1
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Wohlgemuth R. Synthesis of Metabolites and Metabolite-like Compounds Using Biocatalytic Systems. Metabolites 2023; 13:1097. [PMID: 37887422 PMCID: PMC10608848 DOI: 10.3390/metabo13101097] [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: 08/16/2023] [Revised: 10/13/2023] [Accepted: 10/15/2023] [Indexed: 10/28/2023] Open
Abstract
Methodologies for the synthesis and purification of metabolites, which have been developed following their discovery, analysis, and structural identification, have been involved in numerous life science milestones. The renewed focus on the small molecule domain of biological cells has also created an increasing awareness of the rising gap between the metabolites identified and the metabolites which have been prepared as pure compounds. The design and engineering of resource-efficient and straightforward synthetic methodologies for the production of the diverse and numerous metabolites and metabolite-like compounds have attracted much interest. The variety of metabolic pathways in biological cells provides a wonderful blueprint for designing simplified and resource-efficient synthetic routes to desired metabolites. Therefore, biocatalytic systems have become key enabling tools for the synthesis of an increasing number of metabolites, which can then be utilized as standards, enzyme substrates, inhibitors, or other products, or for the discovery of novel biological functions.
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Affiliation(s)
- Roland Wohlgemuth
- MITR, Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego Street 116, 90-924 Lodz, Poland;
- Swiss Coordination Committee Biotechnology (SKB), 8021 Zurich, Switzerland
- European Society of Applied Biocatalysis (ESAB), 1000 Brussels, Belgium
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2
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Morris P, García-Arrazola R, Rios-Solis L, Dalby PA. Biophysical characterization of the inactivation of E. coli transketolase by aqueous co-solvents. Sci Rep 2021; 11:23584. [PMID: 34880340 PMCID: PMC8654844 DOI: 10.1038/s41598-021-03001-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/24/2021] [Indexed: 11/09/2022] Open
Abstract
Transketolase (TK) has been previously engineered, using semi-rational directed evolution and substrate walking, to accept increasingly aliphatic, cyclic, and then aromatic substrates. This has ultimately led to the poor water solubility of new substrates, as a potential bottleneck to further exploitation of this enzyme in biocatalysis. Here we used a range of biophysical studies to characterise the response of both E. coli apo- and holo-TK activity and structure to a range of polar organic co-solvents: acetonitrile (AcCN), n-butanol (nBuOH), ethyl acetate (EtOAc), isopropanol (iPrOH), and tetrahydrofuran (THF). The mechanism of enzyme deactivation was found to be predominantly via solvent-induced local unfolding. Holo-TK is thermodynamically more stable than apo-TK and yet for four of the five co-solvents it retained less activity than apo-TK after exposure to organic solvents, indicating that solvent tolerance was not simply correlated to global conformational stability. The co-solvent concentrations required for complete enzyme inactivation was inversely proportional to co-solvent log(P), while the unfolding rate was directly proportional, indicating that the solvents interact with and partially unfold the enzyme through hydrophobic contacts. Small amounts of aggregate formed in some cases, but this was not sufficient to explain the enzyme inactivation. TK was found to be tolerant to 15% (v/v) iPrOH, 10% (v/v) AcCN, or 6% (v/v) nBuOH over 3 h. This work indicates that future attempts to engineer the enzyme to better tolerate co-solvents should focus on increasing the stability of the protein to local unfolding, particularly in and around the cofactor-binding loops.
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Affiliation(s)
- Phattaraporn Morris
- Department of Biochemical Engineering, University College London, Bernard Katz Building, Gower Street, London, WC1E 6BT, UK
- Chemical Metrology and Biometry Department, National Institute of Metrology, 3/4-5 Moo 3, Klong 5, Klong Luang, 12120, Pathumthani, Thailand
| | - Ribia García-Arrazola
- Department of Biochemical Engineering, University College London, Bernard Katz Building, Gower Street, London, WC1E 6BT, UK
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh, EH9 3JL, UK
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, King's Buildings, Edinburgh, EH9 3JL, UK
| | - Paul A Dalby
- Department of Biochemical Engineering, University College London, Bernard Katz Building, Gower Street, London, WC1E 6BT, UK.
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3
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Getting the Most Out of Enzyme Cascades: Strategies to Optimize In Vitro Multi-Enzymatic Reactions. Catalysts 2021. [DOI: 10.3390/catal11101183] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In vitro enzyme cascades possess great benefits, such as their synthetic capabilities for complex molecules, no need for intermediate isolation, and the shift of unfavorable equilibria towards the products. Their performance, however, can be impaired by, for example, destabilizing or inhibitory interactions between the cascade components or incongruous reaction conditions. The optimization of such systems is therefore often inevitable but not an easy task. Many parameters such as the design of the synthesis route, the choice of enzymes, reaction conditions, or process design can alter the performance of an in vitro enzymatic cascade. Many strategies to tackle this complex task exist, ranging from experimental to in silico approaches and combinations of both. This review collates examples of various optimization strategies and their success. The feasibility of optimization goals, the influence of certain parameters and the usage of algorithm-based optimizations are discussed.
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4
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Cárdenas-Fernández M, Subrizi F, Dobrijevic D, Hailes HC, Ward JM. Characterisation of a hyperthermophilic transketolase from Thermotoga maritima DSM3109 as a biocatalyst for 7-keto-octuronic acid synthesis. Org Biomol Chem 2021; 19:6493-6500. [PMID: 34250527 PMCID: PMC8317047 DOI: 10.1039/d1ob01237a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 07/05/2021] [Indexed: 11/21/2022]
Abstract
Transketolase (TK) is a fundamentally important enzyme in industrial biocatalysis which carries out a stereospecific carbon-carbon bond formation, and is widely used in the synthesis of prochiral ketones. This study describes the biochemical and molecular characterisation of a novel and unusual hyperthermophilic TK from Thermotoga maritima DSM3109 (TKtmar). TKtmar has a low protein sequence homology compared to the already described TKs, with key amino acid residues in the active site highly conserved. TKtmar has a very high optimum temperature (>90 °C) and shows pronounced stability at high temperature (e.g. t1/2 99 and 9.3 h at 50 and 80 °C, respectively) and in presence of organic solvents commonly used in industry (DMSO, acetonitrile and methanol). Substrate screening showed activity towards several monosaccharides and aliphatic aldehydes. In addition, for the first time, TK specificity towards uronic acids was achieved with TKtmar catalysing the efficient conversion of d-galacturonic acid and lithium hydroxypyruvate into 7-keto-octuronic acid, a very rare C8 uronic acid, in high yields (98%, 49 mM).
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Affiliation(s)
- Max Cárdenas-Fernández
- Department of Biochemical Engineering, University College London, Gower Street, London WC1E 6BT, UK. and School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Fabiana Subrizi
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
| | - Dragana Dobrijevic
- Department of Biochemical Engineering, University College London, Gower Street, London WC1E 6BT, UK.
| | - Helen C Hailes
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
| | - John M Ward
- Department of Biochemical Engineering, University College London, Gower Street, London WC1E 6BT, UK.
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5
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Wu R, Song H, Wang Y, Wang L, Zhu Z. Multienzyme co-immobilization-based bioelectrode: Design of principles and bioelectrochemical applications. Chin J Chem Eng 2020. [DOI: 10.1016/j.cjche.2020.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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6
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Wu D, Shu T, Yang X, Song JX, Zhang M, Yao C, Liu W, Huang M, Yu Y, Yang Q, Zhu T, Xu J, Mu J, Wang Y, Wang H, Tang T, Ren Y, Wu Y, Lin SH, Qiu Y, Zhang DY, Shang Y, Zhou X. Plasma metabolomic and lipidomic alterations associated with COVID-19. Natl Sci Rev 2020; 7:1157-1168. [PMID: 34676128 PMCID: PMC7197563 DOI: 10.1093/nsr/nwaa086] [Citation(s) in RCA: 212] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/15/2020] [Accepted: 04/23/2020] [Indexed: 12/19/2022] Open
Abstract
The pandemic of the coronavirus disease 2019 (COVID-19) has become a global public health crisis. The symptoms of COVID-19 range from mild to severe, but the physiological changes associated with COVID-19 are barely understood. In this study, we performed targeted metabolomic and lipidomic analyses of plasma from a cohort of patients with COVID-19 who had experienced different symptoms. We found that metabolite and lipid alterations exhibit apparent correlation with the course of disease in these patients, indicating that the development of COVID-19 affected their whole-body metabolism. In particular, malic acid of the TCA cycle and carbamoyl phosphate of the urea cycle result in altered energy metabolism and hepatic dysfunction, respectively. It should be noted that carbamoyl phosphate is profoundly down-regulated in patients who died compared with patients with mild symptoms. And, more importantly, guanosine monophosphate (GMP), which is mediated not only by GMP synthase but also by CD39 and CD73, is significantly changed between healthy subjects and patients with COVID-19, as well as between the mild and fatal cases. In addition, dyslipidemia was observed in patients with COVID-19. Overall, the disturbed metabolic patterns have been found to align with the progress and severity of COVID-19. This work provides valuable knowledge about plasma biomarkers associated with COVID-19 and potential therapeutic targets, as well as an important resource for further studies of the pathogenesis of COVID-19.
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Affiliation(s)
- Di Wu
- Joint Laboratory of Infectious Diseases and Health, Wuhan Institute of Virology & Wuhan Jinyintan Hospital, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences (CAS), Wuhan 430023, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, CAS, Wuhan 430071, China
| | - Ting Shu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, CAS, Wuhan 430071, China
- Center for Translational Medicine, Jinyintan Hospital, Wuhan 430023, China
- Joint Laboratory of Infectious Diseases and Health, Wuhan Institute of Virology & Wuhan Jinyintan Hospital, Wuhan Jinyintan Hospital, Wuhan 430023, China
| | - Xiaobo Yang
- Department of Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jian-Xin Song
- Department of Infectious Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | | | - Chengye Yao
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wen Liu
- Center for Translational Medicine, Jinyintan Hospital, Wuhan 430023, China
- Joint Laboratory of Infectious Diseases and Health, Wuhan Institute of Virology & Wuhan Jinyintan Hospital, Wuhan Jinyintan Hospital, Wuhan 430023, China
| | - Muhan Huang
- Joint Laboratory of Infectious Diseases and Health, Wuhan Institute of Virology & Wuhan Jinyintan Hospital, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences (CAS), Wuhan 430023, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, CAS, Wuhan 430071, China
| | - Yuan Yu
- Department of Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Qingyu Yang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, CAS, Wuhan 430071, China
- Center for Translational Medicine, Jinyintan Hospital, Wuhan 430023, China
- Joint Laboratory of Infectious Diseases and Health, Wuhan Institute of Virology & Wuhan Jinyintan Hospital, Wuhan Jinyintan Hospital, Wuhan 430023, China
| | - Tingju Zhu
- Center for Translational Medicine, Jinyintan Hospital, Wuhan 430023, China
- Joint Laboratory of Infectious Diseases and Health, Wuhan Institute of Virology & Wuhan Jinyintan Hospital, Wuhan Jinyintan Hospital, Wuhan 430023, China
| | - Jiqian Xu
- Department of Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jingfang Mu
- Joint Laboratory of Infectious Diseases and Health, Wuhan Institute of Virology & Wuhan Jinyintan Hospital, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences (CAS), Wuhan 430023, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, CAS, Wuhan 430071, China
| | - Yaxin Wang
- Department of Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Hong Wang
- Wuhan Metware Biotechnology Co., Ltd., Wuhan 430075, China
| | - Tang Tang
- Wuhan Metware Biotechnology Co., Ltd., Wuhan 430075, China
| | - Yujie Ren
- Joint Laboratory of Infectious Diseases and Health, Wuhan Institute of Virology & Wuhan Jinyintan Hospital, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences (CAS), Wuhan 430023, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, CAS, Wuhan 430071, China
| | - Yongran Wu
- Department of Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shu-Hai Lin
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen 361005, China
| | - Yang Qiu
- Joint Laboratory of Infectious Diseases and Health, Wuhan Institute of Virology & Wuhan Jinyintan Hospital, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences (CAS), Wuhan 430023, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, CAS, Wuhan 430071, China
- Center for Translational Medicine, Jinyintan Hospital, Wuhan 430023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ding-Yu Zhang
- Center for Translational Medicine, Jinyintan Hospital, Wuhan 430023, China
- Joint Laboratory of Infectious Diseases and Health, Wuhan Institute of Virology & Wuhan Jinyintan Hospital, Wuhan Jinyintan Hospital, Wuhan 430023, China
| | - You Shang
- Department of Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Center for Translational Medicine, Jinyintan Hospital, Wuhan 430023, China
- Joint Laboratory of Infectious Diseases and Health, Wuhan Institute of Virology & Wuhan Jinyintan Hospital, Wuhan Jinyintan Hospital, Wuhan 430023, China
| | - Xi Zhou
- Joint Laboratory of Infectious Diseases and Health, Wuhan Institute of Virology & Wuhan Jinyintan Hospital, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences (CAS), Wuhan 430023, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, CAS, Wuhan 430071, China
- Center for Translational Medicine, Jinyintan Hospital, Wuhan 430023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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7
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High Conversion of D-Fructose into D-Allulose by Enzymes Coupling with an ATP Regeneration System. Mol Biotechnol 2019; 61:432-441. [PMID: 30963480 DOI: 10.1007/s12033-019-00174-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
D-Allulose is a rare monosaccharide that exists in extremely small quantities in nature, and it is also hard to prepare at a large scale via chemical or enzyme synthetic route due to low conversion and downstream separation complexity. Using D-psicose epimerase and L-rhamnulose kinase, a method enabling high conversion of D-allulose from D-fructose without the need for a tedious isomer separation step was established recently. However, this method requires expensive ATP to facilitate the reaction. In the present study, an ATP regenerate system was developed coupling with polyphosphate kinase. In our optimized reaction with purified enzymes, the conversion rate of 99% D-fructose was achieved at the concentrations of 2 mM ATP, 5 mM polyphosphate, 20 mM D-fructose, and 20 mM Mg2+ when incubated at 50 °C and at pH 7.5. ATP usage can be reduced to 10% of the theoretical amount compared to that without the ATP regeneration system. A fed-batch mode was also studied to minimize the inhibitory effect of polyphosphate. The biosynthetic system reported here offers a potential and promising platform for the conversion of D-fructose into D-allulose at reduced ATP cost.
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8
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Sánchez-Moreno I, Trachtmann N, Ilhan S, Hélaine V, Lemaire M, Guérard-Hélaine C, Sprenger GA. 2-Ketogluconate Kinase from Cupriavidus necator H16: Purification, Characterization, and Exploration of Its Substrate Specificity. Molecules 2019; 24:molecules24132393. [PMID: 31261738 PMCID: PMC6651773 DOI: 10.3390/molecules24132393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 06/21/2019] [Accepted: 06/27/2019] [Indexed: 11/30/2022] Open
Abstract
We have cloned, overexpressed, purified, and characterized a 2-ketogluconate kinase (2-dehydrogluconokinase, EC 2.7.1.13) from Cupriavidus necator (Ralstonia eutropha) H16. Exploration of its substrate specificity revealed that three ketoacids (2-keto-3-deoxy-d-gluconate, 2-keto-d-gulonate, and 2-keto-3-deoxy-d-gulonate) with structures close to the natural substrate (2-keto-d-gluconate) were successfully phosphorylated at an efficiency lower than or comparable to 2-ketogluconate, as depicted by the measured kinetic constant values. Eleven aldo and keto monosaccharides of different chain lengths and stereochemistries were also assayed but not found to be substrates. 2-ketogluconate-6-phosphate was synthesized at a preparative scale and was fully characterized for the first time.
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Affiliation(s)
- Israel Sánchez-Moreno
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
| | - Natalia Trachtmann
- University of Stuttgart, Institute of Microbiology, D-70569 Stuttgart, Germany
| | - Sibel Ilhan
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
- University of Stuttgart, Institute of Microbiology, D-70569 Stuttgart, Germany
| | - Virgil Hélaine
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
| | - Marielle Lemaire
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
| | - Christine Guérard-Hélaine
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France.
| | - Georg A Sprenger
- University of Stuttgart, Institute of Microbiology, D-70569 Stuttgart, Germany.
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9
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Hardt N, Kind S, Schoenenberger B, Eggert T, Obkircher M, Wohlgemuth R. Facile synthesis of D-xylulose-5-phosphate and L-xylulose-5-phosphate by xylulokinase-catalyzed phosphorylation. BIOCATAL BIOTRANSFOR 2019. [DOI: 10.1080/10242422.2019.1630385] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
| | | | | | | | | | - Roland Wohlgemuth
- Sigma-Aldrich/Merck KGaA, Buchs, Switzerland
- Institute of Technical Biochemistry, Technical University Lodz, Lodz, Poland
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10
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Affiliation(s)
- Ee Taek Hwang
- Center for Convergence Bioceramic Materials, Korea Institute of Ceramic Engineering & Technology, Cheongju-si, Chungcheongbuk-do 28160, Republic of Korea
| | - Seonbyul Lee
- Center for Convergence Bioceramic Materials, Korea Institute of Ceramic Engineering & Technology, Cheongju-si, Chungcheongbuk-do 28160, Republic of Korea
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11
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Vergne-Vaxelaire C, Mariage A, Petit JL, Fossey-Jouenne A, Guérard-Hélaine C, Darii E, Debard A, Nepert S, Pellouin V, Lemaire M, Zaparucha A, Salanoubat M, de Berardinis V. Characterization of a thermotolerant ROK-type mannofructokinase from Streptococcus mitis: application to the synthesis of phosphorylated sugars. Appl Microbiol Biotechnol 2018; 102:5569-5583. [DOI: 10.1007/s00253-018-9018-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 03/29/2018] [Accepted: 04/10/2018] [Indexed: 01/08/2023]
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12
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ATP-free biosynthesis of a high-energy phosphate metabolite fructose 1,6-diphosphate by in vitro metabolic engineering. Metab Eng 2017. [DOI: 10.1016/j.ymben.2017.06.006] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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13
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Affiliation(s)
- Wei-Chih Wei
- Department of Chemistry; Fu Jen Catholic University; 24205 New Taipei City Taiwan
| | - Che-Chien Chang
- Department of Chemistry; Fu Jen Catholic University; 24205 New Taipei City Taiwan
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14
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Gruber P, Marques MP, Sulzer P, Wohlgemuth R, Mayr T, Baganz F, Szita N. Real-time pH monitoring of industrially relevant enzymatic reactions in a microfluidic side-entry reactor (μSER) shows potential for pH control. Biotechnol J 2017; 12. [DOI: 10.1002/biot.201600475] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 01/16/2017] [Accepted: 01/18/2017] [Indexed: 01/23/2023]
Affiliation(s)
- Pia Gruber
- Department of Biochemical Engineering; University College London; Gordon Street London UK
| | - Marco P.C. Marques
- Department of Biochemical Engineering; University College London; Gordon Street London UK
| | - Philipp Sulzer
- Institute of Analytical Chemistry and Food Chemistry; Graz University of Technology; Graz Austria
| | - Roland Wohlgemuth
- Member of Merck Group; Sigma-Aldrich; Member of Merck Group; Buchs Switzerland
| | - Torsten Mayr
- Institute of Analytical Chemistry and Food Chemistry; Graz University of Technology; Graz Austria
| | - Frank Baganz
- Institute of Analytical Chemistry and Food Chemistry; Graz University of Technology; Graz Austria
| | - Nicolas Szita
- Department of Biochemical Engineering; University College London; Gordon Street London UK
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15
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Jeffries JWE, Dawson N, Orengo C, Moody TS, Quinn DJ, Hailes HC, Ward JM. Metagenome Mining: A Sequence Directed Strategy for the Retrieval of Enzymes for Biocatalysis. ChemistrySelect 2016. [DOI: 10.1002/slct.201600515] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jack W. E. Jeffries
- Department of Biochemical Engineering; University College London, Bernard Katz Building; Gordon Street London WC1H 0AH UK
| | - Natalie Dawson
- Department of Structural and Molecular Biology; University College London; Gower Street WC1E 6BT UK
| | - Christine Orengo
- Department of Structural and Molecular Biology; University College London; Gower Street WC1E 6BT UK
| | - Thomas S. Moody
- Department of Biocatalysis and Isotope Chemistry; Almac; 20 Seagoe Industrial Estate Craigavon Northern Ireland (UK
| | - Derek J. Quinn
- Department of Biocatalysis and Isotope Chemistry; Almac; 20 Seagoe Industrial Estate Craigavon Northern Ireland (UK
| | - Helen C. Hailes
- Department of Chemistry; University College London; 20 Gordon Street London WC1H 0AJ UK
| | - John M. Ward
- Department of Biochemical Engineering; University College London, Bernard Katz Building; Gordon Street London WC1H 0AH UK
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16
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Affiliation(s)
- Liuqing Wen
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Kenneth Huang
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Yunpeng Liu
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
- National
Glycoengineering Research Center, Shandong University, Jinan 250100, China
| | - Peng George Wang
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
- National
Glycoengineering Research Center, Shandong University, Jinan 250100, China
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17
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Kim JE, Zhang YHP. Biosynthesis of D-xylulose 5-phosphate from D-xylose and polyphosphate through a minimized two-enzyme cascade. Biotechnol Bioeng 2015; 113:275-82. [PMID: 26241217 DOI: 10.1002/bit.25718] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 07/22/2015] [Accepted: 07/27/2015] [Indexed: 01/20/2023]
Abstract
Sugar phosphates cannot be produced easily by microbial fermentation because negatively-charged compounds cannot be secreted across intact cell membrane. D-xylulose 5-phosphate (Xu5P), a very expensive sugar phosphate, was synthesized from D-xylose and polyphosphate catalyzed by enzyme cascades in one pot. The synthetic enzymatic pathway comprised of xylose isomerase and xylulokinase was designed to produce Xu5P, along with a third enzyme, polyphosphate kinase, responsible for in site ATP regeneration. Due to the promiscuous activity of the ATP-based xylulokinase from a hyperthermophilic bacterium Thermotoga maritima on polyphosphate, the number of enzymes in the pathway was minimized to two without polyphosphate kinase. The reactions catalyzed by the two-enzyme and three-enzyme pathways were compared for Xu5P production, and the reaction conditions were optimized by examining effects of reaction temperature, enzyme ratio and substrate concentration. The optimized two-enzyme system produced 32 mM Xu5P from 50 mM xylose and polyphosphate after 36 h at 45°C. Biosynthesis of less costly Xu5P from D-xylose and polyphosphate could be highly feasible via this minimized two-enzyme pathway.
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Affiliation(s)
- Jae-Eung Kim
- Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, 24061, Virginia
| | - Y-H Percival Zhang
- Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, 24061, Virginia. .,Cell Free Bioinnovations Inc., Blacksburg, Virginia. .,Institute for Critical Technology and Applied Science (ICTAS), Virginia Tech, Blacksburg, Virginia. .,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
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Qi P, You C, Zhang YHP. One-Pot Enzymatic Conversion of Sucrose to Synthetic Amylose by using Enzyme Cascades. ACS Catal 2014. [DOI: 10.1021/cs400961a] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Peng Qi
- Biological
Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, Virginia 24061, United States
| | - Chun You
- Biological
Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, Virginia 24061, United States
| | - Y.-H. Percival Zhang
- Biological
Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, Virginia 24061, United States
- Cell Free Bioinnovations,
Inc., Blacksburg, Virginia 24060, United States
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20
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Lawrence J, O'Sullivan B, Lye GJ, Wohlgemuth R, Szita N. Microfluidic multi-input reactor for biocatalytic synthesis using transketolase. JOURNAL OF MOLECULAR CATALYSIS. B, ENZYMATIC 2013; 95:111-117. [PMID: 24187515 PMCID: PMC3724052 DOI: 10.1016/j.molcatb.2013.05.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 05/08/2013] [Accepted: 05/17/2013] [Indexed: 11/14/2022]
Abstract
Biocatalytic synthesis in continuous-flow microreactors is of increasing interest for the production of specialty chemicals. However, the yield of production achievable in these reactors can be limited by the adverse effects of high substrate concentration on the biocatalyst, including inhibition and denaturation. Fed-batch reactors have been developed in order to overcome this problem, but no continuous-flow solution exists. We present the design of a novel multi-input microfluidic reactor, capable of substrate feeding at multiple points, as a first step towards overcoming these problems in a continuous-flow setting. Using the transketolase-(TK) catalysed reaction of lithium hydroxypyruvate (HPA) and glycolaldehyde (GA) to l-erythrulose (ERY), we demonstrate the transposition of a fed-batch substrate feeding strategy to our microfluidic reactor. We obtained a 4.5-fold increase in output concentration and a 5-fold increase in throughput compared with a single input reactor.
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Affiliation(s)
- James Lawrence
- Department of Biochemical Engineering, University College London, Torrington Place, London WC1E 7JE, UK
| | - Brian O'Sullivan
- Department of Biochemical Engineering, University College London, Torrington Place, London WC1E 7JE, UK
| | - Gary J. Lye
- Department of Biochemical Engineering, University College London, Torrington Place, London WC1E 7JE, UK
| | | | - Nicolas Szita
- Department of Biochemical Engineering, University College London, Torrington Place, London WC1E 7JE, UK
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Sánchez-Moreno I, Hélaine V, Poupard N, Charmantray F, Légeret B, Hecquet L, García-Junceda E, Wohlgemuth R, Guérard-Hélaine C, Lemaire M. One-Pot Cascade Reactions using Fructose-6-phosphate Aldolase: Efficient Synthesis of D-Arabinose 5-Phosphate, D-Fructose 6-Phosphate and Analogues. Adv Synth Catal 2012. [DOI: 10.1002/adsc.201200150] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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23
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Modular microfluidic reactor and inline filtration system for the biocatalytic synthesis of chiral metabolites. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.molcatb.2011.12.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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24
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Ricca E, Brucher B, Schrittwieser JH. Multi-Enzymatic Cascade Reactions: Overview and Perspectives. Adv Synth Catal 2011. [DOI: 10.1002/adsc.201100256] [Citation(s) in RCA: 374] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Jahromi RRF, Morris P, Martinez-Torres RJ, Dalby PA. Structural stability of E. coli transketolase to temperature and pH denaturation. J Biotechnol 2011; 155:209-16. [PMID: 21723889 DOI: 10.1016/j.jbiotec.2011.06.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Revised: 06/07/2011] [Accepted: 06/17/2011] [Indexed: 11/15/2022]
Abstract
We have previously shown that the denaturation of TK with urea follows a non-aggregating though irreversible denaturation pathway in which the cofactor binding appears to become altered but without dissociating, then followed at higher urea by partial denaturation of the homodimer prior to any further unfolding or dissociation of the two monomers. Urea is not typically present during biocatalysis, whereas access to TK enzymes that retain activity at increased temperature and extreme pH would be useful for operation under conditions that increase substrate and product stability or solubility. To provide further insight into the underlying causes of its deactivation in process conditions, we have characterised the effects of temperature and pH on the structure, stability, aggregation and activity of Escherichia coli transketolase. The activity of TK was initially found to progressively improve after pre-incubation at increasing temperatures. Loss of activity at higher temperature and low pH resulted primarily from protein denaturation and subsequent irreversible aggregation. By contrast, high pH resulted in the formation of a native-like state that was only partially inactive. The apo-TK enzyme structure content also increased at pH 9 to converge on that of the holo-TK. While cofactor dissociation was previously proposed for high pH deactivation, the observed structural changes in apo-TK but not holo-TK indicate a more complex mechanism.
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Affiliation(s)
- Raha R F Jahromi
- Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering, University College London, Torrington Place, London, UK
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26
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Brovetto M, Gamenara D, Méndez PS, Seoane GA. C-C bond-forming lyases in organic synthesis. Chem Rev 2011; 111:4346-403. [PMID: 21417217 DOI: 10.1021/cr100299p] [Citation(s) in RCA: 160] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Margarita Brovetto
- Grupo de Fisicoquímica Orgánica y Bioprocesos, Departamento de Química Orgánica, DETEMA, Facultad de Química, Universidad de la República (UdelaR), Gral. Flores 2124, 11800 Montevideo, Uruguay
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Ayhan P, Şimşek İ, Çifçi B, Demir AS. Benzaldehyde lyase catalyzed enantioselective self and cross condensation reactions of acetaldehyde derivatives. Org Biomol Chem 2011; 9:2602-5. [DOI: 10.1039/c0ob01121e] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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Wohlgemuth R. Biocatalysis—key to sustainable industrial chemistry. Curr Opin Biotechnol 2010; 21:713-24. [DOI: 10.1016/j.copbio.2010.09.016] [Citation(s) in RCA: 214] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Revised: 09/24/2010] [Accepted: 09/24/2010] [Indexed: 12/19/2022]
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Wohlgemuth R. Asymmetric biocatalysis with microbial enzymes and cells. Curr Opin Microbiol 2010; 13:283-92. [DOI: 10.1016/j.mib.2010.04.001] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Revised: 04/01/2010] [Accepted: 04/02/2010] [Indexed: 01/05/2023]
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Zhang YHP. Production of biocommodities and bioelectricity by cell-free synthetic enzymatic pathway biotransformations: challenges and opportunities. Biotechnol Bioeng 2010; 105:663-77. [PMID: 19998281 DOI: 10.1002/bit.22630] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Cell-free synthetic (enzymatic) pathway biotransformation (SyPaB) is the assembly of a number of purified enzymes (usually more than 10) and coenzymes for the production of desired products through complicated biochemical reaction networks that a single enzyme cannot do. Cell-free SyPaB, as compared to microbial fermentation, has several distinctive advantages, such as high product yield, great engineering flexibility, high product titer, and fast reaction rate. Biocommodities (e.g., ethanol, hydrogen, and butanol) are low-value products where costs of feedstock carbohydrates often account for approximately 30-70% of the prices of the products. Therefore, yield of biocommodities is the most important cost factor, and the lowest yields of profitable biofuels are estimated to be ca. 70% of the theoretical yields of sugar-to-biofuels based on sugar prices of ca. US$ 0.18 per kg. The opinion that SyPaB is too costly for producing low-value biocommodities are mainly attributed to the lack of stable standardized building blocks (e.g., enzymes or their complexes), costly labile coenzymes, and replenishment of enzymes and coenzymes. In this perspective, I propose design principles for SyPaB, present several SyPaB examples for generating hydrogen, alcohols, and electricity, and analyze the advantages and limitations of SyPaB. The economical analyses clearly suggest that developments in stable enzymes or their complexes as standardized parts, efficient coenzyme recycling, and use of low-cost and more stable biomimetic coenzyme analogs, would result in much lower production costs than do microbial fermentations because the stabilized enzymes have more than 3 orders of magnitude higher weight-based total turn-over numbers than microbial biocatalysts, although extra costs for enzyme purification and stabilization are spent.
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Affiliation(s)
- Y-H Percival Zhang
- Biological Systems Engineering Department, Virginia Polytechnic Institute and State University, 210-A Seitz Hall, Blacksburg, Virginia 24061, USA. USA.
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31
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Cázares A, Galman JL, Crago LG, Smith MEB, Strafford J, Ríos-Solís L, Lye GJ, Dalby PA, Hailes HC. Non-α-hydroxylated aldehydes with evolved transketolase enzymes. Org Biomol Chem 2010; 8:1301-9. [DOI: 10.1039/b924144b] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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Galman JL, Steadman D, Bacon S, Morris P, Smith MEB, Ward JM, Dalby PA, Hailes HC. α,α′-Dihydroxyketone formation using aromatic and heteroaromatic aldehydes with evolved transketolase enzymes. Chem Commun (Camb) 2010; 46:7608-10. [DOI: 10.1039/c0cc02911d] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Wohlgemuth R. Tools and ingredients for the biocatalytic synthesis of metabolites. Biotechnol J 2009; 4:1253-65. [DOI: 10.1002/biot.200900002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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35
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Wohlgemuth R. The locks and keys to industrial biotechnology. N Biotechnol 2009; 25:204-13. [PMID: 19429540 DOI: 10.1016/j.nbt.2009.01.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2008] [Revised: 01/07/2009] [Accepted: 01/08/2009] [Indexed: 11/27/2022]
Abstract
The sustainable use of resources by Nature to synthesize the required products at the right place, when they are needed, continues to be the role model for total synthesis and production in general. The combination of molecular and engineering science and technology in the biotechnological approach needs no protecting groups at all and has therefore been established for numerous large-scale routes to both natural and synthetic products in industry. The use of biobased raw materials for chemical synthesis, and the economy of molecular transformations like atom economy and step economy are of growing importance. As safety, health and environmental issues are key drivers for process improvements in the chemical industry, the development of biocatalytic reactions or pathways replacing hazardous reagents is a major focus. The integration of the biocatalytic reaction and downstream processing with product isolation has led to a variety of in situ product recovery techniques and has found numerous successful applications. With the growing collection of biocatalytic reactions, the retrosynthetic thinking can be applied to biocatalysis as well. The introduction of biocatalytic reactions is uniquely suited to cost reductions and higher quality products, as well as to more sustainable processes. The transfer of Nature's simple and robust sensing and control principles as well as its reaction and separation organization into useful technical systems can be applied to different fermentations, biotransformations and downstream processes. Biocatalyst and pathway discovery and development is the key towards new synthetic transformations in industrial biotechnology.
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Affiliation(s)
- Roland Wohlgemuth
- Sigma-Aldrich, Research Specialities, Industriestrasse 25, 9470 Buchs, Switzerland.
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