Enzymatic C1 reduction using hydrogen in cofactor regeneration

Abstract

Carbon dioxide fixation presents a potential solution for mitigating the greenhouse gas issue. During carbon dioxide fixation, C1 compound reduction requires a high energy supply. Thermodynamic calculations suggest that the energy source for cofactor regeneration plays a vital role in the effective enzymatic C1 reduction. Hydrogenase utilizes renewable hydrogen to achieve the regeneration and supply cofactor nicotinamide adenine dinucleotide (NADH), providing a driving force for the reduction reaction to reduce the thermodynamic barrier of the reaction cascade, and making the forward reduction pathway thermodynamically feasible. Based on the regeneration of cofactor NADH by hydrogenase, and coupled with formaldehyde dehydrogenase and formolase, a favorable thermodynamic mode of the C1 reduction pathway for reducing formate to dihydroxyacetone (DHA) was designed and constructed. This resulted in accumulation of 373.19 μmol·L^–1 DHA after 2 h, and conversion reaching 7.47%. These results indicate that enzymatic utilization of hydrogen as the electron donor to regenerate NADH is of great significance to the sustainable and green development of bio-manufacturing because of its high economic efficiency, no by-products, and environment-friendly operation. Moreover, formolase efficiently and selectively fixed the intermediate formaldehyde (FALD) to DHA, thermodynamically pulled formate to efficiently reduce to DHA, and finally stored the low-grade renewable energy into chemical energy with high energy density.

Graphical abstract

Keywords

[NiFe]-hydrogenase SH / formolase / NADH regeneration / C1 compound reduction / thermodynamic calculation

References

[1] Zhang C , Ottenheim C , Weingarten M , Ji L H . Microbial utilization of next-generation feedstocks for the biomanufacturing of value-added chemicals and food ingredients. Frontiers in Bioengineering and Biotechnology, 2022, 10: 874612

[2] Artz J , Müller T E , Thenert K , Kleinekorte J , Meys R , Sternberg A , Bardow A , Leitner W . Sustainable conversion of carbon dioxide: an integrated review of catalysis and life cycle assessment. Chemical Reviews, 2018, 118(2): 434–504

[3] Yishai O , Lindner S N , de la Cruz J G , Tenenboim H , Bar-Even A . The formate bio-economy. Current Opinion in Chemical Biology, 2016, 35: 1–9

[4] Hu Z C , Zheng Y G , Shen Y C . Dissolved-oxygen-stat fed-batch fermentation of 1,3-dihydroxyacetone from glycerol by Gluconobacter oxydans ZJB09112. Biotechnology and Bioprocess Engineering, 2010, 15(4): 651–656

[5] Wu H , Tian C Y , Song X K , Liu C , Yang D , Jiang Z Y . Methods for the regeneration of nicotinamide coenzymes. Green Chemistry, 2013, 15(7): 1773–1789

[6] Lee Y S , Gerulskis R , Minteer S D . Advances in electrochemical cofactor regeneration: enzymatic and non-enzymatic approaches. Current Opinion in Biotechnology, 2022, 73: 14–21

[7] Sharma V K , Hutchison J M , Allgeier A M . Redox biocatalysis: quantitative comparisons of nicotinamide cofactor regeneration methods. ChemSusChem, 2022, 15(22): e202200888

[8] Lee S H , Choi D S , Kuk S K , Park C B . Photobiocatalysis: activating redox enzymes by direct or indirect transfer of photoinduced electrons. Angewandte Chemie International Edition, 2018, 57(27): 7958–7985

[9] Wang X , Saba T , Yiu H H P , Howe R F , Anderson J A , Shi J . Cofactor NAD(P)H regeneration inspired by heterogeneous pathways. Chem, 2017, 2(5): 621–654

[10] Calvin S J , Mangan D , Miskelly I , Moody T S , Stevenson P J . Overcoming equilibrium issues with carbonyl reductase enzymes. Organic Process Research & Development, 2012, 16(1): 82–86

[11] Hollmann F , Arends I W C E , Holtmann D . Enzymatic reductions for the chemist. Green Chemistry, 2011, 13(9): 2285–2313

[12] Schiffels J , Pinkenburg O , Schelden M , Aboulnaga E A A , Baumann M E M , Selmer T . An innovative cloning platform enables large-scale production and maturation of an oxygen-tolerant NiFe-hydrogenase from Cupriavidus necator in Escherichia coli. PLoS One, 2013, 8(7): e68812

[13] Siegel J B , Smith A L , Poust S , Wargacki A J , Bar-Even A , Louw C , Shen B W , Eiben C B , Tran H M , Noor E . . Computational protein design enables a novel one-carbon assimilation pathway. Proceedings of the National Academy of Sciences of the United States of America, 2015, 112(12): 3704–3709

[14] Friedrich B , Fritsch J , Lenz O . Oxygen-tolerant hydrogenases in hydrogen-based technologies. Current Opinion in Biotechnology, 2011, 22(3): 358–364

[15] Kim K J , Kim H E , Lee K H , Han W , Yi M J , Jeong J , Oh B H . Two-promoter vector is highly efficient for overproduction of protein complexes. Protein Science, 2004, 13(6): 1698–1703

[16] Studier F W . Protein production by auto-induction in high density shaking cultures. Protein Expression and Purification, 2005, 41(1): 207–234

[17] Schiffels J , Selmer T . A flexible toolbox to study protein-assisted metalloenzyme assembly in vitro. Biotechnology and Bioengineering, 2015, 112(11): 2360–2372

[18] Schütte H , Flossdorf J , Sahm H , Kula M R . Purification and properties of formaldehyde dehydrogenase and formate dehydrogenase from Candida boidinii. European Journal of Biochemistry, 1976, 62(1): 151–160

[19] Khana D B , Callaghan M M , Amador-Noguez D . Novel computational and experimental approaches for investigating the thermodynamics of metabolic networks. Current Opinion in Microbiology, 2022, 66: 21–31

[20] Alberty R A . Thermodynamics of systems of biochemical reactions. Journal of Theoretical Biology, 2002, 215(4): 491–501

[21] Zhao T , Li Y , Zhang Y . Biological carbon fixation: a thermodynamic perspective. Green Chemistry, 2021, 23(20): 7852–7864

[22] Flamholz A , Noor E , Bar-Even A , Milo R . eQuilibrator-the biochemical thermodynamics calculator. Nucleic Acids Research, 2012, 40(D1): D770–D775

[23] Lonsdale T H , Lauterbach L , Malca S H , Nestl B M , Hauer B , Lenz O . H₂-driven biotransformation of n-octane to 1-octanol by a recombinant Pseudomonas putida strain co-synthesizing an O₂-tolerant hydrogenase and a P450 monooxygenase. Chemical Communications, 2015, 51(90): 16173–16175

[24] Lv X , Yu W , Zhang C , Ning P , Li J , Liu Y , Du G , Liu L . C1-based biomanufacturing: advances, challenges and perspectives. Bioresource Technology, 2023, 367: 128259

[25] Yishai O , Bouzon M , Doring V , Bar-Even A . In vivo assimilation of one-carbon via a synthetic reductive glycine pathway in Escherichia coli. ACS Synthetic Biology, 2018, 7(9): 2023–2028

[26] Sanchez-Moreno I , Garcia-Garcia J F , Bastida A , Garcia-Junceda E . Multienzyme system for dihydroxyacetone phosphate-dependent aldolase catalyzed C–C bond formation from dihydroxyacetone. Chemical Communications, 2004, (14): 1634–1635

[27] Katryniok B , Kimura H , Skrzynska E , Girardon J S , Fongarland P , Capron M , Ducoulombier R , Mimura N , Paul S , Dumeignil F . Selective catalytic oxidation of glycerol: perspectives for high value chemicals. Green Chemistry, 2011, 13(8): 1960–1979

[28] Cai T , Sun H , Qiao J , Zhu L , Zhang F , Zhang J , Tang Z , Wei X , Yang J , Yuan Q . . Cell-free chemoenzymatic starch synthesis from carbon dioxide. Science, 2021, 373(6562): 1523–1527

[29] Salehizadeh H , Yan N , Farnood R . Recent advances in microbial CO₂ fixation and conversion to value-added products. Chemical Engineering Journal, 2020, 390: 124584

[30] Satanowski A , Bar-Even A . A one-carbon path for fixing CO₂. EMBO Reports, 2020, 21(4): e50273

Competing interests

The authors declare that they have no competing interests.

Acknowledgements

This study was funded by the National Key Research and Development Program of China (Grant No. 2022YFC2105900) and the National Natural Science Foundation of China (Grant Nos. 22378015 and 52073022).

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2024 Higher Education Press