synth Biol 2024; 13:1059-1076. [PMID: 38546129 DOI: 10.1021/acssynbio.4c00061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
Triterpenoids possess a range of biological activities and are extensively utilized in the pharmaceutical, food, cosmetic, and chemical industries. Traditionally, they are acquired through chemical synthesis and plant extraction. However, these methods have drawbacks, including high energy consumption, environmental pollution, and being time-consuming. Recently, the de novo synthesis of triterpenoids in microbial cell factories has been achieved. This represents a promising and environmentally friendly alternative to traditional supply methods. Saccharomyces cerevisiae, known for its robustness, safety, and ample precursor supply, stands out as an ideal candidate for triterpenoid biosynthesis. However, challenges persist in industrial production and economic feasibility of triterpenoid biosynthesis. Consequently, metabolic engineering approaches have been applied to improve the triterpenoid yield, leading to substantial progress. This review explores triterpenoids biosynthesis mechanisms in S. cerevisiae and strategies for efficient production. Finally, the review also discusses current challenges and proposes potential solutions, offering insights for future engineering.
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Affiliation(s)
- Shuai Wang
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Dong Meng
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Meilin Feng
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Chun Li
- Key Laboratory for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Ying Wang
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
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3
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Ghosh S, Baltussen MG, Ivanov NM, Haije R, Jakštaitė M, Zhou T, Huck WTS. Exploring Emergent Properties in Enzymatic Reaction Networks: Design and Control of Dynamic Functional Systems. Chem Rev 2024; 124:2553-2582. [PMID: 38476077 PMCID: PMC10941194 DOI: 10.1021/acs.chemrev.3c00681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/13/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024]
Abstract
The intricate and complex features of enzymatic reaction networks (ERNs) play a key role in the emergence and sustenance of life. Constructing such networks in vitro enables stepwise build up in complexity and introduces the opportunity to control enzymatic activity using physicochemical stimuli. Rational design and modulation of network motifs enable the engineering of artificial systems with emergent functionalities. Such functional systems are useful for a variety of reasons such as creating new-to-nature dynamic materials, producing value-added chemicals, constructing metabolic modules for synthetic cells, and even enabling molecular computation. In this review, we offer insights into the chemical characteristics of ERNs while also delving into their potential applications and associated challenges.
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Affiliation(s)
- Souvik Ghosh
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Mathieu G. Baltussen
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Nikita M. Ivanov
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Rianne Haije
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Miglė Jakštaitė
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Tao Zhou
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Wilhelm T. S. Huck
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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4
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Ducrot L, López IL, Orrego AH, López-Gallego F. Coenzyme A Thioester Intermediates as Platform Molecules in Cell-Free Chemical Biomanufacturing. Chembiochem 2024; 25:e202300673. [PMID: 37994376 DOI: 10.1002/cbic.202300673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 11/06/2023] [Indexed: 11/24/2023]
Abstract
The in vitro synthesis of Coenzyme A (CoA)-thioester intermediates opens new avenues to transform simple molecules into more complex and multifunctional ones by assembling cell-free biosynthetic cascades. In this review, we have systematically cataloged known CoA-dependent enzyme reactions that have been successfully implemented in vitro. To faciliate their identification, we provide their UniProt ID when available. Based on this catalog, we have organized enzymes into three modules: activation, modification, and removal. i) The activation module includes enzymes capable of fusing CoA with organic molecules. ii) The modification module includes enzymes capable of catalyzing chemical modifications in the structure of acyl-CoA intermediates. And iii) the removal module includes enzymes able to remove the CoA and release an organic molecule different from the one activated in the upstream. Based on these reactions, we constructed a reaction network that summarizes the most relevant CoA-dependent biosynthetic pathways reported until today. From the information available in the articles, we have plotted the total turnover number of CoA as a function of the product titer, observing a positive correlation between both parameters. Therefore, the success of a CoA-dependent in vitro pathway depends on its ability to regenerate CoA, but also to regenerate other cofactors such as NAD(P)H and ATP.
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Affiliation(s)
- Laurine Ducrot
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, 20014, Spain
| | - Idania L López
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, 20014, Spain
| | - Alejandro H Orrego
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, 20014, Spain
| | - Fernando López-Gallego
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, 20014, Spain
- Ikerbasque, Basque Foundation for Science, 48009, Bilbao, Spain
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5
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Ditzel A, Zhao F, Gao X, Phillips GN. Utilizing a cell-free protein synthesis platform for the biosynthesis of a natural product, caffeine. Synth Biol (Oxf) 2023; 8:ysad017. [PMID: 38149044 PMCID: PMC10750991 DOI: 10.1093/synbio/ysad017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 10/24/2023] [Accepted: 12/20/2023] [Indexed: 12/28/2023] Open
Abstract
Natural products are a valuable source of pharmaceuticals, providing a majority of the small-molecule drugs in use today. However, their production through organic synthesis or in heterologous hosts can be difficult and time-consuming. Therefore, to allow for easier screening and production of natural products, we demonstrated the use of a cell-free protein synthesis system to partially assemble natural products in vitro using S-Adenosyl Methionine (SAM)-dependent methyltransferase enzyme reactions. The tea caffeine synthase, TCS1, was utilized to synthesize caffeine within a cell-free protein synthesis system. Cell-free systems also provide the benefit of allowing the use of substrates that would normally be toxic in a cellular environment to synthesize novel products. However, TCS1 is unable to utilize a compound like S-adenosyl ethionine as a cofactor to create ethylated caffeine analogs. The automation and reduced metabolic engineering requirements of cell-free protein synthesis systems, in combination with other synthesis methods, may enable the more efficient generation of new compounds. Graphical Abstract.
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Affiliation(s)
| | - Fanglong Zhao
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Xue Gao
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
- Department of Chemistry, Rice University, Houston, TX, USA
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - George N Phillips
- Department of Biosciences, Rice University, Houston, TX, USA
- Department of Chemistry, Rice University, Houston, TX, USA
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6
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Zhang J, Yuan Y, Wang Z, Chen T. Metabolic engineering of Halomonas bluephagenesis for high-level mevalonate production from glucose and acetate mixture. Metab Eng 2023; 79:203-213. [PMID: 37657641 DOI: 10.1016/j.ymben.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/14/2023] [Accepted: 08/27/2023] [Indexed: 09/03/2023]
Abstract
Mevalonate (MVA) plays a crucial role as a building block for the biosynthesis of isoprenoids. In this study, we engineered Halomonas bluephagenesis to efficiently produce MVA. Firstly, by screening MVA synthetases from eight different species, the two efficient candidate modules, specifically NADPH-dependent mvaESEfa from Enterococcus faecalis and NADH-dependent mvaESLca from Lactobacillus casei, were integrated into the chromosome, leading to the construction of the H. bluephagenesis MVA11. Through the synergetic utilization of glucose and acetate as mixed carbon sources, MVA11 produced 11.2 g/L MVA with a yield of 0.45 g/g (glucose + acetic acid) in the shake flask. Subsequently, 10 beneficial genes out of 50 targets that could promote MVA production were identified using CRISPR interference. The simultaneous repression of rpoN (encoding RNA polymerase sigma-54 factor) and IldD (encoding L-lactate dehydrogenase) increased MVA titer (13.3 g/L) by 19.23% and yield (0.53 g/g (glucose + acetic acid)) by 17.78%, respectively. Furthermore, introducing the non-oxidative glycolysis (NOG) pathway into MVA11 enhanced MVA yield by 12.20%. Ultimately, by combining these strategies, the resultant H. bluephagenesis MVA13/pli-63 produced 13.9 g/L MVA in the shake flask, and the yield increased to 0.56 g/g (glucose + acetic acid), which was the highest reported so far. Under open fed-batch fermentation conditions, H. bluephagenesis MVA13/pli-63 produced 121 g/L of MVA with a yield of 0.42 g/g (glucose + acetic acid), representing the highest reported titer and yield in the bioreactor to date. This study demonstrates that H. bluephagenesis is one of the most favorable chassis for MVA production.
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Affiliation(s)
- Jing Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin, 300072, China
| | - Yue Yuan
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin, 300072, China
| | - Zhiwen Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin, 300072, China
| | - Tao Chen
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin, 300072, China.
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7
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Liu J, Hu Y, Gu W, Lan H, Zhang Z, Jiang L, Xu X. Research progress on the application of cell-free synthesis systems for enzymatic processes. Crit Rev Biotechnol 2023; 43:938-955. [PMID: 35994247 DOI: 10.1080/07388551.2022.2090314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 02/24/2022] [Accepted: 04/09/2022] [Indexed: 11/03/2022]
Abstract
Cell-free synthesis systems can complete the transcription and translation process in vitro to produce complex proteins that are difficult to be expressed in traditional cell-based systems. Such systems also can be used for the assembly of efficient localized multienzyme cascades to synthesize products that are toxic to cells. Cell-free synthesis systems provide a simpler and faster engineering solution than living cells, allowing unprecedented design freedom. This paper reviews the latest progress on the application of cell-free synthesis systems in the field of enzymatic catalysis, including cell-free protein synthesis and cell-free metabolic engineering. In cell-free protein synthesis: complex proteins, toxic proteins, membrane proteins, and artificial proteins containing non-natural amino acids can be easily synthesized by directly controlling the reaction conditions in the cell-free system. In cell-free metabolic engineering, the synthesis of desired products can be made more specific and efficient by designing metabolic pathways and screening biocatalysts based on purified enzymes or crude extracts. Through the combination of cell-free synthesis systems and emerging technologies, such as: synthetic biology, microfluidic control, cofactor regeneration, and artificial scaffolds, we will be able to build increasingly complex biomolecule systems. In the next few years, these technologies are expected to mature and reach industrialization, providing innovative platforms for a wide range of biotechnological applications.
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Affiliation(s)
- Jie Liu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Yongqi Hu
- School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Wanyi Gu
- School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Haiquan Lan
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Zhidong Zhang
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Ling Jiang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Xian Xu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
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8
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Yue K, Chen J, Li Y, Kai L. Advancing synthetic biology through cell-free protein synthesis. Comput Struct Biotechnol J 2023; 21:2899-2908. [PMID: 37216017 PMCID: PMC10196276 DOI: 10.1016/j.csbj.2023.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/03/2023] [Accepted: 05/03/2023] [Indexed: 05/24/2023] Open
Abstract
The rapid development of synthetic biology has enabled the production of compounds with revolutionary improvements in biotechnology. DNA manipulation tools have expedited the engineering of cellular systems for this purpose. Nonetheless, the inherent constraints of cellular systems persist, imposing an upper limit on mass and energy conversion efficiencies. Cell-free protein synthesis (CFPS) has demonstrated its potential to overcome these inherent constraints and has been instrumental in the further advancement of synthetic biology. Via the removal of the cell membranes and redundant parts of cells, CFPS has provided flexibility in directly dissecting and manipulating the Central Dogma with rapid feedback. This mini-review summarizes recent achievements of the CFPS technique and its application to a wide range of synthetic biology projects, such as minimal cell assembly, metabolic engineering, and recombinant protein production for therapeutics, as well as biosensor development for in vitro diagnostics. In addition, current challenges and future perspectives in developing a generalized cell-free synthetic biology are outlined.
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Affiliation(s)
- Ke Yue
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
| | - Junyu Chen
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
| | - Yingqiu Li
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
| | - Lei Kai
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
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9
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Dinglasan JLN, Doktycz MJ. Rewiring cell-free metabolic flux in E. coli lysates using a block-push-pull approach. Synth Biol (Oxf) 2023; 8:ysad007. [PMID: 37908558 PMCID: PMC10615139 DOI: 10.1093/synbio/ysad007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/27/2023] [Accepted: 04/12/2023] [Indexed: 11/02/2023] Open
Abstract
Cell-free systems can expedite the design and implementation of biomanufacturing processes by bypassing troublesome requirements associated with the use of live cells. In particular, the lack of survival objectives and the open nature of cell-free reactions afford engineering approaches that allow purposeful direction of metabolic flux. The use of lysate-based systems to produce desired small molecules can result in competitive titers and productivities when compared to their cell-based counterparts. However, pathway crosstalk within endogenous lysate metabolism can compromise conversion yields by diverting carbon flow away from desired products. Here, the 'block-push-pull' concept of conventional cell-based metabolic engineering was adapted to develop a cell-free approach that efficiently directs carbon flow in lysates from glucose and toward endogenous ethanol synthesis. The approach is readily adaptable, is relatively rapid and allows for the manipulation of central metabolism in cell extracts. In implementing this approach, a block strategy is first optimized, enabling selective enzyme removal from the lysate to the point of eliminating by-product-forming activity while channeling flux through the target pathway. This is complemented with cell-free metabolic engineering methods that manipulate the lysate proteome and reaction environment to push through bottlenecks and pull flux toward ethanol. The approach incorporating these block, push and pull strategies maximized the glucose-to-ethanol conversion in an Escherichia coli lysate that initially had low ethanologenic potential. A 10-fold improvement in the percent yield is demonstrated. To our knowledge, this is the first report of successfully rewiring lysate carbon flux without source strain optimization and completely transforming the consumed input substrate to a desired output product in a lysate-based, cell-free system.
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Affiliation(s)
- Jaime Lorenzo N Dinglasan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Mitchel J Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
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10
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Yuan Q, Wu M, Liao Y, Liang S, Lu Y, Lin Y. Rapid prototyping enzyme homologs to improve titer of nicotinamide mononucleotide using a strategy combining cell-free protein synthesis with split GFP. Biotechnol Bioeng 2023; 120:1133-1146. [PMID: 36585353 DOI: 10.1002/bit.28326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/18/2022] [Accepted: 12/29/2022] [Indexed: 01/01/2023]
Abstract
Engineering biological systems to test new pathway variants containing different enzyme homologs is laborious and time-consuming. To tackle this challenge, a strategy was developed for rapidly prototyping enzyme homologs by combining cell-free protein synthesis (CFPS) with split green fluorescent protein (GFP). This strategy featured two main advantages: (1) dozens of enzyme homologs were parallelly produced by CFPS within hours, and (2) the expression level and activity of each homolog was determined simultaneously by using the split GFP assay. As a model, this strategy was applied to optimize a 3-step pathway for nicotinamide mononucleotide (NMN) synthesis. Ten enzyme homologs from different organisms were selected for each step. Here, the most productive homolog of each step was identified within 24 h rather than weeks or months. Finally, the titer of NMN was increased to 1213 mg/L by improving physiochemical conditions, tuning enzyme ratios and cofactor concentrations, and decreasing the feedback inhibition, which was a more than 12-fold improvement over the initial setup. This strategy would provide a promising way to accelerate design-build-test cycles for metabolic engineering to improve the production of desired products.
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Affiliation(s)
- Qingyan Yuan
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Minhui Wu
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Yibo Liao
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Shuli Liang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Yuan Lu
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Ying Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
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11
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Rasor BJ, Karim AS, Alper HS, Jewett MC. Cell Extracts from Bacteria and Yeast Retain Metabolic Activity after Extended Storage and Repeated Thawing. ACS Synth Biol 2023; 12:904-908. [PMID: 36848582 DOI: 10.1021/acssynbio.2c00685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Cell-free synthetic biology enables rapid prototyping of biological parts and synthesis of proteins or metabolites in the absence of cell growth constraints. Cell-free systems are frequently made from crude cell extracts, where composition and activity can vary significantly based on source strain, preparation and processing, reagents, and other considerations. This variability can cause extracts to be treated as black boxes for which empirical observations guide practical laboratory practices, including a hesitance to use dated or previously thawed extracts. To better understand the robustness of cell extracts over time, we assessed the activity of cell-free metabolism during storage. As a model, we studied conversion of glucose to 2,3-butanediol. We found that cell extracts from Escherichia coli and Saccharomyces cerevisiae subjected to an 18-month storage period and repeated freeze-thaw cycles retain consistent metabolic activity. This work gives users of cell-free systems a better understanding of the impacts of storage on extract behavior.
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12
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Aminian A, Motamedian E. Investigating ethanol production using the Zymomonas mobilis crude extract. Sci Rep 2023; 13:1165. [PMID: 36670195 PMCID: PMC9860009 DOI: 10.1038/s41598-023-28396-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/18/2023] [Indexed: 01/22/2023] Open
Abstract
Cell-free systems have become valuable investigating tools for metabolic engineering research due to their easy access to metabolism without the interference of the membrane. Therefore, we applied Zymomonas mobilis cell-free system to investigate whether ethanol production is controlled by the genes of the metabolic pathway or is limited by cofactors. Initially, different glucose concentrations were added to the extract to determine the crude extract's capability to produce ethanol. Then, we investigated the genes of the metabolic pathway to find the limiting step in the ethanol production pathway. Next, to identify the bottleneck gene, a systemic approach was applied based on the integration of gene expression data on a cell-free metabolic model. ZMO1696 was determined as the bottleneck gene and an activator for its enzyme was added to the extract to experimentally assess its effect on ethanol production. Then the effect of NAD+ addition at the high concentration of glucose (1 M) was evaluated, which indicates no improvement in efficiency. Finally, the imbalance ratio of ADP/ATP was found as the controlling factor by measuring ATP levels in the extract. Furthermore, sodium gluconate as a carbon source was utilized to investigate the expansion of substrate consumption by the extract. 100% of the maximum theoretical yield was obtained at 0.01 M of sodium gluconate while it cannot be consumed by Z. mobilis. This research demonstrated the challenges and advantages of using Z. mobilis crude extract for overproduction.
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Affiliation(s)
- Amirhossein Aminian
- Department of Biotechnology, Faculty of Chemical Engineering, Tarbiat Modares University, P.O. Box 14115-143, Tehran, Iran
| | - Ehsan Motamedian
- Department of Biotechnology, Faculty of Chemical Engineering, Tarbiat Modares University, P.O. Box 14115-143, Tehran, Iran.
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13
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Yue K, Li Y, Cao M, Shen L, Gu J, Kai L. Bottom-Up Synthetic Biology Using Cell-Free Protein Synthesis. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 185:1-20. [PMID: 37526707 DOI: 10.1007/10_2023_232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Technical advances in biotechnology have greatly accelerated the development of bottom-up synthetic biology. Unlike top-down approaches, bottom-up synthetic biology focuses on the construction of a minimal cell from scratch and the application of these principles to solve challenges. Cell-free protein synthesis (CFPS) systems provide minimal machinery for transcription and translation, from either a fractionated cell lysate or individual purified protein elements, thus speeding up the development of synthetic cell projects. In this review, we trace the history of the cell-free technique back to the first in vitro fermentation experiment using yeast cell lysate. Furthermore, we summarized progresses of individual cell mimicry modules, such as compartmentalization, gene expression regulation, energy regeneration and metabolism, growth and division, communication, and motility. Finally, current challenges and future perspectives on the field are outlined.
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Affiliation(s)
- Ke Yue
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Yingqiu Li
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Mengjiao Cao
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Lulu Shen
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Jingsheng Gu
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Lei Kai
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China.
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14
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Gonzales DT, Suraritdechachai S, Tang TYD. Compartmentalized Cell-Free Expression Systems for Building Synthetic Cells. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 186:77-101. [PMID: 37306700 DOI: 10.1007/10_2023_221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
One of the grand challenges in bottom-up synthetic biology is the design and construction of synthetic cellular systems. One strategy toward this goal is the systematic reconstitution of biological processes using purified or non-living molecular components to recreate specific cellular functions such as metabolism, intercellular communication, signal transduction, and growth and division. Cell-free expression systems (CFES) are in vitro reconstitutions of the transcription and translation machinery found in cells and are a key technology for bottom-up synthetic biology. The open and simplified reaction environment of CFES has helped researchers discover fundamental concepts in the molecular biology of the cell. In recent decades, there has been a drive to encapsulate CFES reactions into cell-like compartments with the aim of building synthetic cells and multicellular systems. In this chapter, we discuss recent progress in compartmentalizing CFES to build simple and minimal models of biological processes that can help provide a better understanding of the process of self-assembly in molecularly complex systems.
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Affiliation(s)
- David T Gonzales
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
| | | | - T -Y Dora Tang
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
- Center for Systems Biology Dresden, Dresden, Germany.
- Physics of Life, Cluster of Excellence, TU Dresden, Dresden, Germany.
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15
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Hooe SL, Ellis GA, Medintz IL. Alternative design strategies to help build the enzymatic retrosynthesis toolbox. RSC Chem Biol 2022; 3:1301-1313. [PMID: 36349225 PMCID: PMC9627731 DOI: 10.1039/d2cb00096b] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 09/11/2022] [Indexed: 05/30/2024] Open
Abstract
Most of the complex molecules found in nature still cannot be synthesized by current organic chemistry methods. Given the number of enzymes that exist in nature and the incredible potential of directed evolution, the field of synthetic biology contains perhaps all the necessary building blocks to bring about the realization of applied enzymatic retrosynthesis. Current thinking anticipates that enzymatic retrosynthesis will be implemented using conventional cell-based synthetic biology approaches where requisite native, heterologous, designer, and evolved enzymes making up a given multi-enzyme pathway are hosted by chassis organisms to carry out designer synthesis. In this perspective, we suggest that such an effort should not be limited by solely exploiting living cells and enzyme evolution and describe some useful yet less intensive complementary approaches that may prove especially productive in this grand scheme. By decoupling reactions from the environment of a living cell, a significantly larger portion of potential synthetic chemical space becomes available for exploration; most of this area is currently unavailable to cell-based approaches due to toxicity issues. In contrast, in a cell-free reaction a variety of classical enzymatic approaches can be exploited to improve performance and explore and understand a given enzyme's substrate specificity and catalytic profile towards non-natural substrates. We expect these studies will reveal unique enzymatic capabilities that are not accessible in living cells.
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Affiliation(s)
- Shelby L Hooe
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory Washington DC 20375 USA
- National Research Council Washington DC 20001 USA
| | - Gregory A Ellis
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory Washington DC 20375 USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory Washington DC 20375 USA
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16
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Opportunities and Challenges of in vitro Synthetic Biosystem for Terpenoids Production. BIOTECHNOL BIOPROC E 2022. [DOI: 10.1007/s12257-022-0100-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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17
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Copeland CE, Kim J, Copeland PL, Heitmeier CJ, Kwon YC. Characterizing a New Fluorescent Protein for a Low Limit of Detection Sensing in the Cell-Free System. ACS Synth Biol 2022; 11:2800-2810. [PMID: 35850511 PMCID: PMC9396652 DOI: 10.1021/acssynbio.2c00180] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cell-free protein synthesis-based biosensors have been developed as highly accurate, low-cost biosensors. However, since most biomarkers exist at low concentrations in various types of biopsies, the biosensor's dynamic range must be increased in the system to achieve low limits of detection necessary while deciphering from higher background signals. Many attempts to increase the dynamic range have relied on amplifying the input signal from the analyte, which can lead to complications of false positives. In this study, we aimed to increase the protein synthesis capability of the cell-free protein synthesis system and the output signal of the reporter protein to achieve a lower limit of detection. We utilized a new fluorescent protein, mNeonGreen, which produces a higher output than those commonly used in cell-free biosensors. Optimizations of DNA sequence and the subsequent cell-free protein synthesis reaction conditions allowed characterizing protein expression variability by given DNA template types, reaction environment, and storage additives that cause the greatest time constraint on designing the cell-free biosensor. Finally, we characterized the fluorescence kinetics of mNeonGreen compared to the commonly used reporter protein, superfolder green fluorescent protein. We expect that this finely tuned cell-free protein synthesis platform with the new reporter protein can be used with sophisticated synthetic gene circuitry networks to increase the dynamic range of a cell-free biosensor to reach lower detection limits and reduce the false-positive proportion.
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Affiliation(s)
- Caroline E Copeland
- Department of Biological and Agricultural Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Jeehye Kim
- Department of Biological and Agricultural Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Pearce L Copeland
- Department of Biological and Agricultural Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Chloe J Heitmeier
- Department of Biological and Agricultural Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Yong-Chan Kwon
- Department of Biological and Agricultural Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States.,Louisiana State University Agricultural Center, Baton Rouge, Louisiana 70803, United States
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18
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Ji X, Liu WQ, Li J. Recent advances in applying cell-free systems for high-value and complex natural product biosynthesis. Curr Opin Microbiol 2022; 67:102142. [DOI: 10.1016/j.mib.2022.102142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/09/2022] [Accepted: 02/18/2022] [Indexed: 11/03/2022]
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19
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Sierra AMR, Arold ST, Grünberg R. Efficient multi-gene expression in cell-free droplet microreactors. PLoS One 2022; 17:e0260420. [PMID: 35312702 PMCID: PMC8936439 DOI: 10.1371/journal.pone.0260420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 02/28/2022] [Indexed: 11/19/2022] Open
Abstract
Cell-free transcription and translation systems promise to accelerate and simplify the engineering of proteins, biological circuits and metabolic pathways. Their encapsulation on microfluidic platforms can generate millions of cell-free reactions in picoliter volume droplets. However, current methods struggle to create DNA diversity between droplets while also reaching sufficient protein expression levels. In particular, efficient multi-gene expression has remained elusive. We here demonstrate that co-encapsulation of DNA-coated beads with a defined cell-free system allows high protein expression while also supporting genetic diversity between individual droplets. We optimize DNA loading on commercially available microbeads through direct binding as well as through the sequential coupling of up to three genes via a solid-phase Golden Gate assembly or BxB1 integrase-based recombineering. Encapsulation with an off-the-shelf microfluidics device allows for single or multiple protein expression from a single DNA-coated bead per 14 pL droplet. We envision that this approach will help to scale up and parallelize the rapid prototyping of more complex biological systems.
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Affiliation(s)
- Ana Maria Restrepo Sierra
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
- KAUST Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
- Bionanoscience Department/Applied Sciences, Technische Universiteit Delft, Delft, The Netherlands
| | - Stefan T. Arold
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
- KAUST Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
- Centre de Biologie Structurale (CBS)/CNRS/INSERM, Université Montpellier, Montpellier, France
| | - Raik Grünberg
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
- KAUST Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
- * E-mail:
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20
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Rasor BJ, Vögeli B, Jewett MC, Karim AS. Cell-Free Protein Synthesis for High-Throughput Biosynthetic Pathway Prototyping. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2433:199-215. [PMID: 34985746 DOI: 10.1007/978-1-0716-1998-8_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Biological systems provide a sustainable and complimentary approach to synthesizing useful chemical products. Metabolic engineers seeking to establish economically viable biosynthesis platforms strive to increase product titers, rates, and yields. Despite continued advances in genetic tools and metabolic engineering techniques, cellular workflows remain limited in throughput. It may take months to test dozens of unique pathway designs even in a robust model organism, such as Escherichia coli. In contrast, cell-free protein synthesis enables the rapid generation of enzyme libraries that can be combined to reconstitute metabolic pathways in vitro for biochemical synthesis in days rather than weeks. Cell-free reactions thereby enable comparison of hundreds to thousands of unique combinations of enzyme homologs and concentrations, which can quickly identify the most productive pathway variants to test in vivo or further characterize in vitro. This cell-free pathway prototyping strategy provides a complementary approach to accelerate cellular metabolic engineering efforts toward highly productive strains for metabolite production.
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Affiliation(s)
- Blake J Rasor
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.,Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA.,Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Bastian Vögeli
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.,Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA.,Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, Center for Synthetic Biology, Robert H. Lurie Comprehensive Cancer Center, and Simpson Querrey Institute, Northwestern University, Evanston, IL, USA.
| | - Ashty S Karim
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, and Center for Synthetic Biology, Northwestern University, Evanston, IL, USA.
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21
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Sato W, Zajkowski T, Moser F, Adamala KP. Synthetic cells in biomedical applications. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2022; 14:e1761. [PMID: 34725945 PMCID: PMC8918002 DOI: 10.1002/wnan.1761] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 08/23/2021] [Accepted: 08/30/2021] [Indexed: 12/12/2022]
Abstract
Synthetic cells are engineered vesicles that can mimic one or more salient features of life. These features include directed localization, sense-and-respond behavior, gene expression, metabolism, and high stability. In nanomedicine, many of these features are desirable capabilities of drug delivery vehicles but are difficult to engineer. In this focus article, we discuss where synthetic cells offer unique advantages over nanoparticle and living cell therapies. We review progress in the engineering of the above life-like behaviors and how they are deployed in nanomedicine. Finally, we assess key challenges synthetic cells face before being deployed as drugs and suggest ways to overcome these challenges. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Biology-Inspired Nanomaterials > Lipid-Based Structures.
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Affiliation(s)
- Wakana Sato
- 1 Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN US
| | - Tomasz Zajkowski
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
- USRA at NASA Ames Research Center, Mountain View, CA 94035
- Blue Marble Space Institute of Science, 600 1st Avenue, Seattle WA 98104
| | - Felix Moser
- Synlife, Inc., One Kendall Square Suite B4401, Cambridge, MA 20139
| | - Katarzyna P. Adamala
- 1 Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN US
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22
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Key reaction components affect the kinetics and performance robustness of cell-free protein synthesis reactions. Comput Struct Biotechnol J 2022; 20:218-229. [PMID: 35024094 PMCID: PMC8718664 DOI: 10.1016/j.csbj.2021.12.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/08/2021] [Accepted: 12/08/2021] [Indexed: 11/23/2022] Open
Abstract
Novel cell-free protein synthesis reaction buffer improves performance by 400%. Enhanced performance is maintained across the synthesis of different proteins. Protein synthesis performance is robust across different cell lysate batches and E. coli strains. Buffer components affect aspects of reaction kinetics in differing ways.
Cell-free protein synthesis (CFPS) reactions have grown in popularity with particular interest in applications such as gene construct prototyping, biosensor technologies and the production of proteins with novel chemistry. Work has frequently focussed on optimising CFPS protocols for improving protein yield, reducing cost, or developing streamlined production protocols. Here we describe a statistical Design of Experiments analysis of 20 components of a popular CFPS reaction buffer. We simultaneously identify factors and factor interactions that impact on protein yield, rate of reaction, lag time and reaction longevity. This systematic experimental approach enables the creation of a statistical model capturing multiple behaviours of CFPS reactions in response to components and their interactions. We show that a novel reaction buffer outperforms the reference reaction by 400% and importantly reduces failures in CFPS across batches of cell lysates, strains of E. coli, and in the synthesis of different proteins. Detailed and quantitative understanding of how reaction components affect kinetic responses and robustness is imperative for future deployment of cell-free technologies.
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Key Words
- 3-PGA, 3-phosphoglyceric acid
- ATP, adenosine triphosphate
- Automation
- CFE, cell-free extract
- CFPS, cell-free protein synthesis
- CTP, cytidine triphosphate
- Cell-free protein synthesis (CFPS)
- CoA, coenzyme A
- DSD, Definitive Screening Design
- DTT, dithiothreitol
- Design of Experiments (DoE)
- DoE, Design of Experiments
- FEU, fluorescein equivalent units
- G-6-P, glucose-6-phosphate
- GTP, guanosine triphosphate
- HEPES, 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
- K-glutamate, potassium glutamate
- LB, lysogeny broth
- Mg, magnesium glutamate
- NAD, nicotinamide adenine dinucleotide
- NTP, nucleoside triphosphate
- OFAT, one-factor-at-a-time
- PEG-8000, polyethylene glycol 8000
- PEP, phosphoenolpyruvate
- RFU, relative fluorescence units
- RSM, Response Surface Model
- Robustness
- Statistical engineering
- UTP, uridine triphosphate
- X-gal, 5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside
- cAMP, cyclic adenosine monophosphate
- eGFP, enhanced green fluorescent protein
- tRNA, transfer ribonucleic acid
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23
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Brookwell A, Oza JP, Caschera F. Biotechnology Applications of Cell-Free Expression Systems. Life (Basel) 2021; 11:life11121367. [PMID: 34947898 PMCID: PMC8705439 DOI: 10.3390/life11121367] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 12/13/2022] Open
Abstract
Cell-free systems are a rapidly expanding platform technology with an important role in the engineering of biological systems. The key advantages that drive their broad adoption are increased efficiency, versatility, and low cost compared to in vivo systems. Traditionally, in vivo platforms have been used to synthesize novel and industrially relevant proteins and serve as a testbed for prototyping numerous biotechnologies such as genetic circuits and biosensors. Although in vivo platforms currently have many applications within biotechnology, they are hindered by time-constraining growth cycles, homeostatic considerations, and limited adaptability in production. Conversely, cell-free platforms are not hindered by constraints for supporting life and are therefore highly adaptable to a broad range of production and testing schemes. The advantages of cell-free platforms are being leveraged more commonly by the biotechnology community, and cell-free applications are expected to grow exponentially in the next decade. In this study, new and emerging applications of cell-free platforms, with a specific focus on cell-free protein synthesis (CFPS), will be examined. The current and near-future role of CFPS within metabolic engineering, prototyping, and biomanufacturing will be investigated as well as how the integration of machine learning is beneficial to these applications.
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Affiliation(s)
- August Brookwell
- Department of Chemistry & Biochemistry, College of Science & Mathematics, California Polytechnic State University, San Luis Obispo, CA 93407, USA;
| | - Javin P. Oza
- Department of Chemistry & Biochemistry, College of Science & Mathematics, California Polytechnic State University, San Luis Obispo, CA 93407, USA;
- Correspondence: (J.P.O.); (F.C.)
| | - Filippo Caschera
- Nuclera Nucleics Ltd., Cambridge CB4 0GD, UK
- Correspondence: (J.P.O.); (F.C.)
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24
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25
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Moore SJ, Tosi T, Bell D, Hleba YB, Polizzi KM, Freemont PS. High-yield 'one-pot' biosynthesis of raspberry ketone, a high-value fine chemical. Synth Biol (Oxf) 2021; 6:ysab021. [PMID: 34712844 PMCID: PMC8546603 DOI: 10.1093/synbio/ysab021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/14/2021] [Accepted: 08/03/2021] [Indexed: 11/14/2022] Open
Abstract
Cell-free extract and purified enzyme-based systems provide an attractive solution to study biosynthetic strategies towards a range of chemicals. 4-(4-hydroxyphenyl)-butan-2-one, also known as raspberry ketone, is the major fragrance component of raspberry fruit and is used as a natural additive in the food and sports industry. Current industrial processing of the natural form of raspberry ketone involves chemical extraction from a yield of ∼1–4 mg kg−1 of fruit. Due to toxicity, microbial production provides only low yields of up to 5–100 mg L−1. Herein, we report an efficient cell-free strategy to probe into a synthetic enzyme pathway that converts either L-tyrosine or the precursor, 4-(4-hydroxyphenyl)-buten-2-one, into raspberry ketone at up to 100% conversion. As part of this strategy, it is essential to recycle inexpensive cofactors. Specifically, the final enzyme step in the pathway is catalyzed by raspberry ketone/zingerone synthase (RZS1), an NADPH-dependent double bond reductase. To relax cofactor specificity towards NADH, the preferred cofactor for cell-free biosynthesis, we identify a variant (G191D) with strong activity with NADH. We implement the RZS1 G191D variant within a ‘one-pot’ cell-free reaction to produce raspberry ketone at high-yield (61 mg L−1), which provides an alternative route to traditional microbial production. In conclusion, our cell-free strategy complements the growing interest in engineering synthetic enzyme cascades towards industrially relevant value-added chemicals.
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Affiliation(s)
- Simon J Moore
- Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, London, UK
| | - Tommaso Tosi
- Department of Medicine, Imperial College London, South Kensington Campus, London, UK
| | - David Bell
- Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, London, UK
| | - Yonek B Hleba
- Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, London, UK
| | - Karen M Polizzi
- Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, London, UK
| | - Paul S Freemont
- Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, London, UK
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26
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Tang S, Liao D, Li X, Lin Y, Han S, Zheng S. Cell-Free Biosynthesis System: Methodology and Perspective of in Vitro Efficient Platform for Pyruvate Biosynthesis and Transformation. ACS Synth Biol 2021; 10:2417-2433. [PMID: 34529398 DOI: 10.1021/acssynbio.1c00252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The modification of intracellular metabolic pathways by metabolic engineering has generated many engineered strains with relatively high yields of various target products in the past few decades. However, the unpredictable accumulation of toxic products, the cell membrane barrier, and competition between the carbon flux of cell growth and product synthesis have severely retarded progress toward the industrial-scale production of many essential chemicals. On the basis of an in-depth understanding of intracellular metabolic pathways, scientists intend to explore more sustainable methods and construct a cell-free biosynthesis system in vitro. In this review, the synthesis and application of pyruvate as a platform compound is used as an example to introduce cell-free biosynthesis systems. We systematically summarize a proposed methodology workflow of cell-free biosynthesis systems, including pathway design, enzyme mining, enzyme modification, multienzyme assembly, and pathway optimization. Some new methods, such as machine learning, are also mentioned in this review.
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Affiliation(s)
- Shiming Tang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Daocheng Liao
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Xuewen Li
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Ying Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Shuangyan Han
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Suiping Zheng
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
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27
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Chou A, Lee SH, Zhu F, Clomburg JM, Gonzalez R. An orthogonal metabolic framework for one-carbon utilization. Nat Metab 2021; 3:1385-1399. [PMID: 34675440 DOI: 10.1038/s42255-021-00453-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 08/10/2021] [Indexed: 11/09/2022]
Abstract
Metabolic engineering often entails concurrent engineering of substrate utilization, central metabolism and product synthesis pathways, inevitably creating interdependency with native metabolism. Here we report an alternative approach using synthetic pathways for C1 bioconversion that generate multicarbon products directly from C1 units and hence are orthogonal to the host metabolic network. The engineered pathways are based on formyl-CoA elongation (FORCE) reactions catalysed by the enzyme 2-hydroxyacyl-CoA lyase. We use thermodynamic and stoichiometric analyses to evaluate FORCE pathway variants, including aldose elongation, α-reduction and aldehyde elongation. Promising variants were prototyped in vitro and in vivo using the non-methylotrophic bacterium Escherichia coli. We demonstrate the conversion of formate, formaldehyde and methanol into various products including glycolate, ethylene glycol, ethanol and glycerate. FORCE pathways also have the potential to be integrated with the host metabolism for synthetic methylotrophy by the production of native growth substrates as demonstrated in a two-strain co-culture system.
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Affiliation(s)
- Alexander Chou
- Department of Chemical, Biological and Materials Engineering, University of South Florida, Tampa, FL, USA
| | - Seung Hwan Lee
- Department of Chemical, Biological and Materials Engineering, University of South Florida, Tampa, FL, USA
| | - Fayin Zhu
- Department of Chemical, Biological and Materials Engineering, University of South Florida, Tampa, FL, USA
| | - James M Clomburg
- Department of Chemical, Biological and Materials Engineering, University of South Florida, Tampa, FL, USA
| | - Ramon Gonzalez
- Department of Chemical, Biological and Materials Engineering, University of South Florida, Tampa, FL, USA.
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28
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Lehr FX, Kuzembayeva A, Bailey ME, Kleindienst W, Kabisch J, Koeppl H. Functionalizing Cell-Free Systems with CRISPR-Associated Proteins: Application to RNA-Based Circuit Engineering. ACS Synth Biol 2021; 10:2138-2150. [PMID: 34383464 DOI: 10.1021/acssynbio.0c00386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cell-free systems have become a compelling choice for the prototyping of synthetic circuits. Many robust protocols for preparing cell-free systems are now available along with toolboxes designed for a variety of applications. Thus far, the production of cell-free extracts has often been decoupled from the production of functionalized proteins. Here, we leveraged a recent protocol for producing an E. coli-based cell-free expression system with two CRISPR-associated proteins, Csy4 and dCas9, expressed prior to harvest. We found that pre-expression did not affect the resulting extract performance, and the final concentrations of the endonucleases matched the level required for synthetic circuit prototyping. We demonstrated the benefits and versatility of dCas9 and Csy4 through the use of RNA circuitry based on a combination of single guide RNAs, small transcriptional activator RNAs, and toehold switches. For instance, we show that Csy4 processing increased 4-fold the dynamic range of a previously published AND-logic gate. Additionally, blending the CRISPR-enhanced extracts enabled us to reduce leakage in a multiple inputs gate, and to extend the type of Boolean functions available for RNA-based circuits, such as NAND-logic. Finally, we reported the use of simultaneous transcriptional and translational reporters in our RNA-based circuits. In particular, the AND-gate mRNA and protein levels were able to be independently monitored in response to transcriptional and translational activators. We hope this work will facilitate the adoption of advanced processing tools for RNA-based circuit prototyping in a cell-free environment.
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Affiliation(s)
- François-Xavier Lehr
- Centre for Synthetic Biology, Technische Universität Darmstadt, Darmstadt 64287, Germany
- Department of Electrical Engineering and Information Technology, Technische Universität Darmstadt, Darmstadt 64283, Germany
| | - Alina Kuzembayeva
- Centre for Synthetic Biology, Technische Universität Darmstadt, Darmstadt 64287, Germany
- Department of Electrical Engineering and Information Technology, Technische Universität Darmstadt, Darmstadt 64283, Germany
| | - Megan E Bailey
- Centre for Synthetic Biology, Technische Universität Darmstadt, Darmstadt 64287, Germany
- Department of Electrical Engineering and Information Technology, Technische Universität Darmstadt, Darmstadt 64283, Germany
| | - Werner Kleindienst
- Centre for Synthetic Biology, Technische Universität Darmstadt, Darmstadt 64287, Germany
| | - Johannes Kabisch
- Centre for Synthetic Biology, Technische Universität Darmstadt, Darmstadt 64287, Germany
| | - Heinz Koeppl
- Centre for Synthetic Biology, Technische Universität Darmstadt, Darmstadt 64287, Germany
- Department of Electrical Engineering and Information Technology, Technische Universität Darmstadt, Darmstadt 64283, Germany
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An integrated in vivo/in vitro framework to enhance cell-free biosynthesis with metabolically rewired yeast extracts. Nat Commun 2021; 12:5139. [PMID: 34446711 PMCID: PMC8390474 DOI: 10.1038/s41467-021-25233-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/30/2021] [Indexed: 02/07/2023] Open
Abstract
Cell-free systems using crude cell extracts present appealing opportunities for designing biosynthetic pathways and enabling sustainable chemical synthesis. However, the lack of tools to effectively manipulate the underlying host metabolism in vitro limits the potential of these systems. Here, we create an integrated framework to address this gap that leverages cell extracts from host strains genetically rewired by multiplexed CRISPR-dCas9 modulation and other metabolic engineering techniques. As a model, we explore conversion of glucose to 2,3-butanediol in extracts from flux-enhanced Saccharomyces cerevisiae strains. We show that cellular flux rewiring in several strains of S. cerevisiae combined with systematic optimization of the cell-free reaction environment significantly increases 2,3-butanediol titers and volumetric productivities, reaching productivities greater than 0.9 g/L-h. We then show the generalizability of the framework by improving cell-free itaconic acid and glycerol biosynthesis. Our coupled in vivo/in vitro metabolic engineering approach opens opportunities for synthetic biology prototyping efforts and cell-free biomanufacturing.
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Arce A, Guzman Chavez F, Gandini C, Puig J, Matute T, Haseloff J, Dalchau N, Molloy J, Pardee K, Federici F. Decentralizing Cell-Free RNA Sensing With the Use of Low-Cost Cell Extracts. Front Bioeng Biotechnol 2021; 9:727584. [PMID: 34497801 PMCID: PMC8419261 DOI: 10.3389/fbioe.2021.727584] [Citation(s) in RCA: 9] [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: 06/18/2021] [Accepted: 08/06/2021] [Indexed: 11/13/2022] Open
Abstract
Cell-free gene expression systems have emerged as a promising platform for field-deployed biosensing and diagnostics. When combined with programmable toehold switch-based RNA sensors, these systems can be used to detect arbitrary RNAs and freeze-dried for room temperature transport to the point-of-need. These sensors, however, have been mainly implemented using reconstituted PURE cell-free protein expression systems that are difficult to source in the Global South due to their high commercial cost and cold-chain shipping requirements. Based on preliminary demonstrations of toehold sensors working on lysates, we describe the fast prototyping of RNA toehold switch-based sensors that can be produced locally and reduce the cost of sensors by two orders of magnitude. We demonstrate that these in-house cell lysates provide sensor performance comparable to commercial PURE cell-free systems. We further optimize these lysates with a CRISPRi strategy to enhance the stability of linear DNAs by knocking-down genes responsible for linear DNA degradation. This enables the direct use of PCR products for fast screening of new designs. As a proof-of-concept, we develop novel toehold sensors for the plant pathogen Potato Virus Y (PVY), which dramatically reduces the yield of this important staple crop. The local implementation of low-cost cell-free toehold sensors could enable biosensing capacity at the regional level and lead to more decentralized models for global surveillance of infectious disease.
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Affiliation(s)
- Anibal Arce
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Schools of Engineering, Institute for Biological and Medical Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | - Chiara Gandini
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Juan Puig
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Schools of Engineering, Institute for Biological and Medical Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Tamara Matute
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Schools of Engineering, Institute for Biological and Medical Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Jim Haseloff
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | | | - Jenny Molloy
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Keith Pardee
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Fernán Federici
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Schools of Engineering, Institute for Biological and Medical Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
- FONDAP Center for Genome Regulation, Santiago, Chile
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31
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Niu FX, Yan ZB, Huang YB, Liu JZ. Cell-free Biosynthesis of Chlorogenic Acid Using a Mixture of Chassis Cell Extracts and Purified Spy-Cyclized Enzymes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:7938-7947. [PMID: 34237214 DOI: 10.1021/acs.jafc.1c03309] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A novel cell-free biosynthesis system based on a mixture of chassis cell extracts and purified Spy-cyclized enzymes (CFBS-mixture) was developed. As a demonstration, the CFBS-mixture was applied to chlorogenic acid (CGA) biosynthesis. The mix-and-match and Plackett-Burman experiments demonstrated that Lonicera japonica hydroxycinnamate-CoA quinate transferase and p-hydroxyphenylacetate 3-hydroxylase were the key enzymes for the production of CGA. After optimization of the concentrations of the biosynthetic enzymes in the CFBS-mixture reaction using the Plackett-Burman experimental design and the path of the steepest ascent, 711.26 ± 15.63 mg/L CGA was produced after 16 h, which is 71.1-fold the yield obtained using the conventional crude extract-based CFBS and 9.1-fold the reported yield obtained using the living cells. Based on the CFBS-mixture results, the production of CGA was further enhanced in engineered Escherichia coli. The CFBS-mixture strategy is highly effective and will be useful for high-level CFBS of natural products.
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Affiliation(s)
- Fu-Xing Niu
- Institute of Synthetic Biology, MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Zhi-Bo Yan
- Institute of Synthetic Biology, MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yuan-Bin Huang
- Institute of Synthetic Biology, MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Jian-Zhong Liu
- Institute of Synthetic Biology, MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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32
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Xu Y, Wu Y, Lv X, Sun G, Zhang H, Chen T, Du G, Li J, Liu L. Design and construction of novel biocatalyst for bioprocessing: Recent advances and future outlook. BIORESOURCE TECHNOLOGY 2021; 332:125071. [PMID: 33826982 DOI: 10.1016/j.biortech.2021.125071] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
Bioprocess, a biocatalysis-based technology, is becoming popular in many research fields and widely applied in industrial manufacturing. However, low bioconversion, low productivity, and high costs during industrial processes are usually the limitation in bioprocess. Therefore, many biocatalyst strategies have been developed to meet these challenges in recent years. In this review, we firstly discuss protein engineering strategies, which are emerged for improving the biocatalysis activity of biocatalysts. Then, we summarize metabolic engineering strategies that are promoting the development of microbial cell factories. Next, we illustrate the necessity of using the combining strategy of protein engineering and metabolic engineering for efficient biocatalysts. Lastly, future perspectives about the development and application of novel biocatalyst strategies are discussed. This review provides theoretical guidance for the development of efficient, sustainable, and economical bioprocesses mediated by novel biocatalysts.
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Affiliation(s)
- Yameng Xu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China
| | - Yaokang Wu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China
| | - Guoyun Sun
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China
| | - Hongzhi Zhang
- Shandong Runde Biotechnology Co., Ltd., Tai'an 271000, PR China
| | - Taichi Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China.
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Kruyer NS, Sugianto W, Tickman BI, Alba Burbano D, Noireaux V, Carothers JM, Peralta-Yahya P. Membrane Augmented Cell-Free Systems: A New Frontier in Biotechnology. ACS Synth Biol 2021; 10:670-681. [PMID: 33749249 DOI: 10.1021/acssynbio.0c00625] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Membrane proteins are present in a wide array of cellular processes from primary and secondary metabolite synthesis to electron transport and single carbon metabolism. A key barrier to applying membrane proteins industrially is their difficult functional production. Beyond expression, folding, and membrane insertion, membrane protein activity is influenced by the physicochemical properties of the associated membrane, making it difficult to achieve optimal membrane protein performance outside the endogenous host. In this review, we highlight recent work on production of membrane proteins in membrane augmented cell-free systems (CFSs) and applications thereof. CFSs lack membranes and can thus be augmented with user-specified, tunable, mimetic membranes to generate customized environments for production of functional membrane proteins of interest. Membrane augmented CFSs would enable the synthesis of more complex plant secondary metabolites, the growth and division of synthetic cells for drug delivery and cell therapeutic applications, as well as enable green energy applications including methane capture and artificial photosynthesis.
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Affiliation(s)
- Nicholas S. Kruyer
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Widianti Sugianto
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Benjamin I. Tickman
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington 98195, United States
| | - Diego Alba Burbano
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington 98195, United States
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - James M. Carothers
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington 98195, United States
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Pamela Peralta-Yahya
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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Feng J, Yang C, Zhao Z, Xu J, Li J, Li P. Application of Cell-Free Protein Synthesis System for the Biosynthesis of l-Theanine. ACS Synth Biol 2021; 10:620-631. [PMID: 33719397 DOI: 10.1021/acssynbio.0c00618] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
l-Theanine, as an active component of the leaves of the tea plant, possesses many health benefits and broad applications. Chemical synthesis of l-theanine is possible; however, this method generates chiral compounds and needs further isolation of the pure l-isoform. Heterologous biosynthesis is an alternative strategy, but one main limitation is the toxicity of the substrate ethylamine on microbial host cells. In this study, we introduced a cell-free protein synthesis (CFPS) system for l-theanine production. The CFPS expressed l-theanine synthetase 2 from Camellia sinensis (CsTS2) could produce l-theanine at a concentration of 11.31 μM after 32 h of the synthesis reaction. In addition, three isozymes from microorganisms were expressed in CFPS for l-theanine biosynthesis. The γ-glutamylcysteine synthetase from Escherichia coli could produce l-theanine at the highest concentration of 302.96 μM after 24 h of reaction. Furthermore, CFPS was used to validate a hypothetical two-step l-theanine biosynthetic pathway consisting of the l-alanine decarboxylase from C. sinensis (CsAD) and multiple l-theanine synthases. Among them, the combination of CsAD and the l-glutamine synthetase from Pseudomonas taetrolens (PtGS) could synthesize l-theanine at the highest concentration of 13.42 μM. Then, we constructed an engineered E. coli strain overexpressed CsAD and PtGS to further confirm the l-theanine biosynthesis ability in living cells. This engineered E. coli strain could convert l-alanine and l-glutamate in the medium to l-theanine at a concentration of 3.82 mM after 72 h of fermentation. Taken together, these results demonstrated that the CFPS system can be used to produce the l-theanine through the two-step l-theanine biosynthesis pathway, indicating the potential application of CFPS for the biosynthesis of other active compounds.
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Affiliation(s)
- Junchen Feng
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Chen Yang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhehao Zhao
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Junjian Xu
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Jian Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ping Li
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
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35
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Toward sustainable, cell-free biomanufacturing. Curr Opin Biotechnol 2021; 69:136-144. [PMID: 33453438 DOI: 10.1016/j.copbio.2020.12.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 12/10/2020] [Accepted: 12/15/2020] [Indexed: 12/12/2022]
Abstract
Industrial biotechnology is an attractive approach to address the need for low-cost fuels and products from sustainable resources. Unfortunately, cells impose inherent limitations on the effective synthesis and release of target products. One key constraint is that cellular survival objectives often work against the production objectives of biochemical engineers. Additionally, industrial strains release CO2 and struggle to utilize sustainable, potentially profitable feedstocks. Cell-free biotechnology, which uses biological machinery harvested from cells, can address these challenges with advantages including: (i) shorter development times, (ii) higher volumetric production rates, and (iii) tolerance to otherwise toxic molecules. In this review, we highlight recent advances in cell-free technologies toward the production of non-protein products beyond lab-scale demonstrations and describe guiding principles for designing cell-free systems. Specifically, we discuss carbon and energy sources, reaction homeostasis, and scale-up. Expanding the scope of cell-free biomanufacturing practice could enable innovative approaches for the industrial production of green chemicals.
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36
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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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37
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Kitamura S, Shimizu H, Toya Y. Identification of a rate-limiting step in a metabolic pathway using the kinetic model and in vitro experiment. J Biosci Bioeng 2020; 131:271-276. [PMID: 33168471 DOI: 10.1016/j.jbiosc.2020.10.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/19/2020] [Accepted: 10/22/2020] [Indexed: 11/16/2022]
Abstract
Identification of the rate-limiting step in a metabolic pathway is an important challenge in metabolic engineering for enhancing pathway flow. Although specific enzyme activities (Vmax) provide valuable clues for the identification, it is time-consuming and difficult to measure multiple enzymes in the pathway because different assay protocols are required for each enzyme. In the present study, we propose a method to simultaneously determine the Vmax values of multiple enzymes using a kinetic model with a time course of the intermediate concentrations through an in vitro experiment. To demonstrate this method, nine glycolysis reactions for converting glucose-6-phosphate (G6P) to pyruvate in Escherichia coli were considered. In a reaction mixture containing G6P and cofactors, glycolysis was initiated by adding a crude cell extract obtained from stationary phase cells. The Vmax values were optimized to minimize the difference between the measured and simulated time-courses using a kinetic model. Metabolic control analysis using the kinetic model with the estimated Vmax values revealed that fructose bisphosphate aldolase (FBA) was the rate-limiting step in the upper part of glycolysis. The addition of FBA in the reaction mixture successfully increased the glycolytic flux in vitro. Furthermore, in vivo, the specific glucose consumption rate of an FBA overexpression strain was 1.4 times higher than that of the control strain during the stationary phase. These results confirmed that FBA was the rate-limiting step in glycolysis under the stationary phase. This approach provides Vmax values of multiple enzymes in a pathway for metabolic control analysis with a kinetic model.
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Affiliation(s)
- Sayaka Kitamura
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
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38
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Engineered biosynthetic pathways and biocatalytic cascades for sustainable synthesis. Curr Opin Chem Biol 2020; 58:146-154. [PMID: 33152607 DOI: 10.1016/j.cbpa.2020.08.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/13/2020] [Accepted: 08/14/2020] [Indexed: 10/23/2022]
Abstract
Nature exploits biosynthetic cascades to construct numerous molecules from a limited set of starting materials. A deeper understanding of biosynthesis and extraordinary developments in gene technology has allowed the manipulation of natural pathways and construction of artificial cascades for the preparation of a range of molecules, which would be challenging to access using traditional synthetic chemical approaches. Alongside these metabolic engineering strategies, there has been continued interest in developing in vivo and in vitro biocatalytic cascades. Advancements in both metabolic engineering and biocatalysis are complementary, and this article aims to highlight some of the most exciting developments in these two areas with a particular focus on exploring those that have the potential to advance both pathway engineering and more traditional biocatalytic cascade development.
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39
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Malico AA, Calzini MA, Gayen AK, Williams GJ. Synthetic biology, combinatorial biosynthesis, and chemo‑enzymatic synthesis of isoprenoids. J Ind Microbiol Biotechnol 2020; 47:675-702. [PMID: 32880770 PMCID: PMC7666032 DOI: 10.1007/s10295-020-02306-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 08/27/2020] [Indexed: 12/12/2022]
Abstract
Isoprenoids are a large class of natural products with myriad applications as bioactive and commercial compounds. Their diverse structures are derived from the biosynthetic assembly and tailoring of their scaffolds, ultimately constructed from two C5 hemiterpene building blocks. The modular logic of these platforms can be harnessed to improve titers of valuable isoprenoids in diverse hosts and to produce new-to-nature compounds. Often, this process is facilitated by the substrate or product promiscuity of the component enzymes, which can be leveraged to produce novel isoprenoids. To complement rational enhancements and even re-programming of isoprenoid biosynthesis, high-throughput approaches that rely on searching through large enzymatic libraries are being developed. This review summarizes recent advances and strategies related to isoprenoid synthetic biology, combinatorial biosynthesis, and chemo-enzymatic synthesis, focusing on the past 5 years. Emerging applications of cell-free biosynthesis and high-throughput tools are included that culminate in a discussion of the future outlook and perspective of isoprenoid biosynthetic engineering.
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Affiliation(s)
| | - Miles A Calzini
- Department of Chemistry, NC State University, Raleigh, NC, 27695, USA
| | - Anuran K Gayen
- Department of Chemistry, NC State University, Raleigh, NC, 27695, USA
| | - Gavin J Williams
- Department of Chemistry, NC State University, Raleigh, NC, 27695, USA.
- Comparative Medicine Institute, NC State University, Raleigh, NC, 27695, USA.
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40
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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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41
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Tian R, Wang M, Shi J, Qin X, Guo H, Jia X, Li J, Liu L, Du G, Chen J, Liu Y. Cell-free synthesis system-assisted pathway bottleneck diagnosis and engineering in Bacillus subtilis. Synth Syst Biotechnol 2020; 5:131-136. [PMID: 32637666 PMCID: PMC7320236 DOI: 10.1016/j.synbio.2020.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 06/12/2020] [Accepted: 06/15/2020] [Indexed: 11/29/2022] Open
Abstract
Metabolic engineering is a key technology for cell factories construction by rewiring cellular resources to achieve efficient production of target chemicals. However, the existence of bottlenecks in synthetic pathway can seriously affect production efficiency, which is also one of the core issues for metabolic engineers to solve. Therefore, developing an approach for diagnosing potential metabolic bottlenecks in a faster and simpler manner is of great significance to accelerate cell factories construction. The cell-free reaction system based on cell lysates can transfer metabolic reactions from in vivo to in vitro, providing a flexible access to directly change protein and metabolite variables, thus provides a potential solution for rapid identification of bottlenecks. Here, bottleneck diagnosis of the N-acetylneuraminic acid (NeuAc) biosynthesis pathway in industrially important chassis microorganism Bacillus subtilis was performed using cell-free synthesis system. Specifically, a highly efficient B. subtilis cell-free system for NeuAc de novo synthesis was firstly constructed, which had a 305-fold NeuAc synthesis rate than that in vivo and enabled fast pathway dynamics analysis. Next, through the addition of all potential key intermediates in combination with substrate glucose respectively, it was found that insufficient phosphoenolpyruvate supply was one of the NeuAc pathway bottlenecks. Rational in vivo metabolic engineering of NeuAc-producing B. subtilis was further performed to eliminate the bottleneck. By down-regulating the expression level of pyruvate kinase throughout the growth phase or only in the stationary phase using inhibitory N-terminal coding sequences (NCSs) and growth-dependent regulatory NCSs respectively, the maximal NeuAc titer increased 2.0-fold. Our study provides a rapid method for bottleneck diagnosis, which may help to accelerate the cycle of design, build, test and learn cycle for metabolic engineering.
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Affiliation(s)
- Rongzhen Tian
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Minghu Wang
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jintian Shi
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Xiaolong Qin
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Haoyu Guo
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Xuanjie Jia
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jianghua Li
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Long Liu
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Guocheng Du
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jian Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China
| | - Yanfeng Liu
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
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42
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Richardson KN, Black WB, Li H. Aldehyde Production in Crude Lysate- and Whole Cell-Based Biotransformation Using a Noncanonical Redox Cofactor System. ACS Catal 2020; 10:8898-8903. [PMID: 34306803 DOI: 10.1021/acscatal.0c03070] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
It is challenging to biosynthesize industrially important aldehydes, which are readily consumed by the numerous alcohol dehydrogenases (ADHs) in cells. In this work, we demonstrate that a nicotinamide mononucleotide (NMN+)-dependent redox cofactor cycling system enables aldehyde accumulation in Escherichia coli crude lysates and whole cells. By specifically delivering reducing power to a recombinant enoate reductase, but not to endogenous ADHs, we convert citral to citronellal with minimal byproduct formation (97-100% and 83% product purity in crude lysate- and whole cell-based biotransformation, respectively). We envision the system's universal application to lowering the noise in biomanufacturing by silencing the host's metabolic background.
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Affiliation(s)
- Kelly N. Richardson
- Department of Chemical and Biomolecular Engineering, University of California Irvine, Irvine, California 92697-2700, United States
| | - William B. Black
- Department of Chemical and Biomolecular Engineering, University of California Irvine, Irvine, California 92697-2700, United States
| | - Han Li
- Department of Chemical and Biomolecular Engineering, University of California Irvine, Irvine, California 92697-2700, United States
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43
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Jaroentomeechai T, Taw MN, Li M, Aquino A, Agashe N, Chung S, Jewett MC, DeLisa MP. Cell-Free Synthetic Glycobiology: Designing and Engineering Glycomolecules Outside of Living Cells. Front Chem 2020; 8:645. [PMID: 32850660 PMCID: PMC7403607 DOI: 10.3389/fchem.2020.00645] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/22/2020] [Indexed: 12/12/2022] Open
Abstract
Glycans and glycosylated biomolecules are directly involved in almost every biological process as well as the etiology of most major diseases. Hence, glycoscience knowledge is essential to efforts aimed at addressing fundamental challenges in understanding and improving human health, protecting the environment and enhancing energy security, and developing renewable and sustainable resources that can serve as the source of next-generation materials. While much progress has been made, there remains an urgent need for new tools that can overexpress structurally uniform glycans and glycoconjugates in the quantities needed for characterization and that can be used to mechanistically dissect the enzymatic reactions and multi-enzyme assembly lines that promote their construction. To address this technology gap, cell-free synthetic glycobiology has emerged as a simplified and highly modular framework to investigate, prototype, and engineer pathways for glycan biosynthesis and biomolecule glycosylation outside the confines of living cells. From nucleotide sugars to complex glycoproteins, we summarize here recent efforts that harness the power of cell-free approaches to design, build, test, and utilize glyco-enzyme reaction networks that produce desired glycomolecules in a predictable and controllable manner. We also highlight novel cell-free methods for shedding light on poorly understood aspects of diverse glycosylation processes and engineering these processes toward desired outcomes. Taken together, cell-free synthetic glycobiology represents a promising set of tools and techniques for accelerating basic glycoscience research (e.g., deciphering the "glycan code") and its application (e.g., biomanufacturing high-value glycomolecules on demand).
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Affiliation(s)
- Thapakorn Jaroentomeechai
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - May N. Taw
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - Mingji Li
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - Alicia Aquino
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - Ninad Agashe
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - Sean Chung
- Graduate Field of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY, United States
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States
- Center for Synthetic Biology, Northwestern University, Evanston, IL, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, United States
| | - Matthew P. DeLisa
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
- Graduate Field of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY, United States
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44
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Abstract
Metabolic engineering is crucial in the development of production strains for platform chemicals, pharmaceuticals and biomaterials from renewable resources. The central carbon metabolism (CCM) of heterotrophs plays an essential role in the conversion of biomass to the cellular building blocks required for growth. Yet, engineering the CCM ultimately aims toward a maximization of flux toward products of interest. The most abundant dissimilative carbohydrate pathways amongst prokaryotes (and eukaryotes) are the Embden-Meyerhof-Parnas (EMP) and the Entner-Doudoroff (ED) pathways, which build the basics for heterotrophic metabolic chassis strains. Although the EMP is regarded as the textbook example of a carbohydrate pathway owing to its central role in production strains like Escherichia coli, Saccharomyces cerevisiae and Bacillus subtilis, it is either modified, complemented or even replaced by alternative carbohydrate pathways in different organisms. The ED pathway also plays key roles in biotechnological relevant bacteria, like Zymomonas mobilis and Pseudomonas putida, and its importance was recently discovered in photoautotrophs and marine microorganisms. In contrast to the EMP, the ED pathway and its variations are not evolutionary optimized for high ATP production and it differs in key principles such as protein cost, energetics and thermodynamics, which can be exploited in the construction of unique metabolic designs. Single ED pathway enzymes and complete ED pathway modules have been used to rewire carbon metabolisms in production strains and for the construction of cell-free enzymatic pathways. This review focuses on the differences of the ED and EMP pathways including their variations and discusses the use of alternative pathway strategies for in vivo and cell-free metabolic engineering.
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Affiliation(s)
- Dominik Kopp
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Anwar Sunna
- Department of Molecular Sciences, Macquarie University, Sydney, Australia.,Biomolecular Discovery Research Centre, Macquarie University, Sydney, Australia
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45
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Daletos G, Katsimpouras C, Stephanopoulos G. Novel Strategies and Platforms for Industrial Isoprenoid Engineering. Trends Biotechnol 2020; 38:811-822. [DOI: 10.1016/j.tibtech.2020.03.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/16/2020] [Accepted: 03/17/2020] [Indexed: 12/13/2022]
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46
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Khatri Y, Hohlman RM, Mendoza J, Li S, Lowell AN, Asahara H, Sherman DH. Multicomponent Microscale Biosynthesis of Unnatural Cyanobacterial Indole Alkaloids. ACS Synth Biol 2020; 9:1349-1360. [PMID: 32302487 PMCID: PMC7323787 DOI: 10.1021/acssynbio.0c00038] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Genome sequencing and bioinformatics tools have facilitated the identification and expression of an increasing number of cryptic biosynthetic gene clusters (BGCs). However, functional analysis of all components of a metabolic pathway to precisely determine biocatalytic properties remains time-consuming and labor intensive. One way to speed this process involves microscale cell-free protein synthesis (CFPS) for direct gene to biochemical function analysis, which has rarely been applied to study multicomponent enzymatic systems in specialized metabolism. We sought to establish an in vitro transcription/translation (TT)-assay to assess assembly of cyanobacterial-derived hapalindole-type natural products (cNPs) because of their diverse bioactivity profiles and complex structural diversity. Using a CFPS system including a plasmid bearing famD2 prenyltransferase from Fischerella ambigua UTEX 1903, we showed production of the central prenylated intermediate (3GC) in the presence of exogenous geranyl-pyrophosphate (GPP) and cis-indole isonitrile. Further addition of a plasmid bearing the famC1 Stig cyclase resulted in synthesis of both FamD2 and FamC1 enzymes, which was confirmed by proteomics analysis, and catalyzed assembly of 12-epi-hapalindole U. Further combinations of Stig cyclases (FamC1-C4) produced hapalindole U and hapalindole H, while FisC identified from Fischerella sp. SAG46.79 generated 12-epi-fischerindole U. The CFPS system was further employed to screen six unnatural halogenated cis-indole isonitrile substrates using FamC1 and FisC, and the reactions were scaled-up using chemoenzymatic synthesis and identified as 5- and 6-fluoro-12-epi-hapalindole U, and 5- and 6-fluoro-12-epi-fischerindole U, respectively. This approach represents an effective, high throughput strategy to determine the functional role of biosynthetic enzymes from diverse natural product BGCs.
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Affiliation(s)
| | | | | | | | | | - Haruichi Asahara
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, United States
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47
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Karim AS, Dudley QM, Juminaga A, Yuan Y, Crowe SA, Heggestad JT, Garg S, Abdalla T, Grubbe WS, Rasor BJ, Coar DN, Torculas M, Krein M, Liew F, Quattlebaum A, Jensen RO, Stuart JA, Simpson SD, Köpke M, Jewett MC. In vitro prototyping and rapid optimization of biosynthetic enzymes for cell design. Nat Chem Biol 2020; 16:912-919. [DOI: 10.1038/s41589-020-0559-0] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 04/10/2020] [Accepted: 05/06/2020] [Indexed: 01/27/2023]
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48
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Abstract
Cell-free systems are a widely used research tool in systems and synthetic biology and a promising platform for manufacturing of proteins and chemicals. In the past, cell-free biology was primarily used to better understand fundamental biochemical processes. Notably, E. coli cell-free extracts were used in the 1960s to decipher the sequencing of the genetic code. Since then, the transcription and translation capabilities of cell-free systems have been repeatedly optimized to improve energy efficiency and product yield. Today, cell-free systems, in combination with the rise of synthetic biology, have taken on a new role as a promising technology for just-in-time manufacturing of therapeutically important biologics and high-value small molecules. They have also been implemented at an industrial scale for the production of antibodies and cytokines. In this review, we discuss the evolution of cell-free technologies, in particular advancements in extract preparation, cell-free protein synthesis, and cell-free metabolic engineering applications. We then conclude with a discussion of the mathematical modeling of cell-free systems. Mathematical modeling of cell-free processes could be critical to addressing performance bottlenecks and estimating the costs of cell-free manufactured products.
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49
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Dudley QM, Karim AS, Nash CJ, Jewett MC. In vitro prototyping of limonene biosynthesis using cell-free protein synthesis. Metab Eng 2020; 61:251-260. [PMID: 32464283 DOI: 10.1016/j.ymben.2020.05.006] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/13/2020] [Accepted: 05/17/2020] [Indexed: 01/03/2023]
Abstract
Metabolic engineering of microorganisms to produce sustainable chemicals has emerged as an important part of the global bioeconomy. Unfortunately, efforts to design and engineer microbial cell factories are challenging because design-build-test cycles, iterations of re-engineering organisms to test and optimize new sets of enzymes, are slow. To alleviate this challenge, we demonstrate a cell-free approach termed in vitro Prototyping and Rapid Optimization of Biosynthetic Enzymes (or iPROBE). In iPROBE, a large number of pathway combinations can be rapidly built and optimized. The key idea is to use cell-free protein synthesis (CFPS) to manufacture pathway enzymes in separate reactions that are then mixed to modularly assemble multiple, distinct biosynthetic pathways. As a model, we apply our approach to the 9-step heterologous enzyme pathway to limonene in extracts from Escherichia coli. In iterative cycles of design, we studied the impact of 54 enzyme homologs, multiple enzyme levels, and cofactor concentrations on pathway performance. In total, we screened over 150 unique sets of enzymes in 580 unique pathway conditions to increase limonene production in 24 h from 0.2 to 4.5 mM (23-610 mg/L). Finally, to demonstrate the modularity of this pathway, we also synthesized the biofuel precursors pinene and bisabolene. We anticipate that iPROBE will accelerate design-build-test cycles for metabolic engineering, enabling data-driven multiplexed cell-free methods for testing large combinations of biosynthetic enzymes to inform cellular design.
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Affiliation(s)
- Quentin M Dudley
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Ashty S Karim
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Connor J Nash
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA.
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50
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Gregorio NE, Kao WY, Williams LC, Hight CM, Patel P, Watts KR, Oza JP. Unlocking Applications of Cell-Free Biotechnology through Enhanced Shelf Life and Productivity of E. coli Extracts. ACS Synth Biol 2020; 9:766-778. [PMID: 32083847 DOI: 10.1021/acssynbio.9b00433] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cell-free protein synthesis (CFPS) is a platform biotechnology that enables a breadth of applications. However, field applications remain limited due to the poor shelf-stability of aqueous cell extracts required for CFPS. Lyophilization of E. coli extracts improves shelf life but remains insufficient for extended storage at room temperature. To address this limitation, we mapped the chemical space of ten low-cost additives with four distinct mechanisms of action in a combinatorial manner to identify formulations capable of stabilizing lyophilized cell extract. We report three key findings: (1) unique additive formulations that maintain full productivity of cell extracts stored at 4 °C and 23 °C; (2) additive formulations that enhance extract productivity by nearly 2-fold; (3) a machine learning algorithm that provides predictive capacity for the stabilizing effects of additive formulations that were not tested experimentally. These findings provide a simple and low-cost advance toward making CFPS field-ready and cost-competitive for biomanufacturing.
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Affiliation(s)
- Nicole E. Gregorio
- Chemistry and Biochemistry Department, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Wesley Y. Kao
- Chemistry and Biochemistry Department, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Layne C. Williams
- Chemistry and Biochemistry Department, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Christopher M. Hight
- Chemistry and Biochemistry Department, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Pratish Patel
- Department of Finance, Orfalea College of Business, California Polytechnic State University, San Luis Obispo, California 93407, United States
| | - Katharine R. Watts
- Chemistry and Biochemistry Department, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Javin P. Oza
- Chemistry and Biochemistry Department, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
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