1
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Ning X, Li F, Wei X, Zhu Z, You C. A Light-Powered In Vitro Synthetic Enzymatic Biosystem for the Synthesis of 3-Hydroxypropionic Acid via CO 2 Fixation. ACS Synth Biol 2024. [PMID: 39092606 DOI: 10.1021/acssynbio.4c00447] [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: 08/04/2024]
Abstract
3-Hydroxypropionic acid (3-HP) is a highly sought-after platform chemical serving as a precursor to a variety of high value-added chemical products. In this study, we designed and constructed a novel light-powered in vitro synthetic enzymatic biosystem comprising acetyl-CoA ligase, acetyl-CoA carboxylase, malonyl-CoA reductase, and phosphotransferase to efficiently produce 3-HP through CO2 fixation from acetate, a cost-effective and readily available substrate. The system employed natural thylakoid membranes (TMs) for the regeneration of adenosine triphosphate and nicotinamide adenine dinucleotide phosphate. Comprehensive investigations were conducted on the effects of buffer solutions, substrate concentrations, enzyme loading levels, and TMs loading levels to optimize the yield of 3-HP. Following optimization, a production of 0.46 mM 3-HP was achieved within 6 h from an initial 0.5 mM acetate, with a yield nearing 92%. This work underscores the simplicity of 3-HP production via an in vitro biomanufacturing platform and highlights the potential for incorporating TMs as a sustainable and environmentally friendly approach in biomanufacturing processes.
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Affiliation(s)
- Xiao Ning
- University of Chinese Academy of Sciences, Beijing 100049, China
- In Vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Fei Li
- In Vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Xinlei Wei
- In Vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Zhiguang Zhu
- University of Chinese Academy of Sciences, Beijing 100049, China
- In Vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Chun You
- University of Chinese Academy of Sciences, Beijing 100049, China
- In Vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
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2
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Hou C, Tian L, Lian G, Fan LH, Li ZJ. Conversion of acetate and glyoxylate to fumarate by a cell-free synthetic enzymatic biosystem. Synth Syst Biotechnol 2023; 8:235-241. [PMID: 36970069 PMCID: PMC10033897 DOI: 10.1016/j.synbio.2023.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/04/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
Fumarate is a value-added chemical that is widely used in food, medicine, material, and agriculture industries. With the rising attention to the demand for fumarate and sustainable development, many novel alternative ways that can replace the traditional petrochemical routes emerged. The in vitro cell-free multi-enzyme catalysis is an effective method to produce high value chemicals. In this study, a multi-enzyme catalytic pathway comprising three enzymes for fumarate production from low-cost substrates acetate and glyoxylate was designed. The acetyl-CoA synthase, malate synthase, and fumarase from Escherichia coli were selected and the coenzyme A achieved recyclable. The enzymatic properties and optimization of reaction system were investigated, reaching a fumarate yield of 0.34 mM with a conversion rate of 34% after 20 h of reaction. We proposed and realized the conversion of acetate and glyoxylate to fumarate in vitro using a cell-free multi-enzyme catalytic system, thus providing an alternative approach for the production of fumarate.
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3
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Li Q, Meng D, You C. An artificial multi-enzyme cascade biocatalysis for biomanufacturing of nicotinamide mononucleotide from starch and nicotinamide in one-pot. Enzyme Microb Technol 2023; 162:110122. [DOI: 10.1016/j.enzmictec.2022.110122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 08/16/2022] [Accepted: 09/01/2022] [Indexed: 10/14/2022]
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4
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Qin Y, Li Q, Fan L, Ning X, Wei X, You C. Biomanufacturing by In Vitro Biotransformation (ivBT) Using Purified Cascade Multi-enzymes. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 186:1-27. [PMID: 37455283 DOI: 10.1007/10_2023_231] [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: 07/18/2023]
Abstract
In vitro biotransformation (ivBT) refers to the use of an artificial biological reaction system that employs purified enzymes for the one-pot conversion of low-cost materials into biocommodities such as ethanol, organic acids, and amino acids. Unshackled from cell growth and metabolism, ivBT exhibits distinct advantages compared with metabolic engineering, including but not limited to high engineering flexibility, ease of operation, fast reaction rate, high product yields, and good scalability. These characteristics position ivBT as a promising next-generation biomanufacturing platform. Nevertheless, challenges persist in the enhancement of bulk enzyme preparation methods, the acquisition of enzymes with superior catalytic properties, and the development of sophisticated approaches for pathway design and system optimization. In alignment with the workflow of ivBT development, this chapter presents a systematic introduction to pathway design, enzyme mining and engineering, system construction, and system optimization. The chapter also proffers perspectives on ivBT development.
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Affiliation(s)
- Yanmei Qin
- University of Chinese Academy of Sciences, Beijing, China
- In Vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Qiangzi Li
- In Vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Lin Fan
- University of Chinese Academy of Sciences, Beijing, China
- In Vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- University of Chinese Academy of Sciences Sino-Danish College, Beijing, China
| | - Xiao Ning
- University of Chinese Academy of Sciences, Beijing, China
- In Vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Xinlei Wei
- In Vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
- National Technology Innovation Center of Synthetic Biology, Tianjin, China.
| | - Chun You
- In Vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
- National Technology Innovation Center of Synthetic Biology, Tianjin, China.
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5
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Wang J, Qu G, Xie L, Gao C, Jiang Y, Zhang YHPJ, Sun Z, You C. Engineering of a thermophilic dihydroxy-acid dehydratase toward glycerate dehydration for in vitro biosystems. Appl Microbiol Biotechnol 2022; 106:3625-3637. [PMID: 35546366 DOI: 10.1007/s00253-022-11936-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 04/04/2022] [Accepted: 04/21/2022] [Indexed: 12/01/2022]
Abstract
Dihydroxy-acid dehydratase (DHAD) plays an important role in the utilization of glycerol or glucose for the production of value-added chemicals in the in vitro synthetic enzymatic biosystem. The low activity of DHAD in the dehydration of glycerate to pyruvate hampers its applications in biosystems. Protein engineering of a thermophilic DHAD from Sulfolobus solfataricus (SsDHAD) was performed to increase its dehydration activity. A triple mutant (I161M/Y145S/G205K) with a 10-fold higher activity on glycerate dehydration was obtained after three rounds of iterative saturation mutagenesis (ISM) based on computational analysis. The shrunken substrate-binding pocket and newly formed hydrogen bonds were the reason for the activity improvement of the mutant. For the in vitro synthetic enzymatic biosystems of converting glucose or glycerol to L-lactate, the biosystems with the mutant SsDHAD showed 3.32- and 2.34-fold higher reaction rates than the wild type, respectively. This study demonstrates the potential of protein engineering to improve the efficiency of in vitro synthetic enzymatic biosystems by enhancing the enzyme activity of rate-limited enzymes. KEY POINTS: • A screening method was established for the protein engineering of SsDHAD. • A R3 mutant of SsDHAD with 10-fold higher activity was obtained. • The R3 mutant exhibits higher productivity in the in vitro biosystems.
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Affiliation(s)
- Juan Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Ge Qu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Leipeng Xie
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Chao Gao
- State Key Laboratory of Microbial Technology, Shandong University, 27 Shandanan Road, Jinan, 250100, China
| | - Yingying Jiang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Yi-Heng P Job Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China. .,National Technology Innovation Center of Synthetic Biology, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China.
| | - Chun You
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China. .,National Technology Innovation Center of Synthetic Biology, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China.
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6
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Zachos I, Genth R, Sutiono S, Marczynski M, Lieleg O, Sieber V. Hot Flows: Evolving an Archaeal Glucose Dehydrogenase for Ultrastable Carba-NADP+ Using Microfluidics at Elevated Temperatures. ACS Catal 2022. [DOI: 10.1021/acscatal.1c04320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Ioannis Zachos
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, Straubing 94315, Germany
| | - Robert Genth
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, Straubing 94315, Germany
| | - Samuel Sutiono
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, Straubing 94315, Germany
| | - Matthias Marczynski
- TUM School of Engineering and Design, Department of Materials Engineering, Technical University of Munich, Boltzmannstraße 15, Garching 85748, Germany
- Center for Functional Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer Straße 8, Garching 85748, Germany
| | - Oliver Lieleg
- TUM School of Engineering and Design, Department of Materials Engineering, Technical University of Munich, Boltzmannstraße 15, Garching 85748, Germany
- Center for Functional Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer Straße 8, Garching 85748, Germany
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, Straubing 94315, Germany
- Catalytic Research Center, Technical University of Munich, Ernst-Otto-Fischer-Straße 1, Garching 85748, Germany
- SynBiofoundry@TUM, Technical University of Munich, Straubing 94315, Germany
- School of Chemistry and Molecular Biosciences, The University of Queensland, 68 Copper Road, St. Lucia 4072, Australia
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7
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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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8
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Zhou Y, Wu S, Bornscheuer UT. Recent advances in (chemo)enzymatic cascades for upgrading bio-based resources. Chem Commun (Camb) 2021; 57:10661-10674. [PMID: 34585190 DOI: 10.1039/d1cc04243b] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Developing (chemo)enzymatic cascades is very attractive for green synthesis, because they streamline multistep synthetic processes. In this Feature Article, we have summarized the recent advances in in vitro or whole-cell cascade reactions with a focus on the use of renewable bio-based resources as starting materials. This includes the synthesis of rare sugars (such as ketoses, L-ribulose, D-tagatose, myo-inositol or aminosugars) from readily available carbohydrate sources (cellulose, hemi-cellulose, starch), in vitro enzyme pathways to convert glucose to various biochemicals, cascades to convert 5-hydroxymethylfurfural and furfural obtained from lignin or xylose into novel precursors for polymer synthesis, the syntheses of phenolic compounds, cascade syntheses of aliphatic and highly reduced chemicals from plant oils and fatty acids, upgrading of glycerol or ethanol as well as cascades to transform natural L-amino acids into high-value (chiral) compounds. In several examples these processes have demonstrated their efficiency with respect to high space-time yields and low E-factors enabling mature green chemistry processes. Also, the strengths and limitations are discussed and an outlook is provided for improving the existing and developing new cascades.
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Affiliation(s)
- Yi Zhou
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Street, Wuhan 430070, P. R. China.
| | - Shuke Wu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Street, Wuhan 430070, P. R. China. .,Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany.
| | - Uwe T Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany.
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9
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Abstract
The Embden–Meyerhof–Parnas (EMP) and Entner–Doudoroff (ED) pathways are considered the most abundant catabolic pathways found in microorganisms, and ED enzymes have been shown to also be widespread in cyanobacteria, algae and plants. In a large number of organisms, especially common strains used in molecular biology, these pathways account for the catabolism of glucose. The existence of pathways for other carbohydrates that are relevant to biomass utilization has been recognized as new strains have been characterized among thermophilic bacteria and Archaea that are able to transform simple polysaccharides from biomass to more complex and potentially valuable precursors for industrial microbiology. Many of the variants of the ED pathway have the key dehydratase enzyme involved in the oxidation of sugar derived from different families such as the enolase, IlvD/EDD and xylose-isomerase-like superfamilies. There are the variations in structure of proteins that have the same specificity and generally greater-than-expected substrate promiscuity. Typical biomass lignocellulose has an abundance of xylan, and four different pathways have been described, which include the Weimberg and Dahms pathways initially oxidizing xylose to xylono-gamma-lactone/xylonic acid, as well as the major xylose isomerase pathway. The recent realization that xylan constitutes a large proportion of biomass has generated interest in exploiting the compound for value-added precursors, but few chassis microorganisms can grow on xylose. Arabinose is part of lignocellulose biomass and can be metabolized with similar pathways to xylose, as well as an oxidative pathway. Like enzymes in many non-phosphorylative carbohydrate pathways, enzymes involved in L-arabinose pathways from bacteria and Archaea show metabolic and substrate promiscuity. A similar multiplicity of pathways was observed for other biomass-derived sugars such as L-rhamnose and L-fucose, but D-mannose appears to be distinct in that a non-phosphorylative version of the ED pathway has not been reported. Many bacteria and Archaea are able to grow on mannose but, as with other minor sugars, much of the information has been derived from whole cell studies with additional enzyme proteins being incorporated, and so far, only one synthetic pathway has been described. There appears to be a need for further discovery studies to clarify the general ability of many microorganisms to grow on the rarer sugars, as well as evaluation of the many gene copies displayed by marine bacteria.
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10
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Chen H, Zhang YHPJ. Enzymatic regeneration and conservation of ATP: challenges and opportunities. Crit Rev Biotechnol 2020; 41:16-33. [PMID: 33012193 DOI: 10.1080/07388551.2020.1826403] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Adenosine triphosphate (ATP), the universal energy currency of life, has a central role in numerous biochemical reactions with potential for the synthesis of numerous high-value products. ATP can be regenerated by three types of mechanisms: substrate level phosphorylation, oxidative phosphorylation, and photophosphorylation. Current ATP regeneration methods are mainly based on substrate level phosphorylation catalyzed by one enzyme, several cascade enzymes, or in vitro synthetic enzymatic pathways. Among them, polyphosphate kinases and acetate kinase, along with their respective phosphate donors, are the most popular approaches for in vitro ATP regeneration. For in vitro artificial pathways, either ATP-free or ATP-balancing strategies can be implemented via smart pathway design by choosing ATP-independent enzymes. Also, we discuss some remaining challenges and suggest perspectives, especially for industrial biomanufacturing. Development of ATP regeneration systems featuring low cost, high volumetric productivity, long lifetime, flexible compatibility, and great robustness could be one of the bottom-up strategies for cascade biocatalysis and in vitro synthetic biology.
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Affiliation(s)
- Hongge Chen
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Yi-Heng P Job Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin Airport Economic Area, Tianjin, China
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11
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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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12
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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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13
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Sutiono S, Teshima M, Beer B, Schenk G, Sieber V. Enabling the Direct Enzymatic Dehydration of d-Glycerate to Pyruvate as the Key Step in Synthetic Enzyme Cascades Used in the Cell-Free Production of Fine Chemicals. ACS Catal 2020. [DOI: 10.1021/acscatal.9b05068] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Samuel Sutiono
- Chair of Chemistry of Biogenic Resources, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 16, 94315 Straubing, Germany
| | - Mariko Teshima
- Chair of Chemistry of Biogenic Resources, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 16, 94315 Straubing, Germany
| | - Barbara Beer
- Chair of Chemistry of Biogenic Resources, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 16, 94315 Straubing, Germany
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, 68 Copper Road, St. Lucia, Queensland 4072, Australia
- Sustainable Minerals Institute, The University of Queensland, 47 Staff House Road, St. Lucia, Queensland 4072, Australia
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 16, 94315 Straubing, Germany
- Catalytic Research Center, Technical University of Munich, Ernst-Otto-Fischer-Straße 1, 85748 Garching, Germany
- School of Chemistry and Molecular Biosciences, The University of Queensland, 68 Copper Road, St. Lucia, Queensland 4072, Australia
- Straubing Branch BioCat, Fraunhofer IGB, Schulgasse 11a, 94315 Straubing, Germany
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14
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Begander B, Huber A, Döring M, Sperl J, Sieber V. Development of an Improved Peroxidase-Based High-Throughput Screening for the Optimization of D-Glycerate Dehydratase Activity. Int J Mol Sci 2020; 21:ijms21010335. [PMID: 31947885 PMCID: PMC6982167 DOI: 10.3390/ijms21010335] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/22/2019] [Accepted: 12/24/2019] [Indexed: 02/06/2023] Open
Abstract
Successful directed evolution examples span a broad range of improved enzyme properties. Nevertheless, the most challenging step for each single directed evolution approach is an efficient identification of improved variants from a large genetic library. Thus, the development and choice of a proper high-throughput screening is a central key for the optimization of enzymes. The detection of low enzymatic activities is especially complicated when they lead to products that are present in the metabolism of the utilized genetic host. Coupled enzymatic assays based on colorimetric products have enabled the optimization of many of such enzymes, but are susceptible to problems when applied on cell extract samples. The purpose of this study was the development of a high-throughput screening for D-glycerate dehydratase activity in cell lysates. With the aid of an automated liquid handling system, we developed a high-throughput assay that relied on a pre-treatment step of cell extract prior to performing the enzymatic and assay reactions. We could successfully apply our method, which should also be transferable to other cell extract-based peroxidase assays, to identify an improved enzyme for the dehydration of D-glycerate.
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Affiliation(s)
- Benjamin Begander
- Chair of Chemistry of Biogenic Resources, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 16, D-94315 Straubing, Germany
| | - Anna Huber
- Chair of Chemistry of Biogenic Resources, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 16, D-94315 Straubing, Germany
| | - Manuel Döring
- Chair of Chemistry of Biogenic Resources, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 16, D-94315 Straubing, Germany
| | - Josef Sperl
- Chair of Chemistry of Biogenic Resources, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 16, D-94315 Straubing, Germany
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 16, D-94315 Straubing, Germany
- Catalysis Research Center, Technical University of Munich, 85748 Garching, Germany
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
- Correspondence: ; Tel.: +49-9421-187-300
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15
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Zang Y, Zha J, Wu X, Zheng Z, Ouyang J, Koffas MAG. In Vitro Naringenin Biosynthesis from p-Coumaric Acid Using Recombinant Enzymes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:13430-13436. [PMID: 30919618 DOI: 10.1021/acs.jafc.9b00413] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Naringenin is an important precursor for the production of a wide spectrum of flavonoids, and its production is of great interest in metabolic engineering. However, in cellular systems, identification of rate-limiting factors is often difficult because of complex regulatory networks. Cell-free catalytic systems emerge as a promising method to address this issue. Here, we explored the cell-free biosystem for naringenin production by combining different sources of 4-coumaroyl-CoA ligase (4CL), chalcone synthase (CHS), and chalcone isomerase (CHI). After systematic analysis of enzyme levels, substrate concentrations, and cofactors, 4CL and CHS were found to be crucial to the reaction. The best loading ratio of 4CL/CHS/CHI was 10:10:1, and malonyl-CoA was the limiting factor, as identified previously in fermentation. For the first time, we successfully constructed the system for naringenin production in vitro. Our study will deepen our understanding of the key factors in naringenin production and guide further engineering.
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16
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Kopp D, Willows RD, Sunna A. Cell-Free Enzymatic Conversion of Spent Coffee Grounds Into the Platform Chemical Lactic Acid. Front Bioeng Biotechnol 2019; 7:389. [PMID: 31850336 PMCID: PMC6901390 DOI: 10.3389/fbioe.2019.00389] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 11/19/2019] [Indexed: 12/23/2022] Open
Abstract
The coffee industry produces over 10 billion kg beans per year and generates high amounts of different waste products. Spent coffee grounds (SCG) are an industrially underutilized waste resource, which is rich in the polysaccharide galactomannan, a polysaccharide consisting of a mannose backbone with galactose side groups. Here, we present a cell-free reaction cascade for the conversion of mannose, the most abundant sugar in SCG, into L-lactic acid. The enzymatic conversion is based on a so far unknown oxidative mannose metabolism from Thermoplasma acidophilum and uses a previously characterized mannonate dehydratase to convert mannose into lactic acid via 4 enzymatic reactions. In comparison to known in vivo metabolisms the bioconversion is free of phosphorylated intermediates and cofactors. Assessment of enzymes, adjustment of enzyme loadings, substrate and cofactor concentrations, and buffer ionic strength allowed the identification of crucial reaction parameters and bottlenecks. Moreover, reactions with isotope labeled mannose enabled the monitoring of pathway intermediates and revealed a reverse flux in the conversion process. Finally, 4.4 ± 0.1 mM lactic acid was produced from 14.57 ± 0.7 mM SCG-derived mannose. While the conversion efficiency of the process can be further improved by enzyme engineering, the reaction demonstrates the first multi-enzyme cascade for the bioconversion of SCG.
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Affiliation(s)
- Dominik Kopp
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Robert D Willows
- Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, NSW, Australia
| | - Anwar Sunna
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.,Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, NSW, Australia
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