Abstract
Formate dehydrogenase (FDH) is a D-2-hydroxy acid dehydrogenase, which can reversibly reduce CO2 to formate and thus act as non-photosynthetic CO2 reductase. In order to increase catalytic efficiency of formate dehydrogenase for CO2 reduction, two mutants V328I/F285W and V354G/F285W were obtained of which reduction activity was about two times more than the parent CbFDHM2, and the formate production from CO2 catalyzed by mutants were 2.9 and 2.7-fold higher than that of the parent CbFDHM2. The mutants had greater potential in CO2 reduction. The optimal temperature for V328I/F285W and V354G/F285W was 55 °C, and they showed increasement of relative activity under 45 °C to 55 °C compared with parent. The optimal pH for the mutants was 9.0, and they showed excellent stability in pH 4.0–11.5. The kcat/Km values of mutants were 1.75 times higher than that of the parent. Then the molecular basis for its improvement of biochemical characteristics were preliminarily elucidated by computer-aided methods. All of these results further established a solid foundation for molecular modification of formate dehydrogenase and CO2 reduction.
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The data that support the findings of this study are available on request from the corresponding author.
References
Altaş N, Aslan AS, Karataş E, Chronopoulou E, Labrou NE, Binay B (2017) Heterologous production of extreme alkaline thermostable NAD + -dependent formate dehydrogenase with wide-range pH activity from Myceliophthora thermophila. Process Biochem 61:110–118. https://doi.org/10.1016/j.procbio.2017.06.017
Appel AM, Bercaw JE, Bocarsly AB, Dobbek H, DuBois DL, Dupuis M, Ferry JG, Fujita E, Hille R, Kenis PJA, Kerfeld CA, Morris RH, Peden CHF, Portis AR, Ragsdale SW, Rauchfuss TB, Reek JNH, Seefeldt LC, Thauer RK, Waldrop GL (2013) Frontiers, opportunities, and challenges in biochemical and chemical catalysis of CO2 fixation. Chem Rev 113(8):6621–6658. https://doi.org/10.1021/cr300463y
Aslan AS, Valjakka J, Ruupunen J, Yildirim D, Turner NJ, Turunen O, Binay B (2017) Chaetomium thermophilum formate dehydrogenase has high activity in the reduction of hydrogen carbonate (HCO3 -) to formate. Protein Eng Des Sel 30(1):47–55. https://doi.org/10.1093/protein/gzw062
Bernal C, Rodriguez K, Martinez R (2018) Integrating enzyme immobilization and protein engineering: an alternative path for the development of novel and improved industrial biocatalysts. Biotechnol Adv 36(5):1470–1480. https://doi.org/10.1016/j.biotechadv.2018.06.002
Bommarius AS, Karau A (2005) Deactivation of formate dehydrogenase (FDH) in solution and at gas-liquid interfaces. Biotechnol Prog 21(6):1663–1672. https://doi.org/10.1021/bp050249q
Bradford M (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72:248–254
Cakar MM, Ruupunen J, Mangas-Sanchez J, Birmingham WR, Yildirim D, Turunen O, Turner NJ, Valjakka J, Binay B (2020) Engineered formate dehydrogenase from Chaetomium thermophilum, a promising enzymatic solution for biotechnical CO(2) fixation. Biotechnol Lett 42(11):2251–2262. https://doi.org/10.1007/s10529-020-02937-7
Chen F-F, Liu Y-Y, Zheng G-W, Xu J-H (2015) Asymmetric amination of secondary alcohols by using a redox-neutral two-enzyme cascade. ChemCatChem 7(23):3838–3841. https://doi.org/10.1002/cctc.201500785
Choe H, Ha JM, Joo JC, Kim H, Yoon HJ, Kim S, Son SH, Gengan RM, Jeon ST, Chang R, Jung KD, Kim YH, Lee HH (2015) Structural insights into the efficient CO2-reducing activity of an NAD-dependent formate dehydrogenase from Thiobacillus sp. KNK65MA. Acta Crystallogr D Biol Crystallogr 71(2):313–23. https://doi.org/10.1107/S1399004714025474
Cordas CM, Campaniço M, Baptista R, Maia LB, Moura I, Moura JJG (2019) Direct electrochemical reduction of carbon dioxide by a molybdenum-containing formate dehydrogenase. J Inorg Biochem 196:110694. https://doi.org/10.1016/j.jinorgbio.2019.110694
Du C, Li Y, He Y, Su L, Wang H, Yuan W, Bai F (2022) Fixing carbon dioxide in situ during ethanol production by formate dehydrogenase. Green Chem 24(18):6989–6999. https://doi.org/10.1039/d2gc02311c
Gao S-J, Wang J-Q, Wu M-C, Zhang H-M, Yin X, Li J-F (2013) Engineering hyperthermostability into a mesophilic family 11 xylanase from Aspergillus oryzae by in silico design of N-terminus substitution. Biotechnol Bioeng 110(4):1028–1038. https://doi.org/10.1002/bit.24768
Hu D, Zong XC, Xue F, Li C, Hu BC, Wu MC (2020) Manipulating regioselectivity of an epoxide hydrolase for single enzymatic synthesis of (R)-1,2-diols from racemic epoxides. Chem Commun (camb) 56(18):2799–2802. https://doi.org/10.1039/d0cc00283f
Kim D, Sathesh-Prabu C, JooYeon Y, Lee SK (2019) High-level production of 4-hydroxyvalerate from levulinic acid via whole-cell biotransformation decoupled from cell metabolism. J Agric Food Chem 67(38):10678–10684. https://doi.org/10.1021/acs.jafc.9b04304
Li A, Yuchi Q, Li X, Pang W, Li B, Xue F, Zhang L (2019a) Discovery of a novel ortho-haloacetophenones-specific carbonyl reductase from Bacillus aryabhattai and insight into the molecular basis for its catalytic performance. Int J Biol Macromol 138:781–790. https://doi.org/10.1016/j.ijbiomac.2019.07.153
Li M, Meng X, Sun Z, Zhu C, Ji H (2019b) Effects of NADH availability on 3-phenyllactic acid production by lactobacillus plantarum expressing formate dehydrogenase. Curr Microbiol 76(6):706–712. https://doi.org/10.1007/s00284-019-01681-0
Liao Q, Liu W, Meng Z (2022) Strategies for overcoming the limitations of enzymatic carbon dioxide reduction. Biotechnol Adv 60:108024. https://doi.org/10.1016/j.biotechadv.2022.108024
Min K, Moon M, Park GW, Lee JP, Kim SJ, Lee JS (2022) Newly explored formate dehydrogenases from Clostridium species catalyze carbon dioxide to formate. Bioresour Technol 348:126832. https://doi.org/10.1016/j.biortech.2022.126832
Miyaji A, Amao Y (2020) Theoretical study on CO(2) reduction catalyzed by formate dehydrogenase using the cation radical of a bipyridinium salt with an ionic substituent as a co-enzyme. Phys Chem Chem Phys 22(46):26987–26994. https://doi.org/10.1039/d0cp05261b
Nikolaos ELABROUDJR (2001) Active-site characterization of Candida boidinii formate dehydrogenase. Biochem J 354:455–463. https://doi.org/10.1042/0264-6021:3540455
Obert R, Dave BC (1999) Enzymatic conversion of carbon dioxide to methanol: enhanced methanol production in silica sol-gel matrices. J Am Chem Soc 121(51):12192–12193. https://doi.org/10.1021/ja991899r
Oliveira AR, Mota C, Mourato C, Domingos RM, Santos MFA, Gesto D, Guigliarelli B, Santos-Silva T, Romão MJ, Cardoso Pereira IA (2020) Toward the mechanistic understanding of enzymatic CO2 reduction. ACS Catal 10(6):3844–3856. https://doi.org/10.1021/acscatal.0c00086
Rouf S, Greish YE, Al-Zuhair S (2021) Immobilization of formate dehydrogenase in metal organic frameworks for enhanced conversion of carbon dioxide to formate. Chemosphere 267:128921. https://doi.org/10.1016/j.chemosphere.2020.128921
Sanchis J, Fernández L, Carballeira JD, Drone J, Gumulya Y, Höbenreich H, Kahakeaw D, Kille S, Lohmer R, Peyralans JJ-P, Podtetenieff J, Prasad S, Soni P, Taglieber A, Wu S, Zilly FE, Reetz MT (2008) Improved PCR method for the creation of saturation mutagenesis libraries in directed evolution: application to difficult-to-amplify templates. Appl Microbiol Biotechnol 81(2):387–397. https://doi.org/10.1007/s00253-008-1678-9
Sato R, Amao Y (2022) Carbonic anhydrase/formate dehydrogenase bienzymatic system for CO2 capture, utilization and storage. React Chem Eng 7(1):181–191. https://doi.org/10.1039/d1re00405k
Shi J, Jiang Y, Jiang Z, Wang X, Wang X, Zhang S, Han P, Yang C (2015) Enzymatic conversion of carbon dioxide. Chem Soc Rev 44(17):5981–6000. https://doi.org/10.1039/C5CS00182J
Slusarczyk H, Felber S, Kula M-R, Pohl M (2000) Stabilization of NAD-dependent formate dehydrogenase from Candida boidinii by site-directed mutagenesis of cysteine residues. Eur J Biochem 267(5):1280–1289. https://doi.org/10.1046/j.1432-1327.2000.01123.x
Sultana S, Chandra Sahoo P, Martha S, Parida K (2016) A review of harvesting clean fuels from enzymatic CO2 reduction. RSC Adv 6(50):44170–44194. https://doi.org/10.1039/C6RA05472B
Takeda H, Cometto C, Ishitani O, Robert M (2017) Electrons, photons, protons and earth-abundant metal complexes for molecular catalysis of CO2 reduction. ACS Catal 7(1):70–88. https://doi.org/10.1021/acscatal.6b02181
Tang C-D, Ding P-J, Shi H-L, Jia Y-y, Zhou M-z, Yu H-l, Xu J-H, Yao L-G, Kan Y-C (2019) One-pot synthesis of phenylglyoxylic acid from racemic mandelic acids via cascade biocatalysis. J Agric Food Chem 67(10):2946–2953. https://doi.org/10.1021/acs.jafc.8b07295
Tang C-D, Zhang Z-H, Shi H-L, Xie Y-L, Yang T-T, Lu Y-F, Zhang S-P, Bai F-H, Kan Y-C, Yao L-G (2021) Directed evolution of formate dehydrogenase and its application in the biosynthesis of L-phenylglycine from phenylglyoxylic acid. Molecular Catal. https://doi.org/10.1016/j.mcat.2021.111666
Tang C-D, Zhang X, Shi H-L, Liu X-X, Wang H-Y, Lu Y-F, Zhang S-P, Kan Y-C, Yao L-G (2022) Improving catalytic activity of Lactobacillus harbinensis -mandelate dehydrogenase toward -o-chloromandelic acid by laboratory evolution. Molecular Catal. https://doi.org/10.1016/j.mcat.2022.112700
Tishkov VI, Popov VO (2004) Catalytic mechanism and application of formate dehydrogenase. Biochemistry-Moscow 69(11):1252–1267. https://doi.org/10.1007/s10541-005-0071-x
Tishkov VI, Popov VO (2006) Protein engineering of formate dehydrogenase. Biomol Eng 23(2–3):89–110. https://doi.org/10.1016/j.bioeng.2006.02.003
Tülek A, Günay E, Servili B, Essiz S, Binay B, Yildirim D (2023) Sustainable production of formic acid from CO2 by a novel immobilized mutant formate dehydrogenase. Sep Purif Technol. https://doi.org/10.1016/j.seppur.2022.123090
Wu R, Li F, Cui X, Li Z, Ma C, Jiang H, Zhang L, Zhang YPJ, Zhao T, Zhang Y, Li Y, Chen H, Zhu Z (2023) Enzymatic Electrosynthesis of Glycine from CO(2) and NH(3). Angew Chem Int Ed Engl. https://doi.org/10.1002/anie.202218387
Ÿzgün G, Karagüler NG, Turunen O, Turner NJ, Binay B (2015) Characterization of a new acidic NAD + -dependent formate dehydrogenase from thermophilic fungus Chaetomium thermophilum. J Molecular Catal 122:212–217. https://doi.org/10.1016/j.molcatb.2015.09.014
Acknowledgements
This work was supported by the Grants from Scientific and Technological Project of China (31900916), the Program for Science&Technology Innovation Talents in Universities of Henan Province (No. 21HASTIT041) and the Central Government Guide Local Science and Technology Development Fund Project of Henan Province (Z20221343035), Henan Province Young Scientist Project (225200810076).
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H-LS: Methodology, Investigation. S-WY: Investigation, Software. X-QX：Investigation, Data curation. Y-LX：Investigation. CY: Conceptualization, Writing—Original Draft. Y-JZ: Investigation, Data curation. L-GY: Writing—Reviewing and Editing. CX: Funding acquisition and Editing. C-DT: Conceptualization, Writing— Reviewing and Editing
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Shi, HL., Yuan, SW., Xi, XQ. et al. Engineering of formate dehydrogenase for improving conversion potential of carbon dioxide to formate. World J Microbiol Biotechnol 39, 352 (2023). https://doi.org/10.1007/s11274-023-03739-5
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DOI: https://doi.org/10.1007/s11274-023-03739-5