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Meliawati M, Volke DC, Nikel PI, Schmid J. Engineering the carbon and redox metabolism of Paenibacillus polymyxa for efficient isobutanol production. Microb Biotechnol 2024; 17:e14438. [PMID: 38529712 DOI: 10.1111/1751-7915.14438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 02/15/2024] [Accepted: 02/21/2024] [Indexed: 03/27/2024] Open
Abstract
Paenibacillus polymyxa is a non-pathogenic, Gram-positive bacterium endowed with a rich and versatile metabolism. However interesting, this bacterium has been seldom used for bioproduction thus far. In this study, we engineered P. polymyxa for isobutanol production, a relevant bulk chemical and next-generation biofuel. A CRISPR-Cas9-based genome editing tool facilitated the chromosomal integration of a synthetic operon to establish isobutanol production. The 2,3-butanediol biosynthesis pathway, leading to the main fermentation product of P. polymyxa, was eliminated. A mutant strain harbouring the synthetic isobutanol operon (kdcA from Lactococcus lactis, and the native ilvC, ilvD and adh genes) produced 1 g L-1 isobutanol under microaerobic conditions. Improving NADPH regeneration by overexpression of the malic enzyme subsequently increased the product titre by 50%. Network-wide proteomics provided insights into responses of P. polymyxa to isobutanol and revealed a significant metabolic shift caused by alcohol production. Glucose-6-phosphate 1-dehydrogenase, the key enzyme in the pentose phosphate pathway, was identified as a bottleneck that hindered efficient NADPH regeneration through this pathway. Furthermore, we conducted culture optimization towards cultivating P. polymyxa in a synthetic minimal medium. We identified biotin (B7), pantothenate (B5) and folate (B9) to be mutual essential vitamins for P. polymyxa. Our rational metabolic engineering of P. polymyxa for the production of a heterologous chemical sheds light on the metabolism of this bacterium towards further biotechnological exploitation.
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Affiliation(s)
- Meliawati Meliawati
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
| | - Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jochen Schmid
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
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2
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Boecker S, Schulze P, Klamt S. Growth-coupled anaerobic production of isobutanol from glucose in minimal medium with Escherichia coli. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:148. [PMID: 37789464 PMCID: PMC10548627 DOI: 10.1186/s13068-023-02395-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 09/18/2023] [Indexed: 10/05/2023]
Abstract
BACKGROUND The microbial production of isobutanol holds promise to become a sustainable alternative to fossil-based synthesis routes for this important chemical. Escherichia coli has been considered as one production host, however, due to redox imbalance, growth-coupled anaerobic production of isobutanol from glucose in E. coli is only possible if complex media additives or small amounts of oxygen are provided. These strategies have a negative impact on product yield, productivity, reproducibility, and production costs. RESULTS In this study, we propose a strategy based on acetate as co-substrate for resolving the redox imbalance. We constructed the E. coli background strain SB001 (ΔldhA ΔfrdA ΔpflB) with blocked pathways from glucose to alternative fermentation products but with an enabled pathway for acetate uptake and subsequent conversion to ethanol via acetyl-CoA. This strain, if equipped with the isobutanol production plasmid pIBA4, showed robust exponential growth (µ = 0.05 h-1) under anaerobic conditions in minimal glucose medium supplemented with small amounts of acetate. In small-scale batch cultivations, the strain reached a glucose uptake rate of 4.8 mmol gDW-1 h-1, a titer of 74 mM and 89% of the theoretical maximal isobutanol/glucose yield, while secreting only small amounts of ethanol synthesized from acetate. Furthermore, we show that the strain keeps a high metabolic activity also in a pulsed fed-batch bioreactor cultivation, even if cell growth is impaired by the accumulation of isobutanol in the medium. CONCLUSIONS This study showcases the beneficial utilization of acetate as a co-substrate and redox sink to facilitate growth-coupled production of isobutanol under anaerobic conditions. This approach holds potential for other applications with different production hosts and/or substrate-product combinations.
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Affiliation(s)
- Simon Boecker
- Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106, Magdeburg, Germany
- University of Applied Sciences Berlin, Seestr. 64, 13347, Berlin, Germany
| | - Peter Schulze
- Physical and Chemical Foundations of Process Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106, Magdeburg, Germany
| | - Steffen Klamt
- Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106, Magdeburg, Germany.
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3
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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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4
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Gupta M, Wong M, Jawed K, Gedeon K, Barrett H, Bassalo M, Morrison C, Eqbal D, Yazdani SS, Gill RT, Huang J, Douaisi M, Dordick J, Belfort G, Koffas MA. Isobutanol production by combined in vivo and in vitro metabolic engineering. Metab Eng Commun 2022; 15:e00210. [PMID: 36325486 PMCID: PMC9619177 DOI: 10.1016/j.mec.2022.e00210] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/03/2022] [Accepted: 10/16/2022] [Indexed: 12/12/2022] Open
Abstract
The production of the biofuel, isobutanol, in E. coli faces limitations due to alcohol toxicity, product inhibition, product recovery, and long-term industrial feasibility. Here we demonstrate an approach of combining both in vivo with in vitro metabolic engineering to produce isobutanol. The in vivo production of α-ketoisovalerate (KIV) was conducted through CRISPR mediated integration of the KIV pathway in bicistronic design (BCD) in E. coli and inhibition of competitive valine pathway using CRISPRi technology. The subsequent in vitro conversion to isobutanol was carried out with engineered enzymes for 2-ketoacid decarboxylase (KIVD) and alcohol dehydrogenase (ADH). For the in vivo production of KIV and subsequent in vitro production of isobutanol, this two-step serial approach resulted in yields of 56% and 93%, productivities of 0.62 and 0.074 g L-1 h-1, and titers of 5.6 and 1.78 g L-1, respectively. Thus, this combined biosynthetic system can be used as a modular approach for producing important metabolites, like isobutanol, without the limitations associated with in vivo production using a consolidated bioprocess.
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Affiliation(s)
- Mamta Gupta
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA,Department of Botany and Environmental Studies, DAV University, Jalandhar, 144 001, Punjab, India
| | - Matthew Wong
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA,Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Kamran Jawed
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA,DBT-ICGEB Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Kamil Gedeon
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Hannah Barrett
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Marcelo Bassalo
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, 80309, USA
| | - Clifford Morrison
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Danish Eqbal
- DBT-ICGEB Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Syed Shams Yazdani
- DBT-ICGEB Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Ryan T. Gill
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, 80309, USA
| | - Jiaqi Huang
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Marc Douaisi
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Jonathan Dordick
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA,Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Georges Belfort
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA,Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Mattheos A.G. Koffas
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA,Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA,Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA,Corresponding author. Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
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5
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Gambacorta FV, Wagner ER, Jacobson TB, Tremaine M, Muehlbauer LK, McGee MA, Baerwald JJ, Wrobel RL, Wolters JF, Place M, Dietrich JJ, Xie D, Serate J, Gajbhiye S, Liu L, Vang-Smith M, Coon JJ, Zhang Y, Gasch AP, Amador-Noguez D, Hittinger CT, Sato TK, Pfleger BF. Comparative functional genomics identifies an iron-limited bottleneck in a Saccharomyces cerevisiae strain with a cytosolic-localized isobutanol pathway. Synth Syst Biotechnol 2022; 7:738-749. [PMID: 35387233 PMCID: PMC8938195 DOI: 10.1016/j.synbio.2022.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/17/2021] [Accepted: 02/14/2022] [Indexed: 11/20/2022] Open
Abstract
Metabolic engineering strategies have been successfully implemented to improve the production of isobutanol, a next-generation biofuel, in Saccharomyces cerevisiae. Here, we explore how two of these strategies, pathway re-localization and redox cofactor-balancing, affect the performance and physiology of isobutanol producing strains. We equipped yeast with isobutanol cassettes which had either a mitochondrial or cytosolic localized isobutanol pathway and used either a redox-imbalanced (NADPH-dependent) or redox-balanced (NADH-dependent) ketol-acid reductoisomerase enzyme. We then conducted transcriptomic, proteomic and metabolomic analyses to elucidate molecular differences between the engineered strains. Pathway localization had a large effect on isobutanol production with the strain expressing the mitochondrial-localized enzymes producing 3.8-fold more isobutanol than strains expressing the cytosolic enzymes. Cofactor-balancing did not improve isobutanol titers and instead the strain with the redox-imbalanced pathway produced 1.5-fold more isobutanol than the balanced version, albeit at low overall pathway flux. Functional genomic analyses suggested that the poor performances of the cytosolic pathway strains were in part due to a shortage in cytosolic Fe-S clusters, which are required cofactors for the dihydroxyacid dehydratase enzyme. We then demonstrated that this cofactor limitation may be partially recovered by disrupting iron homeostasis with a fra2 mutation, thereby increasing cellular iron levels. The resulting isobutanol titer of the fra2 null strain harboring a cytosolic-localized isobutanol pathway outperformed the strain with the mitochondrial-localized pathway by 1.3-fold, demonstrating that both localizations can support flux to isobutanol.
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Affiliation(s)
- Francesca V. Gambacorta
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Ellen R. Wagner
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
| | - Tyler B. Jacobson
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Mary Tremaine
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Mick A. McGee
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Justin J. Baerwald
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Russell L. Wrobel
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, USA
| | - John F. Wolters
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, USA
| | - Mike Place
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Joshua J. Dietrich
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Dan Xie
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Jose Serate
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Shabda Gajbhiye
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Lisa Liu
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Maikayeng Vang-Smith
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Yaoping Zhang
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Audrey P. Gasch
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
| | - Daniel Amador-Noguez
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Chris Todd Hittinger
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory of Genetics, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI, USA
| | - Trey K. Sato
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Brian F. Pfleger
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
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6
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Xiao C, Toldrá F, Zhou F, Mora L, Luo L, Zheng L, Luo D, Zhao M. Chicken-derived tripeptide KPC (Lys-Pro-Cys) stabilizes alcohol dehydrogenase (ADH) through peptide-enzyme interaction. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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7
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Dedov AG, Karavaev AA, Loktev AS, Mitinenko AS, Moiseev II. Isobutanol conversion to petrochemicals using MFI-based catalysts synthesized by a hydrothermal-microwave method. Catal Today 2021. [DOI: 10.1016/j.cattod.2020.04.064] [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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8
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Ma ZX, Zhang M, Zhang CT, Zhang H, Mo XH, Xing XH, Yang S. Metabolomic analysis improves bioconversion of methanol to isobutanol in Methylorubrum extorquens AM1. Biotechnol J 2021; 16:e2000413. [PMID: 33595188 DOI: 10.1002/biot.202000413] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/09/2021] [Accepted: 02/15/2021] [Indexed: 11/12/2022]
Abstract
BACKGROUND Methylorubrum extorquens AM1 can be engineered to convert methanol to value-added chemicals. Most of these chemicals derive from acetyl-CoA involved in the serine cycle. However, recent studies on methylotrophic metabolism have suggested that C3 pyruvate is a good potential precursor for broadening the types of synthesized products. METHODS AND RESULTS In the present study, we found that isobutanol was a model chemical that could be generated from pyruvate through a 2-keto acid pathway. Initially, the engineered M. extorquens AM1 could only produce a trace amount of isobutanol at 0.62 mgL-1 after introducing the heterologous 2-ketoisovalerate decarboxylase and alcohol dehydrogenase. Furthermore, the metabolomic analysis revealed that insufficient carbon fluxes through 2-ketoisovalerate and pyruvate were the key limitation steps for efficient biosynthesis of isobutanol. Based on this analysis, the titer of isobutanol was improved by over 20-fold after overexpressing alsS gene encoding acetolactate synthase and deleting ldhA gene for lactate dehydrogenase. Moreover, substituting the cell chassis with the isobutanol-tolerant strain isolated from adaptive evolution of M. extorquens AM1 further increased the production of isobutanol by 1.7-fold, resulting in the final titer of 19 mgL-1 in flask cultivation. CONCLUSION Our current findings provided promising insights into engineering methylotrophic cell factories capable of converting methanol to isobutanol or value-added chemicals using pyruvate as the precursor.
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Affiliation(s)
- Zeng-Xin Ma
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Min Zhang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China.,Shandong Longkete Enzyme Co., Ltd., Linyi, Shandong, People's Republic of China
| | - Chang-Tai Zhang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Hui Zhang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Xu-Hua Mo
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Xin-Hui Xing
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, People's Republic of China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing, People's Republic of China.,Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, and Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen, People's Republic of China
| | - Song Yang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, People's Republic of China
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9
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Acedos MG, de la Torre I, Santos VE, García-Ochoa F, García JL, Galán B. Modulating redox metabolism to improve isobutanol production in Shimwellia blattae. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:8. [PMID: 33407735 PMCID: PMC7789792 DOI: 10.1186/s13068-020-01862-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/17/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Isobutanol is a candidate to replace gasoline from fossil resources. This higher alcohol can be produced from sugars using genetically modified microorganisms. Shimwellia blattae (p424IbPSO) is a robust strain resistant to high concentration of isobutanol that can achieve a high production rate of this alcohol. Nevertheless, this strain, like most strains developed for isobutanol production, has some limitations in its metabolic pathway. Isobutanol production under anaerobic conditions leads to a depletion of NADPH, which is necessary for two enzymes in the metabolic pathway. In this work, two independent approaches have been studied to mitigate the co-substrates imbalance: (i) using a NADH-dependent alcohol dehydrogenase to reduce the NADPH dependence of the pathway and (ii) using a transhydrogenase to increase NADPH level. RESULTS The addition of the NADH-dependent alcohol dehydrogenase from Lactococcus lactis (AdhA) to S. blattae (p424IbPSO) resulted in a 19.3% higher isobutanol production. The recombinant strain S. blattae (p424IbPSO, pIZpntAB) harboring the PntAB transhydrogenase produced 39.0% more isobutanol than the original strain, reaching 5.98 g L-1 of isobutanol. In both strains, we observed a significant decrease in the yields of by-products such as lactic acid or ethanol. CONCLUSIONS The isobutanol biosynthesis pathway in S. blattae (p424IbPSO) uses the endogenous NADPH-dependent alcohol dehydrogenase YqhD to complete the pathway. The addition of NADH-dependent AdhA leads to a reduction in the consumption of NADPH that is a bottleneck of the pathway. The higher consumption of NADH by AdhA reduces the availability of NADH required for the transformation of pyruvate into lactic acid and ethanol. On the other hand, the expression of PntAB from E. coli increases the availability of NADPH for IlvC and YqhD and at the same time reduces the availability of NADH and thus, the production of lactic acid and ethanol. In this work it is shown how the expression of AdhA and PntAB enzymes in Shimwellia blattae increases yield from 11.9% to 14.4% and 16.4%, respectively.
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Affiliation(s)
- Miguel G Acedos
- Chemical and Materials Engineering Department, Chemical Sciences School, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Isabel de la Torre
- Chemical and Materials Engineering Department, Chemical Sciences School, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Victoria E Santos
- Chemical and Materials Engineering Department, Chemical Sciences School, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Félix García-Ochoa
- Chemical and Materials Engineering Department, Chemical Sciences School, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - José L García
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, CSIC, 28040, Madrid, Spain
| | - Beatriz Galán
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, CSIC, 28040, Madrid, Spain.
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10
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Abstract
Biocatalysts provide a number of advantages such as high selectivity, the ability to operate under mild reaction conditions and availability from renewable resources that are of interest in the development of bioreactors for applications in the pharmaceutical and other sectors. The use of oxidoreductases in biocatalytic reactors is primarily focused on the use of NAD(P)-dependent enzymes, with the recycling of the cofactor occurring via an additional enzymatic system. The use of electrochemically based systems has been limited. This review focuses on the development of electrochemically based biocatalytic reactors. The mechanisms of mediated and direct electron transfer together with methods of immobilising enzymes are briefly reviewed. The use of electrochemically based batch and flow reactors is reviewed in detail with a focus on recent developments in the use of high surface area electrodes, enzyme engineering and enzyme cascades. A future perspective on electrochemically based bioreactors is presented.
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11
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Liu Y, Ghosh IN, Martien J, Zhang Y, Amador-Noguez D, Landick R. Regulated redirection of central carbon flux enhances anaerobic production of bioproducts in Zymomonas mobilis. Metab Eng 2020; 61:261-274. [PMID: 32590077 DOI: 10.1016/j.ymben.2020.06.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 06/06/2020] [Accepted: 06/07/2020] [Indexed: 01/25/2023]
Abstract
The microbial production of chemicals and fuels from plant biomass offers a sustainable alternative to fossilized carbon but requires high rates and yields of bioproduct synthesis. Z. mobilis is a promising chassis microbe due to its high glycolytic rate in anaerobic conditions that are favorable for large-scale production. However, diverting flux from its robust ethanol fermentation pathway to nonnative pathways remains a major engineering hurdle. To enable controlled, high-yield synthesis of bioproducts, we implemented a central-carbon metabolism control-valve strategy using regulated, ectopic expression of pyruvate decarboxylase (Pdc) and deletion of chromosomal pdc. Metabolomic and genetic analyses revealed that glycolytic intermediates and NADH accumulate when Pdc is depleted and that Pdc is essential for anaerobic growth of Z. mobilis. Aerobically, all flux can be redirected to a 2,3-butanediol pathway for which respiration maintains redox balance. Anaerobically, flux can be redirected to redox-balanced lactate or isobutanol pathways with ≥65% overall yield from glucose. This strategy provides a promising path for future metabolic engineering of Z. mobilis.
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Affiliation(s)
- Yang Liu
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, United States; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, United States
| | - Indro Neil Ghosh
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, United States
| | - Julia Martien
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, United States; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, United States
| | - Yaoping Zhang
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, United States
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, United States; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, United States
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, United States; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, United States; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, United States.
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12
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Collins CH, Cirino PC. Commemorating Frances Arnold. AIChE J 2020. [DOI: 10.1002/aic.16924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Cynthia H. Collins
- Department of Chemical and Biological EngineeringRensselaer Polytechnic Institute Troy New York
| | - Patrick C. Cirino
- Department of Chemical & Biomolecular EngineeringUniversity of Houston Houston Texas
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13
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Wong M, Zha J, Sorci M, Gasparis C, Belfort G, Koffas M. Cell-free production of isobutanol: A completely immobilized system. BIORESOURCE TECHNOLOGY 2019; 294:122104. [PMID: 31542497 DOI: 10.1016/j.biortech.2019.122104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 08/30/2019] [Accepted: 08/31/2019] [Indexed: 06/10/2023]
Abstract
A completely immobilized cell-free enzyme reaction system was used to convert ketoisovaleric acid to isobutanol, a desirable biofuel, with a molar yield of 43% and a titer of 2 g/L, which are comparable to high performing in vivo systems (e.g. 41% and 5.4 g/L, respectively, for Clostridium thermocellum). The approach utilizes, for the first time, a series of previously reported enzyme mutants that either overproduce the product or are more stable when compared with their wild type. The selected enzyme variants include keto-acid decarboxylase attached to a maltose binding protein, alcohol dehydrogenase, and formate dehydrogenase. These enzymes were screened for thermal, pH, and product stability to choose optima for this system which were pH 7.4 and 35 °C. This system is designed to address well-known limitations of in vivo systems such as low product concentrations due to product feedback inhibition, instability of cells, and lack of economic product recovery.
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Affiliation(s)
- Matthew Wong
- Howard P. Isermann Department of Chemical and Biological Engineering and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180-3590, United States
| | - Jian Zha
- Howard P. Isermann Department of Chemical and Biological Engineering and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180-3590, United States
| | - Mirco Sorci
- Howard P. Isermann Department of Chemical and Biological Engineering and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180-3590, United States
| | - Christopher Gasparis
- Howard P. Isermann Department of Chemical and Biological Engineering and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180-3590, United States
| | - Georges Belfort
- Howard P. Isermann Department of Chemical and Biological Engineering and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180-3590, United States.
| | - Mattheos Koffas
- Howard P. Isermann Department of Chemical and Biological Engineering and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180-3590, United States.
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14
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Ghosh IN, Martien J, Hebert AS, Zhang Y, Coon JJ, Amador-Noguez D, Landick R. OptSSeq explores enzyme expression and function landscapes to maximize isobutanol production rate. Metab Eng 2019; 52:324-340. [DOI: 10.1016/j.ymben.2018.12.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 11/26/2018] [Accepted: 12/25/2018] [Indexed: 10/27/2022]
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15
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Substitutions of a buried glutamate residue hinder the conformational change in horse liver alcohol dehydrogenase and yield a surprising complex with endogenous 3'-Dephosphocoenzyme A. Arch Biochem Biophys 2018; 653:97-106. [PMID: 30018019 DOI: 10.1016/j.abb.2018.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 06/30/2018] [Accepted: 07/05/2018] [Indexed: 11/22/2022]
Abstract
Glu-267 is highly conserved in alcohol dehydrogenases and buried as a negatively-charged residue in a loop of the NAD coenzyme binding domain. Glu-267 might have a structural role and contribute to a rate-promoting vibration that facilitates catalysis. Substitutions of Glu-267 with histidine or asparagine residues increase the dissociation constants for the coenzymes (NAD+ by ∼40-fold, NADH by ∼200-fold) and significantly decrease catalytic efficiencies by 16-1200-fold various substrates and substituted enzymes. The turnover numbers modestly change with the substitutions, but hydride transfer is at least partially rate-limiting for turnover for alcohol oxidation. X-ray structures of the E267H and E267 N enzymes are similar to the apoenzyme (open) conformation of the wild-type enzyme, and the substitutions are accommodated by local changes in the structure. Surprisingly, the E267H and E267 N enzymes have endogenous (from the expression in E. coli) 3'-dephosphocoenzyme A bound in the active site with the ADP moiety in the NAD binding site and the pantethiene sulfhydryl bound to the catalytic zinc. The kinetics and crystallography show that the substitutions of Glu-267 hinder the conformational change, which occurs when wild-type enzyme binds coenzymes, and affect productive binding of substrates.
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16
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Zhao EM, Zhang Y, Mehl J, Park H, Lalwani MA, Toettcher JE, Avalos JL. Optogenetic regulation of engineered cellular metabolism for microbial chemical production. Nature 2018; 555:683-687. [PMID: 29562237 PMCID: PMC5876151 DOI: 10.1038/nature26141] [Citation(s) in RCA: 207] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 02/13/2018] [Indexed: 12/29/2022]
Abstract
The optimization of engineered metabolic pathways requires careful control over the levels and timing of metabolic enzyme expression1-4. Optogenetic tools are ideal for achieving such precise control, as light can be applied and removed instantly without complex media changes. Here we show that light-controlled transcription can be used to enhance the biosynthesis of valuable products in engineered Saccharomyces cerevisiae. We introduce new optogenetic circuits to shift cells from a light-induced growth phase to a darkness-induced production phase, which allows us to control fermentation purely with light. Furthermore, optogenetic control of engineered pathways enables a new mode of bioreactor operation using periodic light pulses to tune enzyme expression during the production phase of fermentation to increase yields. Using these advances, we control the mitochondrial isobutanol pathway to produce up to 8.49 ± 0.31 g/L of isobutanol and 2.38 ± 0.06 g/L of 2-methyl-1-butanol micro-aerobically from glucose. These results make a compelling case for the application of optogenetics to metabolic engineering for valuable products.
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Affiliation(s)
- Evan M Zhao
- Department of Chemical and Biological Engineering, Hoyt Laboratory, Princeton University, 25 William Street, Princeton, New Jersey 08544, USA
| | - Yanfei Zhang
- Department of Chemical and Biological Engineering, Hoyt Laboratory, Princeton University, 25 William Street, Princeton, New Jersey 08544, USA
| | - Justin Mehl
- Department of Chemical and Biological Engineering, Hoyt Laboratory, Princeton University, 25 William Street, Princeton, New Jersey 08544, USA
| | - Helen Park
- Department of Chemical and Biological Engineering, Hoyt Laboratory, Princeton University, 25 William Street, Princeton, New Jersey 08544, USA
| | - Makoto A Lalwani
- Department of Chemical and Biological Engineering, Hoyt Laboratory, Princeton University, 25 William Street, Princeton, New Jersey 08544, USA
| | - Jared E Toettcher
- Department of Molecular Biology, 140 Lewis Thomas Laboratory, Washington Road, Princeton, New Jersey 08544, USA
| | - José L Avalos
- Department of Chemical and Biological Engineering, Hoyt Laboratory, Princeton University, 25 William Street, Princeton, New Jersey 08544, USA.,The Andlinger Center for Energy and the Environment, Princeton University, 86 Olden Street, Princeton, New Jersey 08544, USA
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17
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Uchida M, McCoy K, Fukuto M, Yang L, Yoshimura H, Miettinen HM, LaFrance B, Patterson DP, Schwarz B, Karty JA, Prevelige PE, Lee B, Douglas T. Modular Self-Assembly of Protein Cage Lattices for Multistep Catalysis. ACS NANO 2018; 12:942-953. [PMID: 29131580 PMCID: PMC5870838 DOI: 10.1021/acsnano.7b06049] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The assembly of individual molecules into hierarchical structures is a promising strategy for developing three-dimensional materials with properties arising from interaction between the individual building blocks. Virus capsids are elegant examples of biomolecular nanostructures, which are themselves hierarchically assembled from a limited number of protein subunits. Here, we demonstrate the bio-inspired modular construction of materials with two levels of hierarchy: the formation of catalytically active individual virus-like particles (VLPs) through directed self-assembly of capsid subunits with enzyme encapsulation, and the assembly of these VLP building blocks into three-dimensional arrays. The structure of the assembled arrays was successfully altered from an amorphous aggregate to an ordered structure, with a face-centered cubic lattice, by modifying the exterior surface of the VLP without changing its overall morphology, to modulate interparticle interactions. The assembly behavior and resultant lattice structure was a consequence of interparticle interaction between exterior surfaces of individual particles and thus independent of the enzyme cargos encapsulated within the VLPs. These superlattice materials, composed of two populations of enzyme-packaged VLP modules, retained the coupled catalytic activity in a two-step reaction for isobutanol synthesis. This study demonstrates a significant step toward the bottom-up fabrication of functional superlattice materials using a self-assembly process across multiple length scales and exhibits properties and function that arise from the interaction between individual building blocks.
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Affiliation(s)
- Masaki Uchida
- Department of Chemistry, Indiana University, 800 East Kirkwood Ave., Bloomington, IN 47405, USA
| | - Kimberly McCoy
- Department of Chemistry, Indiana University, 800 East Kirkwood Ave., Bloomington, IN 47405, USA
| | - Masafumi Fukuto
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
- Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Lin Yang
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Hideyuki Yoshimura
- Department of Chemistry, Indiana University, 800 East Kirkwood Ave., Bloomington, IN 47405, USA
- Department of Physics, Meiji University, 1-1-1 Higashimita, Tama-ku, Kawasaki, 214-8571, Japan
| | - Heini M. Miettinen
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717, USA
| | - Ben LaFrance
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, USA
| | - Dustin P. Patterson
- Department of Chemistry and Biochemistry, University of Texas at Tyler, Tyler, Texas 75799, USA
| | - Benjamin Schwarz
- Department of Chemistry, Indiana University, 800 East Kirkwood Ave., Bloomington, IN 47405, USA
| | - Jonathan A. Karty
- Department of Chemistry, Indiana University, 800 East Kirkwood Ave., Bloomington, IN 47405, USA
| | - Peter E. Prevelige
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Byeongdu Lee
- X-ray science division, Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Ave., Argonne, IL 60439, USA
| | - Trevor Douglas
- Department of Chemistry, Indiana University, 800 East Kirkwood Ave., Bloomington, IN 47405, USA
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18
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Qu G, Lonsdale R, Yao P, Li G, Liu B, Reetz MT, Sun Z. Methodology Development in Directed Evolution: Exploring Options when Applying Triple-Code Saturation Mutagenesis. Chembiochem 2018; 19:239-246. [PMID: 29314451 DOI: 10.1002/cbic.201700562] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Ge Qu
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; 32 West 7th Avenue Tianjin Airport Economic Area Tianjin 300308 China
| | - Richard Lonsdale
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
- Fachbereich Chemie; Philipps-Universität Marburg; Hans-Meerwein-Strasse 35032 Marburg Germany
| | - Peiyuan Yao
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; 32 West 7th Avenue Tianjin Airport Economic Area Tianjin 300308 China
| | - Guangyue Li
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
- Fachbereich Chemie; Philipps-Universität Marburg; Hans-Meerwein-Strasse 35032 Marburg Germany
| | - Beibei Liu
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; 32 West 7th Avenue Tianjin Airport Economic Area Tianjin 300308 China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; 32 West 7th Avenue Tianjin Airport Economic Area Tianjin 300308 China
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
- Fachbereich Chemie; Philipps-Universität Marburg; Hans-Meerwein-Strasse 35032 Marburg Germany
| | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; 32 West 7th Avenue Tianjin Airport Economic Area Tianjin 300308 China
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19
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Dhoke GV, Ensari Y, Davari MD, Ruff AJ, Schwaneberg U, Bocola M. What's My Substrate? Computational Function Assignment of Candida parapsilosis ADH5 by Genome Database Search, Virtual Screening, and QM/MM Calculations. J Chem Inf Model 2016; 56:1313-23. [PMID: 27387009 DOI: 10.1021/acs.jcim.6b00076] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Zinc-dependent medium chain reductase from Candida parapsilosis can be used in the reduction of carbonyl compounds to pharmacologically important chiral secondary alcohols. To date, the nomenclature of cpADH5 is differing (CPCR2/RCR/SADH) in the literature, and its natural substrate is not known. In this study, we utilized a substrate docking based virtual screening method combined with KEGG, MetaCyc pathway, and Candida genome databases search for the discovery of natural substrates of cpADH5. The virtual screening of 7834 carbonyl compounds from the ZINC database provided 94 aldehydes or methyl/ethyl ketones as putative carbonyl substrates. Out of which, 52 carbonyl substrates of cpADH5 with catalytically active docking pose were identified by employing mechanism based substrate docking protocol. Comparison of the virtual screening results with KEGG, MetaCyc database search, and Candida genome pathway analysis suggest that cpADH5 might be involved in the Ehrlich pathway (reduction of fusel aldehydes in leucine, isoleucine, and valine degradation). Our QM/MM calculations and experimental activity measurements affirmed that butyraldehyde substrates are the potential natural substrates of cpADH5, suggesting a carbonyl reductase role for this enzyme in butyraldehyde reduction in aliphatic amino acid degradation pathways. Phylogenetic tree analysis of known ADHs from Candida albicans shows that cpADH5 is close to caADH5. We therefore propose, according to the experimental substrate identification and sequence similarity, the common name butyraldehyde dehydrogenase cpADH5 for Candida parapsilosis CPCR2/RCR/SADH.
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Affiliation(s)
- Gaurao V Dhoke
- Lehrstuhl für Biotechnologie, RWTH Aachen University , Worringerweg 3, 52074 Aachen, Germany
| | - Yunus Ensari
- Lehrstuhl für Biotechnologie, RWTH Aachen University , Worringerweg 3, 52074 Aachen, Germany
| | - Mehdi D Davari
- Lehrstuhl für Biotechnologie, RWTH Aachen University , Worringerweg 3, 52074 Aachen, Germany
| | - Anna Joëlle Ruff
- Lehrstuhl für Biotechnologie, RWTH Aachen University , Worringerweg 3, 52074 Aachen, Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University , Worringerweg 3, 52074 Aachen, Germany.,DWI-Leibniz Institut für Interaktive Materialien , Forckenbeckstraße 50, 52056 Aachen, Germany
| | - Marco Bocola
- Lehrstuhl für Biotechnologie, RWTH Aachen University , Worringerweg 3, 52074 Aachen, Germany
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20
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Cahn JKB, Baumschlager A, Brinkmann-Chen S, Arnold FH. Mutations in adenine-binding pockets enhance catalytic properties of NAD(P)H-dependent enzymes. Protein Eng Des Sel 2016; 29:31-8. [PMID: 26512129 PMCID: PMC4678007 DOI: 10.1093/protein/gzv057] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 09/28/2015] [Indexed: 11/14/2022] Open
Abstract
NAD(P)H-dependent enzymes are ubiquitous in metabolism and cellular processes and are also of great interest for pharmaceutical and industrial applications. Here, we present a structure-guided enzyme engineering strategy for improving catalytic properties of NAD(P)H-dependent enzymes toward native or native-like reactions using mutations to the enzyme's adenine-binding pocket, distal to the site of catalysis. Screening single-site saturation mutagenesis libraries identified mutations that increased catalytic efficiency up to 10-fold in 7 out of 10 enzymes. The enzymes improved in this study represent three different cofactor-binding folds (Rossmann, DHQS-like, and FAD/NAD binding) and utilize both NADH and NADPH. Structural and biochemical analyses show that the improved activities are accompanied by minimal changes in other properties (cooperativity, thermostability, pH optimum, uncoupling), and initial tests on two enzymes (ScADH6 and EcFucO) show improved functionality in Escherichia coli.
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Affiliation(s)
- J K B Cahn
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E California Blvd, MC 210-41, Pasadena, CA 91125, USA
| | - A Baumschlager
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E California Blvd, MC 210-41, Pasadena, CA 91125, USA
| | - S Brinkmann-Chen
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E California Blvd, MC 210-41, Pasadena, CA 91125, USA
| | - F H Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E California Blvd, MC 210-41, Pasadena, CA 91125, USA
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21
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Combinatorial application of two aldehyde oxidoreductases on isobutanol production in the presence of furfural. ACTA ACUST UNITED AC 2016; 43:37-44. [DOI: 10.1007/s10295-015-1718-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 11/29/2015] [Indexed: 11/26/2022]
Abstract
Abstract
Furfural is a toxic by-product formulated from pretreatment processes of lignocellulosic biomass. In order to utilize the lignocellulosic biomass on isobutanol production, inhibitory effect of the furfural on isobutanol production was investigated and combinatorial application of two oxidoreductases, FucO and YqhD, was suggested as an alternative strategy. Furfural decreased cell growth and isobutanol production when only YqhD or FucO was employed as an isobutyraldehyde oxidoreductase. However, combinatorial overexpression of FucO and YqhD could overcome the inhibitory effect of furfural giving higher isobutanol production by 110 % compared with overexpression of YqhD. The combinatorial oxidoreductases increased furfural detoxification rate 2.1-fold and also accelerated glucose consumption 1.4-fold. When it compares to another known system increasing furfural tolerance, membrane-bound transhydrogenase (pntAB), the combinatorial aldehyde oxidoreductases were better on cell growth and production. Thus, to control oxidoreductases is important to produce isobutanol using furfural-containing biomass and the combinatorial overexpression of FucO and YqhD can be an alternative strategy.
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22
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Boock JT, Gupta A, Prather KLJ. Screening and modular design for metabolic pathway optimization. Curr Opin Biotechnol 2015; 36:189-98. [DOI: 10.1016/j.copbio.2015.08.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 08/07/2015] [Accepted: 08/10/2015] [Indexed: 11/26/2022]
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23
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Loderer C, Dhoke GV, Davari MD, Kroutil W, Schwaneberg U, Bocola M, Ansorge-Schumacher MB. Investigation of Structural Determinants for the Substrate Specificity in the Zinc-Dependent Alcohol Dehydrogenase CPCR2 fromCandida parapsilosis. Chembiochem 2015; 16:1512-9. [DOI: 10.1002/cbic.201500100] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Indexed: 11/06/2022]
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24
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Nealon CM, Musa MM, Patel JM, Phillips RS. Controlling Substrate Specificity and Stereospecificity of Alcohol Dehydrogenases. ACS Catal 2015. [DOI: 10.1021/cs501457v] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christopher M. Nealon
- Department
of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Musa M. Musa
- Department
of Chemistry, King Fahd University of Petroleum and Minerals, Dhahran 31261, Kingdom of Saudi Arabia
| | - Jay M. Patel
- Department
of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Robert S. Phillips
- Department
of Chemistry, University of Georgia, Athens, Georgia 30602, United States
- Department
of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
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25
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Engineering redox balance through cofactor systems. Trends Biotechnol 2014; 32:337-43. [DOI: 10.1016/j.tibtech.2014.04.003] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 03/26/2014] [Accepted: 04/02/2014] [Indexed: 12/12/2022]
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26
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Recent advances in engineering proteins for biocatalysis. Biotechnol Bioeng 2014; 111:1273-87. [DOI: 10.1002/bit.25240] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 02/10/2014] [Accepted: 03/19/2014] [Indexed: 01/14/2023]
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27
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Man H, Loderer C, Ansorge-Schumacher MB, Grogan G. Structure of NADH-Dependent Carbonyl Reductase (CPCR2) from Candida parapsilosis
Provides Insight into Mutations that Improve Catalytic Properties. ChemCatChem 2014. [DOI: 10.1002/cctc.201300788] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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28
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Blikstad C, Dahlström KM, Salminen TA, Widersten M. Stereoselective Oxidation of Aryl-Substituted Vicinal Diols into Chiral α-Hydroxy Aldehydes by Re-Engineered Propanediol Oxidoreductase. ACS Catal 2013. [DOI: 10.1021/cs400824h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Cecilia Blikstad
- Department
of Chemistry−BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Käthe M. Dahlström
- Structural
Bioinformatics Laboratory, Åbo Akademi University, Tykistökatu
6A, FIN-20520 Turku, Finland
| | - Tiina A. Salminen
- Structural
Bioinformatics Laboratory, Åbo Akademi University, Tykistökatu
6A, FIN-20520 Turku, Finland
| | - Mikael Widersten
- Department
of Chemistry−BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
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29
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Wang Y, San KY, Bennett GN. Cofactor engineering for advancing chemical biotechnology. Curr Opin Biotechnol 2013; 24:994-9. [PMID: 23611567 DOI: 10.1016/j.copbio.2013.03.022] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 03/21/2013] [Accepted: 03/22/2013] [Indexed: 11/26/2022]
Abstract
Cofactors provide redox carriers for biosynthetic reactions, catabolic reactions and act as important agents in transfer of energy for the cell. Recent advances in manipulating cofactors include culture conditions or additive alterations, genetic modification of host pathways for increased availability of desired cofactor, changes in enzyme cofactor specificity, and introduction of novel redox partners to form effective circuits for biochemical processes and biocatalysts. Genetic strategies to employ ferredoxin, NADH and NADPH most effectively in natural or novel pathways have improved yield and efficiency of large-scale processes for fuels and chemicals and have been demonstrated with a variety of microbial organisms.
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Affiliation(s)
- Yipeng Wang
- Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77005, USA
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