Biotransformation of 2-keto-4-hydroxybutyrate via aldol condensation using an efficient and thermostable carboligase from Deinococcus radiodurans

Yeon-Ju Jeong , Min-Ju Seo , Bong Hyun Sung , Jeong-Sun Kim , Soo-Jin Yeom

Bioresources and Bioprocessing ›› 2024, Vol. 11 ›› Issue (1) : 9

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Bioresources and Bioprocessing ›› 2024, Vol. 11 ›› Issue (1) : 9 DOI: 10.1186/s40643-024-00727-x
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Biotransformation of 2-keto-4-hydroxybutyrate via aldol condensation using an efficient and thermostable carboligase from Deinococcus radiodurans

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Abstract

The bioconversion of 4-hydroxy-2-keto acid derivatives via aldol condensation of formaldehyde and pyruvate has received substantial attention as potential source of chemicals for production of amino acids, hydroxy carboxylic acids, and chiral aldehydes. We developed an environmentally friendly biocatalyst consisting of a novel thermostable class II pyruvate aldolase from Deinococcus radiodurans with maltose-binding protein (MBP-DrADL), which has specific activity of 46.3 µmol min–1 mg–1. Surprisingly, MBP-DrADL maintained over 60% of enzyme activity for 4 days at 50 to 65 °C, we used MBP-DrADL as the best candidate enzyme to produce 2-keto-4-hydroxybutyrate (2-KHB) from formaldehyde and pyruvate via aldol condensation. The optimum reaction conditions for 2-KHB production were 50 °C, pH 8.0, 5 mM Mg2+, 100 mM formaldehyde, and 200 mM pyruvate. Under these optimized conditions, MBP-DrADL produced 76.5 mM (8.94 g L–1) 2-KHB over 60 min with a volumetric productivity of 8.94 g L–1 h–1 and a specific productivity of 357.6 mg mg-enzyme–1 h–1. Furthermore, 2-KHB production was improved by continuous addition of substrates, which produced approximately 124.8 mM (14.6 g L–1) of 2-KHB over 60 min with a volumetric productivity and specific productivity of 14.6 g L–1 h–1 and 583.4 mg mg-enzyme–1 h–1, respectively. MBP-DrADL showed the highest specific productivity for 2-KHB production yet reported. Our study provides a highly efficient biocatalyst for the synthesis of 2-KHB and lays the foundation for large-scale production and application of high-value compounds from formaldehyde.

Keywords

Formaldehyde / Pyruvate / Pyruvate aldolase / 2-keto-4-hydroxybutyrate / Deinococcus radiodurans

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Yeon-Ju Jeong, Min-Ju Seo, Bong Hyun Sung, Jeong-Sun Kim, Soo-Jin Yeom. Biotransformation of 2-keto-4-hydroxybutyrate via aldol condensation using an efficient and thermostable carboligase from Deinococcus radiodurans. Bioresources and Bioprocessing, 2024, 11(1): 9 DOI:10.1186/s40643-024-00727-x

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References

[1]

Aslanidis C, de Jong PJ. Ligation-independent cloning of PCR products (LIC-PCR). Nucleic Acids Res, 1990, 18(20): 6069-6074.

[2]

Baker P, Seah SYK. Rational design of stereoselectivity in the class II pyruvate aldolase BphI. J Am Chem Soc, 2012, 134(1): 507-513.

[3]

Bosch S, Sanchez-Freire E, Del Pozo ML, C̆esnik M, Quesada J, Mate DM, Hernández K, Qi Y, Clapés P, Vasić-Račk D. Thermostability engineering of a class II pyruvate aldolase from Escherichia coli by in vivo folding interference. ACS Sustain Chem Eng, 2021, 9(15): 5430-5436.

[4]

Bouzon M, Perret A, Loreau O, Delmas V, Perchat N, Weissenbach J, Taran F, Marliere P. A synthetic alternative to canonical one-carbon metabolism. ACS Synth Biol, 2017, 6(8): 1520-1533.

[5]

Bradford MM. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem, 1976, 72(1): 248-254.

[6]

Cesnik M, Sudar M, Hernandez K, Charnock S, Vasic-Racki D, Clapes P, Blazevic FZ. Cascade enzymatic synthesis of l-homoserine - mathematical modelling as a tool for process optimisation and design. React Chem Eng, 2020, 5(4): 747-759.

[7]

Chen Z, Geng F, Zeng AP. Protein design and engineering of a de novo pathway for microbial production of 1,3-propanediol from glucose. Biotechnol J, 2015, 10(2): 284-289.

[8]

Dekker EE, Lane RS, Shapley AJB. 2-keto-4-hydroxybutyrate aldolase. Identification as 2-keto-4-hydroxyglutarate aldolase, catalytic properties, and role in the mammalian metabolism of l-homoserine. Biochemistry, 1971, 10(8): 1353-1364.

[9]

Desmons S, Fauré R, Bontemps S. Formaldehyde as a promising C1 source: the instrumental role of biocatalysis for stereocontrolled reactions. ACS Catal, 2019, 9(10): 9575-9588.

[10]

Dick M, Hartmann R, Weiergräber OH, Bisterfeld C, Classen T, Schwarten M, Neudecker P, Willbold D, Pietruszka J. Mechanism-based inhibition of an aldolase at high concentrations of its natural substrate acetaldehyde: structural insights and protective strategies. Chem Sci, 2016, 7(7): 4492-4502.

[11]

Fei H, Xu G, Wu J-P, Yang L-R. Improvement of the thermal stability and aldehyde tolerance of deoxyriboaldolase via immobilization on nano-magnet material. J Mol Catal B Enzym, 2014, 101: 87-91.

[12]

Feldman MY. Reactions of nucleic acids and nucleoproteins with formaldehyde. Prog Nucleic Acid Res Mol Biol, 1973, 13: 1-49.

[13]

Frazao CJR, Trichez D, Serrano-Bataille H, Dagkesamanskaia A, Topham CM, Walther T, Francois JM. Construction of a synthetic pathway for the production of 1,3-propanediol from glucose. Sci Rep, 2019, 9(1): 11576.

[14]

Gastaldi C, Mekhloufi G, Forano C, Gautier A, Guérard-Hélaine C. Mixing chemo- and biocatalysis for rare monosaccharide production by combining aldolase and N-heterocyclic carbene gold catalysts. Green Chem, 2022, 24(9): 3634-3639.

[15]

Gibson DG, Young L, Chuang R-Y, Venter JC, Hutchison CA, Smith HO. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods, 2009, 6(5): 343-345.

[16]

Gong L, Xiu Y, Dong J, Han R, Xu G, Ni Y. Sustainable one-pot chemo-enzymatic synthesis of chiral furan amino acid from biomass via magnetic solid acid and threonine aldolase. Bioresour Technol, 2021, 337.

[17]

Güner S, Wegat V, Pick A, Sieber V. Design of a synthetic enzyme cascade for the in vitro fixation of a C1 carbon source to a functional C4 sugar. Green Chem, 2021, 23(17): 6583-6590.

[18]

Hansen BA, Lane RS, Dekker EE. Formaldehyde binding by 2-Keto-4-hydroxyglutarate aldolase: formation and characterization of an inactive aldolase-formaldehyde-cyanide adduct. J Biol Chem, 1974, 249(15): 4891-4896.

[19]

Hartley CJ, French NG, Scoble JA, Williams CC, Churches QI, Frazer AR, Taylor MC, Coia G, Simpson G, Turner NJ, Scott C. Sugar analog synthesis by in vitro biocatalytic cascade: a comparison of alternative enzyme complements for dihydroxyacetone phosphate production as a precursor to rare chiral sugar synthesis. PLoS ONE, 2017, 12(11

[20]

He H, Hoper R, Dodenhoft M, Marliere P, Bar-Even A. An optimized methanol assimilation pathway relying on promiscuous formaldehyde-condensing aldolases in E. coli. Metab Eng, 2020, 60: 1-13.

[21]

Hernandez K, Bujons J, Joglar J, Charnock SJ, de Maria PD, Fessner WD, Clapes P. Combining aldolases and transaminases for the synthesis of 2-amino-4-hydroxybutanoic acid. ACS Catal, 2017, 7(3): 1707-1711.

[22]

Hernandez K, Joglar J, Bujons J, Parella T, Clapes P. Nucleophile promiscuity of engineered class II pyruvate aldolase YfaU from E. coli. Angew Chem Int Ed Engl, 2018, 57(14): 3583-3587.

[23]

Hixon M, Sinerius G, Schneider A, Walter C, Fessner WD, Schloss JV. Quo vadis photorespiration: a tale of two aldolases. Febs Lett, 1996, 392(3): 281-284.

[24]

Jeong Y-J, Seo P-W, Seo M-J, Ju S-B, Kim J-S, Yeom S-J. One-pot biosynthesis of 2-Keto-4-hydroxybutyrate from cheap C1 compounds using rationally designed pyruvate aldolase and methanol dehydrogenase. J Agric Food Chem, 2023, 71(10): 4328-4336.

[25]

Jo HJ, Kim JH, Kim YN, Seo PW, Kim CY, Kim JW, Yu HN, Cheon H, Lee EY, Kim JS, Park JB. Glyoxylate carboligase-based whole-cell biotransformation of formaldehyde into ethylene glycol via glycotaldehyde. Green Chem, 2022, 24(1): 218-226.

[26]

Ju S-B, Seo M-J, Yeom S-J. In vitro one-pot 3-hydroxypropanal production from cheap C1 and C2 compounds. Int J Mol Sci, 2022, 23(7): 3990.

[27]

Katulic MC, Sudar M, Hernandez K, Qi YY, Charnock SJ, Vasic-Racki D, Clapes P, Blazevic ZF. Cascade synthesis of l-homoserine catalyzed by lyophilized whole cells containing transaminase and aldolase activities: the mathematical modeling approach. Ind Eng Chem Res, 2021, 60(38): 13846-13858.

[28]

Laemmli UK. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature, 1970, 227(5259): 680-685.

[29]

Laurent V, Uzel A, Hélaine V, Nauton L, Traïkia M, Gefflaut T, Salanoubat M, de Berardinis V, Lemaire M, Guérard-Hélaine C. Exploration of aldol reactions catalyzed by stereoselective pyruvate aldolases with 2-oxobutyric acid as nucleophile. Adv Synth Catal, 2019, 361(11): 2713-2717.

[30]

Li Y, Yao P, Zhang S, Feng J, Su H, Liu X, Sheng X, Wu Q, Zhu D, Ma Y. Creating a new benzaldehyde lyase for atom-economic synthesis of chiral 1,2,4-butanetriol and 2-aminobutane-1,4-diol from formaldehyde. Chem Catal, 2023, 3(1

[31]

Liu Q, Wei G, Yang P, Wang C, Chen K, Ouyang P, Zhang A. One-pot biosynthesis of N-acetylneuraminic acid from chitin via combination of chitin-degrading enzymes, N-acetylglucosamine-2-epimerase, and N-neuraminic acid aldolase. Front Microbiol, 2023

[32]

Meng H, Wang C, Yuan Q, Ren J, Zeng A-P. An aldolase-based new pathway for bioconversion of formaldehyde and ethanol into 1,3-propanediol in Escherichia coli. ACS Synth Biol, 2021, 10(4): 799-809.

[33]

Nara TY, Togashi H, Ono S, Egami M, Sekikawa C, Suzuki Y-h, Masuda I, Ogawa J, Horinouchi N, Shimizu S, Mizukami F, Tsunoda T. Improvement of aldehyde tolerance and sequential aldol condensation activity of deoxyriboaldolase via immobilization on interparticle pore type mesoporous silica. J Mol Catal B Enzym, 2011, 68(2): 181-186.

[34]

Rea D, Hovington R, Rakus JF, Gerlt JA, Fulop V, Bugg TDH, Roper DI. Crystal structure and functional assignment of YfaU, a metal ion dependent class II aldolase from Escherichia coli K12. Biochem, 2008, 47(38): 9955-9965.

[35]

Royer SF, Haslett L, Crennell SJ, Hough DW, Danson MJ, Bull SD. Structurally informed site-directed mutagenesis of a stereochemically promiscuous aldolase to afford stereochemically complementary biocatalysts. J Am Chem Soc, 2010, 132(33): 11753-11758.

[36]

Siegel JB, Smith AL, Poust S, Wargacki AJ, Bar-Even A, Louw C, Shen BW, Eiben CB, Tran HM, Noor E, Gallaher JL, Bale J, Yoshikuni Y, Gelb MH, Keasling JD, Stoddard BL, Lidstrom ME, Baker D. Computational protein design enables a novel one-carbon assimilation pathway. Proc Natl Acad Sci USA, 2015, 112(12): 3704-3709.

[37]

Sugiyama M, Hong Z, Liang P-H, Dean SM, Whalen LJ, Greenberg WA, Wong C-H. d-Fructose-6-phosphate aldolase-catalyzed one-pot synthesis of iminocyclitols. J Am Chem Soc, 2007, 129(47): 14811-14817.

[38]

Teng S, Beard K, Pourahmad J, Moridani M, Easson E, Poon R, O'Brien PJ. The formaldehyde metabolic detoxification enzyme systems and molecular cytotoxic mechanism in isolated rat hepatocytes. Chem Biol Interact, 2001, 130–132: 285-296.

[39]

Wang C, Ren J, Zhou LB, Li ZD, Chen L, Zeng AP. An aldolase-catalyzed new metabolic pathway for the assimilation of formaldehyde and methanol to synthesize 2-Keto-4-hydroxybutyrate and 1,3-propanediol in Escherichia coli. ACS Synth Biol, 2019, 8(11): 2483-2493.

[40]

Wang W, Baker P, Seah SYK. Comparison of two metal-dependent pyruvate aldolases related by convergent evolution: substrate specificity, kinetic mechanism, and substrate channeling. Biochem, 2010, 49(17): 3774-3782.

[41]

Wang W, Mazurkewich S, Kimber MS, Seah SY. Structural and kinetic characterization of 4-hydroxy-4-methyl-2-oxoglutarate/4-carboxy-4-hydroxy-2-oxoadipate aldolase, a protocatechuate degradation enzyme evolutionarily convergent with the HpaI and DmpG pyruvate aldolases. J Biol Chem, 2010, 285(47): 36608-36615.

[42]

Williams GJ, Woodhall T, Farnsworth LM, Nelson A, Berry A. Creation of a pair of stereochemically complementary biocatalysts. J Am Chem Soc, 2006, 128(50): 16238-16247.

[43]

Xu YY, Meng H, Ren J, Zeng AP. Formaldehyde formation in the glycine cleavage system and its use for an aldolase-based biosynthesis of 1,3-propanediol. J Biol Eng, 2020

[44]

Zhang Y, Ma C, Dischert W, Soucaille P, Zeng AP. Engineering of phosphoserine aminotransferase increases the conversion of l-homoserine to 4-hydroxy-2-ketobutyrate in a glycerol-independent pathway of 1,3-propanediol production from glucose. Biotechnol J, 2019, 14(9

[45]

Zhong WQ, Zhang Y, Wu WJ, Liu DH, Chen Z. Metabolic engineering of a homoserine-derived non-natural pathway for the de novo production of 1,3-propanediol from glucose. ACS Synth Biol, 2019, 8(3): 587-595.

Funding

C1 Gas Refinery Program(NRF-2018M3D3A1A01056181)

Enzyme engineering for next generation biorefinery(NRF-2022M3J5A1056169)

Korea Research Institute of Bioscience and the Biotechnology (KRIBB) Research Initiative Program(KGM5402322)

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