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Teshima M, Sutiono S, Döring M, Beer B, Boden M, Schenk G, Sieber V. Development of a Highly Selective NAD + -Dependent Glyceraldehyde Dehydrogenase and its Application in Minimal Cell-Free Enzyme Cascades. CHEMSUSCHEM 2024; 17:e202301132. [PMID: 37872118 DOI: 10.1002/cssc.202301132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/18/2023] [Accepted: 10/23/2023] [Indexed: 10/25/2023]
Abstract
Anthropogenic climate change has been caused by over-exploitation of fossil fuels and CO2 emissions. To counteract this, the chemical industry has shifted its focus to sustainable chemical production and the valorization of renewable resources. However, the biggest challenges in biomanufacturing are technical efficiency and profitability. In our minimal cell-free enzyme cascade generating pyruvate as the central intermediate, the NAD+ -dependent, selective oxidation of D-glyceraldehyde was identified as a key reaction step to improve the overall cascade flux. Successive genome mining identified one candidate enzyme with 24-fold enhanced activity and another whose stability is unaffected in 10 % (v/v) ethanol, the final product of our model cascade. Semi-rational engineering improved the substrate selectivity of the enzyme up to 21-fold, thus minimizing side reactions in the one-pot enzyme cascade. The final biotransformation of D-glucose showed a continuous linear production of ethanol (via pyruvate) to a final titer of 4.9 % (v/v) with a molar product yield of 98.7 %. Due to the central role of pyruvate in diverse biotransformations, the optimized production module has great potential for broad biomanufacturing applications.
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Affiliation(s)
- Mariko Teshima
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, 94315, Straubing, Germany
| | - Samuel Sutiono
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, 94315, Straubing, Germany
- Current address: CarboCode Germany GmbH, Byk-Gulden-Straße 2, 78467, Constance, Germany
| | - Manuel Döring
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, 94315, Straubing, Germany
| | - Barbara Beer
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, 94315, Straubing, Germany
- Current address: CASCAT GmbH, Europaring 4, 94315, Straubing, Germany
| | - Mikael Boden
- School of Chemistry and Molecular Biosciences, The University of Queensland, 68 Cooper Rd, St. Lucia, 4072, Brisbane, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, 68 Cooper Rd, St. Lucia, 4072, Brisbane, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Corner of College and Cooper Rds, St. Lucia, 4072, Brisbane, Australia
- Sustainable Minerals Institute, The University of Queensland, Corner of College and Staff House Rds, St. Lucia, 4072, Brisbane, Australia
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, 94315, Straubing, Germany
- School of Chemistry and Molecular Biosciences, The University of Queensland, 68 Cooper Rd, St. Lucia, 4072, Brisbane, Australia
- SynBioFoundry@TUM, Technical University of Munich, Schulgasse 22, 94315, Straubing, Germany
- Catalytic Research Center, Technical University of Munich, Ernst-Otto-Fischer Straße 1, 85748, Garching, Germany
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Ganjave SD, O'Niel RA, Wangikar PP. Rate of dilution and redox ratio influence the refolding efficiency of recombinant fungal dehydrogenases. Int J Biol Macromol 2023; 250:126163. [PMID: 37549766 DOI: 10.1016/j.ijbiomac.2023.126163] [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: 05/06/2023] [Revised: 07/19/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023]
Abstract
Dehydrogenases from fungi are attracting attention as industrial biocatalysts due to their high activity and chiral selectivity. However, these enzymes form insoluble aggregates when overexpressed in E. coli, limiting their industrial application. In the present study, we report the systematic development of a refolding process for selected, industrially relevant fungal dehydrogenases, viz., formate dehydrogenase from Candida boidinii (CbFDH) and formate and alcohol dehydrogenases from Geotrichum candium (GcFDH and GcADH, respectively). We first employed a screen to evaluate the effects of different variables on refolding including the buffer system, additives, and rate of dilution. The extent of refolding was determined by enzyme assays, circular dichroism, and tryptophan fluorescence. Our results showed that glycerol and reducing environment are essential for refolding of these dehydrogenases. Further, slow dilution of solubilized protein over 16 h dramatically improved the recovery of refolded enzymes compared to rapid dilution. The importance of slow dilution was further confirmed in a 10-fold scaled-up refolding trial. Overall, we demonstrate a robust method for refolding of fungal dehydrogenases, thus improving their availability for various biocatalytic applications.
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Affiliation(s)
- Snehal D Ganjave
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Ruchika Annie O'Niel
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Pramod P Wangikar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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Shanbhag AP. Stairway to Stereoisomers: Engineering Short- and Medium-Chain Ketoreductases To Produce Chiral Alcohols. Chembiochem 2023; 24:e202200687. [PMID: 36640298 DOI: 10.1002/cbic.202200687] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/14/2023] [Accepted: 01/14/2023] [Indexed: 01/15/2023]
Abstract
The short- and medium-chain dehydrogenase/reductase superfamilies are responsible for most chiral alcohol production in laboratories and industries. In nature, they participate in diverse roles such as detoxification, housekeeping, secondary metabolite production, and catalysis of several chemicals with commercial and environmental significance. As a result, they are used in industries to create biopolymers, active pharmaceutical intermediates (APIs), and are also used as components of modular enzymes like polyketide synthases for fabricating bioactive molecules. Consequently, random, semi-rational and rational engineering have helped transform these enzymes into product-oriented efficient catalysts. The rise of newer synthetic chemicals and their enantiopure counterparts has proved challenging, and engineering them has been the subject of numerous studies. However, they are frequently limited to the synthesis of a single chiral alcohol. The study attempts to defragment and describe hotspots of engineering short- and medium-chain dehydrogenases/reductases for the production of chiral synthons.
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Affiliation(s)
- Anirudh P Shanbhag
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, 700009, India.,Bugworks Research India Pvt. Ltd., C-CAMP, National Centre for Biological Sciences (NCBS-TIFR), Bellary Road, Bangalore, 560003, India
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Stark F, Loderer C, Petchey M, Grogan G, Ansorge-Schumacher M. Advanced Insights into Catalytic and Structural Features of the Zinc-Dependent Alcohol Dehydrogenase from Thauera aromatica. Chembiochem 2022; 23:e202200149. [PMID: 35557486 PMCID: PMC9400901 DOI: 10.1002/cbic.202200149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/12/2022] [Indexed: 11/10/2022]
Abstract
The asymmetric reduction of ketones to chiral hydroxyl compounds by alcohol dehydrogenases (ADHs) is an established strategy for the provision of valuable precursors for fine chemicals and pharmaceutics. However, most ADHs favor linear aliphatic and aromatic carbonyl compounds, and suitable biocatalysts with preference for cyclic ketones and diketones are still scarce. Among the few candidates, the alcohol dehydrogenase from Thauera aromatica (ThaADH) stands out with a high activity for the reduction of the cyclic α‐diketone 1,2‐cyclohexanedione to the corresponding α‐hydroxy ketone. This study elucidates catalytic and structural features of the enzyme. ThaADH showed a remarkable thermal and pH stability as well as stability in the presence of polar solvents. A thorough description of the substrate scope combined with the resolution and description of the crystal structure, demonstrated a strong preference of ThaADH for cyclic α‐substituted cyclohexanones, and indicated structural determinants responsible for the unique substrate acceptance.
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Affiliation(s)
- Frances Stark
- TU Dresden: Technische Universitat Dresden, Molecular Biotechnology, GERMANY
| | - Christoph Loderer
- TU Dresden: Technische Universitat Dresden, Molecular Biotechnology, GERMANY
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An NAD-Specific 6-Hydroxy-3-Succinoyl-Semialdehyde-Pyridine Dehydrogenase from Nicotine-Degrading Agrobacterium tumefaciens Strain S33. Microbiol Spectr 2021; 9:e0092421. [PMID: 34378958 PMCID: PMC8552603 DOI: 10.1128/spectrum.00924-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Agrobacterium tumefaciens strain S33 can catabolize nicotine via a hybrid of the pyridine and pyrrolidine pathways. Most of the enzymes involved in this biochemical pathway have been identified and characterized, except for the one catalyzing the oxidation of 6-hydroxy-3-succinoyl-semialdehyde-pyridine to 6-hydroxy-3-succinoylpyridine. Based on a previous genomic and transcriptomic analysis, an open reading frame (ORF) annotated to encode aldehyde dehydrogenase (Ald) in the nicotine-degrading cluster was predicted to be responsible for this step. In this study, we heterologously expressed the enzyme and identified its function by biochemical assay and mass spectrum analysis. It was found that Ald catalyzes the NAD-specific dehydrogenation of 6-hydroxy-3-succinoyl-semialdehyde-pyridine to 6-hydroxy-3-succinoylpyridine. With the nonhydroxylated analog 3-succinoyl-semialdehyde-pyridine (SAP) as a substrate, Ald had a specific activity of 10.05 U/mg at pH 9.0 and apparent Km values of around 58.68 μM and 0.41 mM for SAP and NAD+, respectively. Induction at low temperature and purification and storage in low-salt buffers were helpful to prevent its aggregation and precipitation. Disruption of the ald gene caused a lower growth rate and biomass of strain S33 on nicotine but not on 6-hydroxy-3-succinoylpyridine. Ald has a broad range of substrates, including benzaldehyde, furfural, and acetaldehyde. Recombinant Escherichia coli cells harboring the ald gene can efficiently convert furfural to 2-furoic acid at a specific rate of 0.032 mmol min−1 g dry cells−1, extending the application of Ald in the catalysis of bio-based furan compounds. These findings provide new insights into the biochemical mechanism of the nicotine-degrading hybrid pathway and the possible application of Ald in industrial biocatalysis. IMPORTANCE Nicotine is one of the major toxic N-heterocyclic aromatic alkaloids produced in tobacco plants. Manufacturing tobacco and smoking may lead to some environmental and public health problems. Microorganisms can degrade nicotine by various biochemical pathways, but the biochemical mechanism for nicotine degradation has not been fully elucidated. In this study, we identified an aldehyde dehydrogenase responsible for the oxidation of 6-hydroxy-3-succinoyl-semialdehyde-pyridine to 6-hydroxy-3-succinoylpyridine; this was the only uncharacterized enzyme in the hybrid of the pyridine and pyrrolidine pathways in Agrobacterium tumefaciens S33. Similar to the known aldehyde dehydrogenase, the NAD-specific homodimeric enzyme presents a broad substrate range with high activity in alkaline and low-salt-containing buffers. It can catalyze not only the aldehyde from nicotine degradation but also those of benzaldehyde, furfural, and acetaldehyde. It was found that recombinant Escherichia coli cells harboring the ald gene could efficiently convert furfural to valuable 2-furoic acid, demonstrating its potential application for enzymatic catalysis.
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Gmelch TJ, Sperl JM, Sieber V. Molecular Dynamics Analysis of a Rationally Designed Aldehyde Dehydrogenase Gives Insights into Improved Activity for the Non-Native Cofactor NAD .. ACS Synth Biol 2020; 9:920-929. [PMID: 32208678 DOI: 10.1021/acssynbio.9b00527] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The aldehyde dehydrogenase from Thermoplasma acidophilum was previously implemented as a key enzyme in a synthetic cell-free reaction cascade for the production of alcohols. In order to engineer the enzyme's cofactor specificity from NADP+ to NAD+, we identified selectivity-determining residues with the CSR-SALAD tool and investigated further positions based on the crystal structure. Stepwise combination of the initially discovered six point mutations allowed us to monitor the cross effects of each mutation, resulting in a final variant with reduced KM for the non-native cofactor NAD+ (from 18 to 0.6 mM) and an increased activity for the desired substrate d-glyceraldehyde (from 0.4 to 1.5 U/mg). Saturation mutagenesis of the residues at the entrance of the substrate pocket could eliminate substrate inhibition. Molecular dynamics simulations showed a significant gain of flexibility at the cofactor binding site for the final variant. The concomitant increase in stability against isobutanol and only a minor reduction in its temperature stability render the final variant a promising candidate for future optimization of our synthetic cell-free enzymatic cascade.
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Affiliation(s)
- Tobias J. Gmelch
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, D-94315 Straubing, Germany
| | - Josef M. Sperl
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, D-94315 Straubing, Germany
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, D-94315 Straubing, Germany
- Catalysis Research Center, Technical University of Munich, Garching 85748, Germany
- Bio-, Electro- and Chemocatalysis (BioCat) Branch, Fraunhofer Institute of Interfacial Biotechnology (IGB), Straubing 94315, Germany
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
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7
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Gmelch TJ, Sperl JM, Sieber V. Optimization of a reduced enzymatic reaction cascade for the production of L-alanine. Sci Rep 2019; 9:11754. [PMID: 31409820 PMCID: PMC6692406 DOI: 10.1038/s41598-019-48151-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 07/25/2019] [Indexed: 11/09/2022] Open
Abstract
Cell-free enzymatic reaction cascades combine the advantages of well-established in vitro biocatalysis with the power of multi-step in vivo pathways. The absence of a regulatory cell environment enables direct process control including methods for facile bottleneck identification and process optimization. Within this work, we developed a reduced, enzymatic reaction cascade for the direct production of L-alanine from D-glucose and ammonium sulfate. An efficient, activity based enzyme selection is demonstrated for the two branches of the cascade. The resulting redox neutral cascade is composed of a glucose dehydrogenase, two dihydroxyacid dehydratases, a keto-deoxy-aldolase, an aldehyde dehydrogenase and an L-alanine dehydrogenase. This artificial combination of purified biocatalysts eliminates the need for phosphorylation and only requires NAD as cofactor. We provide insight into in detail optimization of the process parameters applying a fluorescamine based L-alanine quantification assay. An optimized enzyme ratio and the necessary enzyme load were identified and together with the optimal concentrations of cofactor (NAD), ammonium and buffer yields of >95% for the main branch and of 8% for the side branch were achieved.
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Affiliation(s)
- Tobias J Gmelch
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, 94315, Straubing, Germany
| | - Josef M Sperl
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, 94315, Straubing, Germany
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, 94315, Straubing, Germany. .,Catalysis Research Center, Technical University of Munich, Garching, Germany. .,Fraunhofer Institute of Interfacial Biotechnology (IGB), Bio-, Electro- and Chemo Catalysis (BioCat) Branch, Straubing, Germany. .,School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia.
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Karim AS, Dudley QM, Jewett MC. Cell-Free Synthetic Systems for Metabolic Engineering and Biosynthetic Pathway Prototyping. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Ashty S. Karim
- Northwestern University; Department of Chemical and Biological Engineering; 2145 Sheridan Road Evanston IL 60208 USA
- Northwestern University; Chemistry of Life Processes Institute; 2170 Campus Drive Evanston IL 60208 USA
| | - Quentin M. Dudley
- Northwestern University; Department of Chemical and Biological Engineering; 2145 Sheridan Road Evanston IL 60208 USA
- Northwestern University; Chemistry of Life Processes Institute; 2170 Campus Drive Evanston IL 60208 USA
| | - Michael C. Jewett
- Northwestern University; Department of Chemical and Biological Engineering; 2145 Sheridan Road Evanston IL 60208 USA
- Northwestern University; Chemistry of Life Processes Institute; 2170 Campus Drive Evanston IL 60208 USA
- Northwestern University; Robert H. Lurie Comprehensive Cancer Center; 676 North St. Clair Chicago IL 60611 USA
- Northwestern University; Simpson Querrey Institute for Bionanotechnology; 303 E. Superior Chicago IL 60611 USA
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Wu X, Xu L, Yan M. A new NAD +-dependent glyceraldehyde dehydrogenase obtained by rational design of l-lactaldehyde dehydrogenase from Escherichia coli. Biosci Biotechnol Biochem 2016; 80:2306-2310. [PMID: 27671251 DOI: 10.1080/09168451.2016.1194181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
NAD + -dependent glyceraldehyde dehydrogenases usually had lower activity in the nonphosphorylated Entner-Doudoroff (nED) pathway. In the present study, a new NAD + -dependent glyceraldehyde dehydrogenase was engineered from l-lactaldehyde dehydrogenase of E. coli (EC: 1.2.1.22). Through comparison of the sequence alignment and the active center model, we found that a residue N286 of l-lactaldehyde dehydrogenase contributed an important structure role to substrate identification. By free energy calculation, three mutations (N286E, N286H, N286T) were chosen to investigate the change of substrate specificity of the enzyme. All mutants were able to oxidate glyceraldehyde. Especially, N286T showed the highest activity of 1.1U/mg, which was 5-fold higher than the reported NAD + -dependent glyceraldehyde dehydrogenases, and 70% activity was retained at 55 °C after an hour. Compared to l-lactaldehyde, N286T had a one-third lower Km value to glyceraldehyde.
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Affiliation(s)
- Xing Wu
- a College of Biotechnology and Pharmaceutical Engineering , Nanjing Tech University , Nanjing , P.R. China
| | - Lin Xu
- a College of Biotechnology and Pharmaceutical Engineering , Nanjing Tech University , Nanjing , P.R. China
| | - Ming Yan
- a College of Biotechnology and Pharmaceutical Engineering , Nanjing Tech University , Nanjing , P.R. China
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Iermak I, Degtjarik O, Steffler F, Sieber V, Kuta Smatanova I. Crystallization behaviour of glyceraldehyde dehydrogenase from Thermoplasma acidophilum. Acta Crystallogr F Struct Biol Commun 2015; 71:1475-80. [PMID: 26625289 PMCID: PMC4666475 DOI: 10.1107/s2053230x15020270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 10/27/2015] [Indexed: 11/10/2022] Open
Abstract
The glyceraldehyde dehydrogenase from Thermoplasma acidophilum (TaAlDH) is a microbial enzyme that catalyzes the oxidation of D-glyceraldehyde to D-glycerate in the artificial enzyme cascade designed for the conversion of glucose to the organic solvents isobutanol and ethanol. Various mutants of TaAlDH were constructed by a random approach followed by site-directed and saturation mutagenesis in order to improve the properties of the enzyme that are essential for its functioning within the cascade. Two enzyme variants, wild-type TaAlDH (TaAlDHwt) and an F34M+S405N variant (TaAlDH F34M+S405N), were successfully crystallized. Crystals of TaAlDHwt belonged to the monoclinic space group P1211 with eight molecules per asymmetric unit and diffracted to a resolution of 1.95 Å. TaAlDH F34M+S405N crystallized in two different space groups: triclinic P1 with 16 molecules per asymmetric unit and monoclinic C121 with four molecules per asymmetric unit. These crystals diffracted to resolutions of 2.14 and 2.10 Å for the P1 and C121 crystals, respectively.
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Affiliation(s)
- Iuliia Iermak
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 31, 37005 Ceske Budejovice, Czech Republic
| | - Oksana Degtjarik
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 31, 37005 Ceske Budejovice, Czech Republic
- Institute of Nanobiology and Structural Biology GCRC, Academy of Sciences of the Czech Republic, Zamek 136, 37333 Nove Hrady, Czech Republic
| | - Fabian Steffler
- Bio, Electro- and Chemocatalysis BioCat, Straubing Branch of the Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Schulgasse 11a, 94315 Straubing, Germany
| | - Volker Sieber
- Chemistry of Biogenic Resources, Straubing Centre of Science, Technische Universität München, Schulgasse 16, 94315 Straubing, Germany
| | - Ivana Kuta Smatanova
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 31, 37005 Ceske Budejovice, Czech Republic
- Institute of Nanobiology and Structural Biology GCRC, Academy of Sciences of the Czech Republic, Zamek 136, 37333 Nove Hrady, Czech Republic
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Zhang YHP. Production of biofuels and biochemicals by in vitro synthetic biosystems: Opportunities and challenges. Biotechnol Adv 2015; 33:1467-83. [DOI: 10.1016/j.biotechadv.2014.10.009] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Revised: 10/09/2014] [Accepted: 10/19/2014] [Indexed: 12/20/2022]
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12
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Dudley QM, Karim AS, Jewett MC. Cell-free metabolic engineering: biomanufacturing beyond the cell. Biotechnol J 2015; 10:69-82. [PMID: 25319678 PMCID: PMC4314355 DOI: 10.1002/biot.201400330] [Citation(s) in RCA: 231] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 07/24/2014] [Accepted: 08/22/2014] [Indexed: 12/20/2022]
Abstract
Industrial biotechnology and microbial metabolic engineering are poised to help meet the growing demand for sustainable, low-cost commodity chemicals and natural products, yet the fraction of biochemicals amenable to commercial production remains limited. Common problems afflicting the current state-of-the-art include low volumetric productivities, build-up of toxic intermediates or products, and byproduct losses via competing pathways. To overcome these limitations, cell-free metabolic engineering (CFME) is expanding the scope of the traditional bioengineering model by using in vitro ensembles of catalytic proteins prepared from purified enzymes or crude lysates of cells for the production of target products. In recent years, the unprecedented level of control and freedom of design, relative to in vivo systems, has inspired the development of engineering foundations for cell-free systems. These efforts have led to activation of long enzymatic pathways (>8 enzymes), near theoretical conversion yields, productivities greater than 100 mg L(-1) h(-1) , reaction scales of >100 L, and new directions in protein purification, spatial organization, and enzyme stability. In the coming years, CFME will offer exciting opportunities to: (i) debug and optimize biosynthetic pathways; (ii) carry out design-build-test iterations without re-engineering organisms; and (iii) perform molecular transformations when bioconversion yields, productivities, or cellular toxicity limit commercial feasibility.
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Affiliation(s)
| | | | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
- Member, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
- Member, Institute for Bionanotechnology in Medicine, Northwestern University, Chicago, IL, USA
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Improvement of thermostable aldehyde dehydrogenase by directed evolution for application in Synthetic Cascade Biomanufacturing. Enzyme Microb Technol 2013; 53:307-14. [PMID: 24034429 DOI: 10.1016/j.enzmictec.2013.07.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Revised: 07/06/2013] [Accepted: 07/08/2013] [Indexed: 11/22/2022]
Abstract
The aldehyde dehydrogenase from Thermoplasma acidophilum, which was previously implemented as a key enzyme in a synthetic cell-free reaction cascade for the production of alcohols, was optimized by directed evolution. Improvements have been made to enhance reaction velocity and solubility. Using a random approach followed by site-directed and saturation mutagenesis, three beneficial amino acid mutations were found after screening of ca. 20,000 variants. Mutation Y399C enhanced the protein solubility after recombinant expression in Escherichia coli 6-fold. Two further mutations, F34M and S405N, enhanced enzyme activity with the cofactor NAD(+) by a factor of eight. Impacts on enzyme stability and substrate specificity were negligible. Modeling of the enzyme structure did not reveal any direct interactions between the amino acid substitutions and residues of the active site or the enzyme's substrates. Thus, a directed evolution approach allowed for the generation of improved enzyme variants which were unlikely to be found by rational or semi-rational strategies.
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