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Wu T, Gómez-Coronado PA, Kubis A, Lindner SN, Marlière P, Erb TJ, Bar-Even A, He H. Engineering a synthetic energy-efficient formaldehyde assimilation cycle in Escherichia coli. Nat Commun 2023; 14:8490. [PMID: 38123535 PMCID: PMC10733421 DOI: 10.1038/s41467-023-44247-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
One-carbon (C1) substrates, such as methanol or formate, are attractive feedstocks for circular bioeconomy. These substrates are typically converted into formaldehyde, serving as the entry point into metabolism. Here, we design an erythrulose monophosphate (EuMP) cycle for formaldehyde assimilation, leveraging a promiscuous dihydroxyacetone phosphate dependent aldolase as key enzyme. In silico modeling reveals that the cycle is highly energy-efficient, holding the potential for high bioproduct yields. Dissecting the EuMP into four modules, we use a stepwise strategy to demonstrate in vivo feasibility of the modules in E. coli sensor strains with sarcosine as formaldehyde source. From adaptive laboratory evolution for module integration, we identify key mutations enabling the accommodation of the EuMP reactions with endogenous metabolism. Overall, our study demonstrates the proof-of-concept for a highly efficient, new-to-nature formaldehyde assimilation pathway, opening a way for the development of a methylotrophic platform for a C1-fueled bioeconomy in the future.
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Affiliation(s)
- Tong Wu
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Biochemistry, Charitéplatz 1, 10117, Berlin, Germany
| | - Paul A Gómez-Coronado
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Armin Kubis
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Steffen N Lindner
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Biochemistry, Charitéplatz 1, 10117, Berlin, Germany
| | - Philippe Marlière
- TESSSI, The European Syndicate of Synthetic Scientists and Industrialists, 81 rue Réaumur, 75002, Paris, France
| | - Tobias J Erb
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Hai He
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany.
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Hartley CJ, Williams CC, Scoble JA, Churches QI, North A, French NG, Nebl T, Coia G, Warden AC, Simpson G, Frazer AR, Jensen CN, Turner NJ, Scott C. Engineered enzymes that retain and regenerate their cofactors enable continuous-flow biocatalysis. Nat Catal 2019. [DOI: 10.1038/s41929-019-0353-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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3
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Desmons S, Fauré R, Bontemps S. Formaldehyde as a Promising C1 Source: The Instrumental Role of Biocatalysis for Stereocontrolled Reactions. ACS Catal 2019. [DOI: 10.1021/acscatal.9b03128] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Sarah Desmons
- LCC-CNRS, Université de Toulouse, CNRS, Toulouse, France
- TBI, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Régis Fauré
- TBI, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
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4
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Palazzolo MA, Nigro MJ, Iribarren AM, Lewkowicz ES. A Chemoenzymatic Route To Prepare Acyclic Nucleoside Analogues. European J Org Chem 2016. [DOI: 10.1002/ejoc.201501412] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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5
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DHAP-dependent aldolases from (hyper)thermophiles: biochemistry and applications. Extremophiles 2013; 18:1-13. [DOI: 10.1007/s00792-013-0593-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2013] [Accepted: 10/10/2013] [Indexed: 12/20/2022]
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6
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Li Z, Cai L, Wei M, Wang PG. One-pot four-enzyme synthesis of ketoses with fructose 1,6-bisphosphate aldolases from Staphylococcus carnosus and rabbit muscle. Carbohydr Res 2012; 357:143-6. [PMID: 22727596 DOI: 10.1016/j.carres.2012.05.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 05/04/2012] [Accepted: 05/07/2012] [Indexed: 10/28/2022]
Abstract
By the action of D-fructose 1,6-bisphosphate aldolases (FruA) from rabbit muscle and Staphylococcus carnosus, various ketoses were synthesized from glyceraldehydes or other aliphatic aldehydes as acceptors in a one-pot four-enzyme system.
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Affiliation(s)
- Zijie Li
- National Glycoengineering Research Center, The State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250100, China
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7
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Bujara M, Schümperli M, Billerbeck S, Heinemann M, Panke S. Exploiting cell-free systems: Implementation and debugging of a system of biotransformations. Biotechnol Bioeng 2010; 106:376-89. [DOI: 10.1002/bit.22666] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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8
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Elshafei AM, Elsayed MA, Abdel-Fatah OM, Ali NH, Mohamed LA. Some properties of two aldolases in extracts ofAspergillus oryzae. J Basic Microbiol 2005; 45:31-40. [PMID: 15678561 DOI: 10.1002/jobm.200410440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Fructose 1,6-diphosphate (FDP) aldolase and 2-keto-3-deoxy-D-gluconate (KDG) aldolase the two key enzymes of Embden-Meyerhof-Parnas (EMP) and the nonphosphorolytic Entner-Doudoroff (ED) pathways respectively, were identified in cell-free extracts of four Aspergillus oryzae strains grown on D-glucose as sole source of carbon. A. oryzae NRRL 3435 gave the highest enzymatic activity for the two enzymes and selected for further studies. Studies on the properties of the two key enzymes indicated that the optimum conditions for the activities of FDP aldolase and KDG aldolases occurred at pH 8.5, 45 degrees C and pH 8.0, 55 degrees C, respectively. Tris-acetate buffer and phosphate buffer showed the highest enzymatic activity for these two enzymes respectively. KDG aldolase was stable at 55 degrees C for 60 minutes however FDP aldolase was found to be less stable above 45 degrees C. On the other hand the two aldolases showed a high degree of stability towards frequent freezing and thawing. Dialysis of the extracts caused a decrease in the enzymatic activity of KDG aldolase, and an increase in FDP aldolase activity. The addition of ethylene diamine tetraacetate to the crude extracts caused an inhibition of KDG aldolase, whileas FDP aldolase was not affected. Addition of MnCl(2), CoSO(4), MgCl(2) and ZnSO(4) to the dialyzed extracts increased the activity of KDG aldolase by 67%, 54%, 61% and 37%, respectively. On the other hand the addition of some metal salts caused an inhibition of FDP aldolase. The results obtained indicate the absence of evidence for the involvement of sulfhydryl groups in the catalytic sites of the two aldolases.
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Affiliation(s)
- Ali M Elshafei
- Department of Microbial Chemistry, National Research Centre, El-Tahrir Street, Dokki, Cairo, Egypt.
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9
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Charmantray F, El Blidi L, Gefflaut T, Hecquet L, Bolte J, Lemaire M. Improved Straightforward Chemical Synthesis of Dihydroxyacetone Phosphate through Enzymatic Desymmetrization of 2,2-Dimethoxypropane-1,3-diol. J Org Chem 2004; 69:9310-2. [PMID: 15609974 DOI: 10.1021/jo048697k] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dihydroxyacetone phosphate (DHAP) was synthesized in high purity and yield in four steps starting from dihydroxyacetone dimer (DHA) (47% overall yield). DHA was converted into 2,2-dimethoxypropane-1,3-diol, which was desymmetrized by acetylation with lipase AK. The alcohol function was phosphorylated to give dibenzyl phosphate ester 4. From 4, two routes were investigated for large-scale synthesis of DHAP. First, acetate hydrolysis was performed prior to hydrogenolysis of the phosphate protective groups. The acetal hydrolysis was finally catalyzed by the phosphate group itself. Second, acetate and acetal hydrolysis were performed in one single step after hydrogenolysis.
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Affiliation(s)
- Franck Charmantray
- Laboratoire SEESIB, UMR 6504 CNRS, Université Blaise Pascal, 24 avenue des Landais, 63177 Aubière Cedex, France
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10
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Meyer O, Rohmer M, Grosdemange-Billiard C. Short and efficient synthesis of a stock material of dihydroxyacetone phosphate from glycidol. Tetrahedron Lett 2004. [DOI: 10.1016/j.tetlet.2004.08.148] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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11
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Bruggink A, Schoevaart R, Kieboom T. Concepts of Nature in Organic Synthesis: Cascade Catalysis and Multistep Conversions in Concert. Org Process Res Dev 2003. [DOI: 10.1021/op0340311] [Citation(s) in RCA: 334] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alle Bruggink
- Organic Chemistry, University of Nijmegen, DSM Research, Geleen, Leiden Institute of Chemistry, Leiden University, and DSM Food Specialties R&D, Delft, The Netherlands
| | - Rob Schoevaart
- Organic Chemistry, University of Nijmegen, DSM Research, Geleen, Leiden Institute of Chemistry, Leiden University, and DSM Food Specialties R&D, Delft, The Netherlands
| | - Tom Kieboom
- Organic Chemistry, University of Nijmegen, DSM Research, Geleen, Leiden Institute of Chemistry, Leiden University, and DSM Food Specialties R&D, Delft, The Netherlands
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12
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At the interface of organic synthesis and biosynthesis. ACTA ACUST UNITED AC 2002. [DOI: 10.1016/s0165-7208(02)80006-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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13
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Abstract
A coupled enzymatic assay was developed for quantitative determination of the stereoisomeric products formed in aldol reactions catalyzed by dihydroxyacetone phosphate (DHAP)-dependent aldolases. Three of the four stereoisomers could be determined directly; the fourth one was calculated. This procedure is based on the reversibility of the aldol reaction and requires no derivatization or work-up of the product samples, only removal or inactivation of the biocatalyst. In comparison with other methods the enzymatic assay is highly accurate and fast. Determination of isomer formation with 10 different acceptor substrates applying this procedure gave unprecedented insight in the stereochemistry of fructose-1,6-bisphosphate aldolase from Staphylococcus carnosus and l-rhamnulose-1-phosphate aldolase from E. coli.
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Affiliation(s)
- R Schoevaart
- Laboratory of Organic Chemistry and Catalysis, Delft University of Technology, Julianalaan 1362628 BL Delft, The Netherlands
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14
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Chênevert R, Dasser M. Chemoenzymatic synthesis of the microbial elicitor (-)-syringolide via a fructose 1,6-diphosphate aldolase-catalyzed condensation reaction. J Org Chem 2000; 65:4529-31. [PMID: 10959854 DOI: 10.1021/jo991989e] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Syringolide 2, an elicitor of the bacterial plant pathogen Pseudomonas syringae pv. tomato which triggers a hypersensitive defense response in resistant soybean plants, has been synthesized in five steps via a fructose 1,6-diphosphate aldolase reaction.
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Affiliation(s)
- R Chênevert
- Départment de chimie, Faculté des sciences et de génie, Univerisité Laval, Québec, Canada.
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