Coenzyme engineering of a hyperthermophilic 6-phosphogluconate dehydrogenase from NADP+ to NAD+ with its application to biobatteries

Chen, Hui; Zhu, Zhiguang; Huang, Rui; Zhang, Yi-Heng Percival

doi:10.1038/srep36311

Title: Coenzyme engineering of a hyperthermophilic 6-phosphogluconate dehydrogenase from NADP⁺ to NAD⁺ with its application to biobatteries

Journal Article · Wed Nov 02 00:00:00 EDT 2016 · Scientific Reports

DOI:https://doi.org/10.1038/srep36311· OSTI ID:1363908

Chen, Hui ^[1]; Zhu, Zhiguang ^[2]; Huang, Rui ^[1]; Zhang, Yi-Heng Percival ^[3]

Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States)
Cell Free Bioinnovations Inc., Blacksburg, VA (United States); Chinese Academy of Sciences, Tianjin (China)
Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States); Cell Free Bioinnovations Inc., Blacksburg, VA (United States); Chinese Academy of Sciences, Tianjin (China)

Engineering the coenzyme specificity of redox enzymes plays an important role in metabolic engineering, synthetic biology, and biocatalysis, but it has rarely been applied to bioelectrochemistry. Here we develop a rational design strategy to change the coenzyme specificity of 6-phosphogluconate dehydrogenase (6PGDH) from a hyperthermophilic bacterium Thermotoga maritima from its natural coenzyme NADP⁺ to NAD⁺. Through amino acid-sequence alignment of NADP⁺- and NAD⁺-preferred 6PGDH enzymes and computer-aided substrate-coenzyme docking, the key amino acid residues responsible for binding the phosphate group of NADP⁺ were identified. Four mutants were obtained via site-directed mutagenesis. The best mutant N32E/R33I/T34I exhibited a ~6.4 × 10⁴-fold reversal of the coenzyme selectivity from NADP⁺ to NAD⁺. The maximum power density and current density of the biobattery catalyzed by the mutant were 0.135 mW cm^-2 and 0.255 mA cm^-2, ~25% higher than those obtained from the wide-type 6PGDH-based biobattery at the room temperature. By using this 6PGDH mutant, the optimal temperature of running the biobattery was as high as 65 °C, leading to a high power density of 1.75 mW cm^-2. As a result, this study demonstrates coenzyme engineering of a hyperthermophilic 6PGDH and its application to high-temperature biobatteries.

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Research Organization:: Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States)

Sponsoring Organization:: USDOE Office of Energy Efficiency and Renewable Energy (EERE), Sustainable Transportation Office. Bioenergy Technologies Office (BETO)

Grant/Contract Number:: EE0006968

OSTI ID:: 1363908

Journal Information:: Scientific Reports, Vol. 6, Issue 1; ISSN 2045-2322

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 27 works

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References (44)

Protein Engineering - An Option for Enzymatic Biofuel Cell Design Güven, Güray; Prodanovic, Radivoje; Schwaneberg, Ulrich Electroanalysis, Vol. 22, Issue 7-8 https://doi.org/10.1002/elan.200980017	journal	February 2010
Stability of NADPH: effect of various factors on the kinetics of degradation. Wu, J. T.; Wu, L. H.; Knight, J. A. Clinical Chemistry, Vol. 32, Issue 2 https://doi.org/10.1093/clinchem/32.2.314	journal	February 1986
Biohydrogenation from Biomass Sugar Mediated by In Vitro Synthetic Enzymatic Pathways Wang, Yiran; Huang, Weidong; Sathitsuksanoh, Noppadon Chemistry & Biology, Vol. 18, Issue 3 https://doi.org/10.1016/j.chembiol.2010.12.019	journal	March 2011
Relaxing the Nicotinamide Cofactor Specificity of Phosphite Dehydrogenase by Rational Design ^† Woodyer, Ryan; van der Donk, Wilfred A.; Zhao, Huimin Biochemistry, Vol. 42, Issue 40 https://doi.org/10.1021/bi035018b	journal	October 2003
Enzymatic Biofuel Cells for Implantable and Microscale Devices Calabrese Barton, Scott; Gallaway, Josh; Atanassov, Plamen Chemical Reviews, Vol. 104, Issue 10 https://doi.org/10.1021/cr020719k	journal	October 2004
Engineering a d-lactate dehydrogenase that can super-efficiently utilize NADPH and NADH as cofactors Meng, Hengkai; Liu, Pi; Sun, Hongbing Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep24887	journal	April 2016
Engineered ketol-acid reductoisomerase and alcohol dehydrogenase enable anaerobic 2-methylpropan-1-ol production at theoretical yield in Escherichia coli Bastian, Sabine; Liu, Xiang; Meyerowitz, Joseph T. Metabolic Engineering, Vol. 13, Issue 3, p. 345-352 https://doi.org/10.1016/j.ymben.2011.02.004	journal	May 2011
Crystallographic analysis and structure-guided engineering of NADPH-dependent Ralstonia sp. Alcohol dehydrogenase toward NADH cosubstrate specificity: Structure-Guided Engineering of RasADH Lerchner, Alexandra; Jarasch, Alexander; Meining, Winfried Biotechnology and Bioengineering, Vol. 110, Issue 11 https://doi.org/10.1002/bit.24956	journal	July 2013
Conformational changes associated with cofactor/substrate binding of 6-phosphogluconate dehydrogenase from Escherichia coli and Klebsiella pneumoniae: Implications for enzyme mechanism Chen, Ying-Yin; Ko, Tzu-Ping; Chen, Wei-Hung Journal of Structural Biology, Vol. 169, Issue 1 https://doi.org/10.1016/j.jsb.2009.08.006	journal	January 2010
Enzyme-catalyzed organic synthesis: NAD(P)H cofactor regeneration by using glucose-6-phosphate and the glucose-5-phosphate dehydrogenase from Leuconostoc mesenteroides Wong, Chi-Huey; Whitesides, George M. Journal of the American Chemical Society, Vol. 103, Issue 16 https://doi.org/10.1021/ja00406a037	journal	August 1981
High-Throughput Screening of Coenzyme Preference Change of Thermophilic 6-Phosphogluconate Dehydrogenase from NADP+ to NAD+ Huang, Rui; Chen, Hui; Zhong, Chao Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep32644	journal	September 2016
A high-energy-density sugar biobattery based on a synthetic enzymatic pathway Zhu, Zhiguang; Kin Tam, Tsz; Sun, Fangfang Nature Communications, Vol. 5, Issue 1 https://doi.org/10.1038/ncomms4026	journal	January 2014
A Bioanode Using Thermostable Alcohol Dehydrogenase for an Ethanol Biofuel Cell Operating at High Temperatures Kontani, Aya; Masuda, Miyuki; Matsumura, Hirotoshi Electroanalysis, Vol. 26, Issue 4 https://doi.org/10.1002/elan.201300514	journal	March 2014
Alteration of the specificity of the cofactor-binding pocket of Corynebacterium 2,5-diketo-D-gluconic acid reductase A Banta, Scott; Swanson, Barbara A.; Wu, Shan Protein Engineering, Design and Selection, Vol. 15, Issue 2 https://doi.org/10.1093/protein/15.2.131	journal	February 2002
New biotechnology paradigm: cell-free biosystems for biomanufacturing Rollin, Joseph A.; Tam, Tsz Kin; Zhang, Y. -H. Percival Green Chemistry, Vol. 15, Issue 7 https://doi.org/10.1039/c3gc40625c	journal	January 2013
Toward low-cost biomanufacturing through in vitro synthetic biology: bottom-up design Zhang, Y. -H. Percival; Myung, Suwan; You, Chun Journal of Materials Chemistry, Vol. 21, Issue 47 https://doi.org/10.1039/c1jm12078f	journal	January 2011
Molecular Basis for Enantioselectivity of Lipase from Pseudomonas cepacia toward Primary Alcohols. Modeling, Kinetics, and Chemical Modification of Tyr29 to Increase or Decrease Enantioselectivity Tuomi, W. Victor; Kazlauskas, Romas J. The Journal of Organic Chemistry, Vol. 64, Issue 8 https://doi.org/10.1021/jo981783y	journal	April 1999
Protein engineering in bioelectrocatalysis Wong, Tuck Seng; Schwaneberg, Ulrich Current Opinion in Biotechnology, Vol. 14, Issue 6 https://doi.org/10.1016/j.copbio.2003.09.008	journal	December 2003
Enzyme catalysed biofuel cells Cooney, M. J.; Svoboda, V.; Lau, C. Energy & Environmental Science, Vol. 1, Issue 3 https://doi.org/10.1039/b809009b	journal	January 2008
Uncovering rare NADH-preferring ketol-acid reductoisomerases Brinkmann-Chen, S.; Cahn, J. K. B.; Arnold, F. H. Metabolic Engineering, Vol. 26 https://doi.org/10.1016/j.ymben.2014.08.003	journal	November 2014
Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega Sievers, Fabian; Wilm, Andreas; Dineen, David Molecular Systems Biology, Vol. 7, Issue 1 https://doi.org/10.1038/msb.2011.75	journal	January 2011
Deep oxidation of glucose in enzymatic fuel cells through a synthetic enzymatic pathway containing a cascade of two thermostable dehydrogenases Zhu, Zhiguang; Sun, Fangfang; Zhang, Xiaozhou Biosensors and Bioelectronics, Vol. 36, Issue 1 https://doi.org/10.1016/j.bios.2012.04.001	journal	June 2012
Strategies for the discovery and engineering of enzymes for biocatalysis Davids, Timo; Schmidt, Marlen; Böttcher, Dominique Current Opinion in Chemical Biology, Vol. 17, Issue 2 https://doi.org/10.1016/j.cbpa.2013.02.022	journal	April 2013
Enzyme-based biofuel cells Minteer, Shelley D.; Liaw, Bor Yann; Cooney, Michael J. Current Opinion in Biotechnology, Vol. 18, Issue 3 https://doi.org/10.1016/j.copbio.2007.03.007	journal	June 2007
Structure of NADP ⁺ -dependent glutamate dehydrogenase from Escherichia coli - reflections on the basis of coenzyme specificity in the family of glutamate dehydrogenases Sharkey, Michael A.; Oliveira, Tânia F.; Engel, Paul C. FEBS Journal, Vol. 280, Issue 18 https://doi.org/10.1111/febs.12439	journal	August 2013
6-Phosphogluconate dehydrogenase from Lactococcus lactis: a role for arginine residues in binding substrate and coenzyme Tetaud, Emmanuel; Hanau, Stefania; Wells, Jeremy M. Biochemical Journal, Vol. 338, Issue 1 https://doi.org/10.1042/bj3380055	journal	February 1999
Sequence logos: a new way to display consensus sequences Schneider, Thomas D.; Stephens, R. Michael Nucleic Acids Research, Vol. 18, Issue 20 https://doi.org/10.1093/nar/18.20.6097	journal	January 1990
Regulated functional alternative splicing in Drosophila Venables, J. P.; Tazi, J.; Juge, F. Nucleic Acids Research, Vol. 40, Issue 1 https://doi.org/10.1093/nar/gkr648	journal	September 2011
Engineering the third wave of biocatalysis Bornscheuer, U. T.; Huisman, G. W.; Kazlauskas, R. J. Nature, Vol. 485, Issue 7397 https://doi.org/10.1038/nature11117	journal	May 2012
Novel expression hosts for complex secondary metabolite megasynthetases: Production of myxochromide in the thermopilic isolate Corallococcus macrosporus GT-2 Perlova, Olena; Gerth, Klaus; Kuhlmann, Silvia Microbial Cell Factories, Vol. 8, Issue 1 https://doi.org/10.1186/1475-2859-8-1	journal	January 2009
Engineering Cofactor Preference of Ketone Reducing Biocatalysts: A Mutagenesis Study on a γ-Diketone Reductase from the Yeast Saccharomyces cerevisiae Serving as an Example Katzberg, Michael; Skorupa-Parachin, Nàdia; Gorwa-Grauslund, Marie-Françoise International Journal of Molecular Sciences, Vol. 11, Issue 4 https://doi.org/10.3390/ijms11041735	journal	April 2010
Biofuel cell system employing thermostable glucose dehydrogenase Okuda-Shimazaki, Junko; Kakehi, Noriko; Yamazaki, Tomohiko Biotechnology Letters, Vol. 30, Issue 10 https://doi.org/10.1007/s10529-008-9749-7	journal	May 2008
Mediatorless high-power glucose biofuel cells based on compressed carbon nanotube-enzyme electrodes Zebda, Abdelkader; Gondran, Chantal; Le Goff, Alan Nature Communications, Vol. 2, Issue 1 https://doi.org/10.1038/ncomms1365	journal	June 2011
Enzymatic biofuel cells utilizing a biomimetic cofactor Campbell, Elliot; Meredith, Matthew; Minteer, Shelley D. Chemical Communications, Vol. 48, Issue 13 https://doi.org/10.1039/c2cc16156g	journal	January 2012
Thermophilic biocathode with bilirubin oxidase from Bacillus pumilus Suraniti, Emmanuel; Tsujimura, Seiya; Durand, Fabien Electrochemistry Communications, Vol. 26 https://doi.org/10.1016/j.elecom.2012.10.004	journal	January 2013
WebLogo: A Sequence Logo Generator Crooks, Gavin E.; Hon, Gary; Chandonia, John-Marc Genome Research, Vol. 14, Issue 6, p. 1188-1190 https://doi.org/10.1101/gr.849004	journal	May 2004
General approach to reversing ketol-acid reductoisomerase cofactor dependence from NADPH to NADH Brinkmann-Chen, S.; Flock, T.; Cahn, J. K. B. Proceedings of the National Academy of Sciences, Vol. 110, Issue 27, p. 10946-10951 https://doi.org/10.1073/pnas.1306073110	journal	June 2013
A high-power glucose/oxygen biofuel cell operating under quiescent conditions Sakai, Hideki; Nakagawa, Takaaki; Tokita, Yuichi Energy Environ. Sci., Vol. 2, Issue 1 https://doi.org/10.1039/B809841G	journal	January 2009
The 2′-Phosphate of NADP Is Responsible for Proper Orientation of the Nicotinamide Ring in the Oxidative Decarboxylation Reaction Catalyzed by Sheep Liver 6-Phosphogluconate Dehydrogenase Li, Lei; Cook, Paul F. Journal of Biological Chemistry, Vol. 281, Issue 48 https://doi.org/10.1074/jbc.M604609200	journal	September 2006
Complete Reversal of Coenzyme Specificity of Xylitol Dehydrogenase and Increase of Thermostability by the Introduction of Structural Zinc Watanabe, Seiya; Kodaki, Tsutomu; Makino, Keisuke Journal of Biological Chemistry, Vol. 280, Issue 11 https://doi.org/10.1074/jbc.M409443200	journal	December 2004
Simple Cloning via Direct Transformation of PCR Product (DNA Multimer) to Escherichia coli and Bacillus subtilis You, Chun; Zhang, Xiao-Zhou; Zhang, Y. -H. Percival Applied and Environmental Microbiology, Vol. 78, Issue 5 https://doi.org/10.1128/AEM.07105-11	journal	December 2011
PROCHECK: a program to check the stereochemical quality of protein structures Laskowski, R. A.; MacArthur, M. W.; Moss, D. S. Journal of Applied Crystallography, Vol. 26, Issue 2 https://doi.org/10.1107/S0021889892009944	journal	April 1993
A High-Power Glucose/Oxygen Biofuel Cell Operating under Quiescent Conditions Sakai, Hideki; Nakagawa, Takaaki; Mita, Hiroki ECS Meeting Abstracts, Vol. MA2008-02, Issue 14, p. 1432-1432 https://doi.org/10.1149/ma2008-02/14/1432	journal	August 2008
Enzymatic Biofuel Cells for Implantable and Microscale Devices Calabrese Barton, Scott; Gallaway, Josh; Atanassov, Plamen ChemInform, Vol. 35, Issue 51 https://doi.org/10.1002/chin.200451259	journal	December 2004

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Strategies and Methodologies for Developing Microbial Detoxification Systems to Mitigate Mycotoxins Zhu, Yan; Hassan, Yousef; Lepp, Dion Toxins, Vol. 9, Issue 4 https://doi.org/10.3390/toxins9040130	journal	April 2017

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Title: Coenzyme engineering of a hyperthermophilic 6-phosphogluconate dehydrogenase from NADP+ to NAD+ with its application to biobatteries

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Title: Coenzyme engineering of a hyperthermophilic 6-phosphogluconate dehydrogenase from NADP⁺ to NAD⁺ with its application to biobatteries