Discovery of an acidic, thermostable and highly NADP+ dependent formate dehydrogenase from Lactobacillus buchneri NRRL B-30929

  • Saadet Alpdağtaş
  • Sevil Yücel
  • Handan Açelya Kapkaç
  • Siqing Liu
  • Barış Binay
Original Research Paper
  • 1 Downloads

Abstract

Objectives

To identify a robust NADP+ dependent formate dehydrogenase from Lactobacillus buchneri NRRL B-30929 (LbFDH) with unique biochemical properties.

Results

A new NADP+ dependent formate dehydrogenase gene (fdh) was cloned from genomic DNA of L. buchneri NRRL B-30929. The recombinant construct was expressed in Escherichia coli BL21(DE3) with 6 × histidine at the C-terminus and the purified protein obtained as a single band of approx. 44 kDa on SDS-PAGE and 90 kDa on native-PAGE. The LbFDH was highly active at acidic conditions (pH 4.8–6.2). Its optimum temperature was 60 °C and 50 °C with NADP+ and NAD+, respectively and its Tm value was 78 °C. Its activity did not decrease after incubation in a solution containing 20% of DMSO and acetonitrile for 6 h. The KM constants were 49.8, 0.12 and 1.68 mM for formate (with NADP+), NADP+ and NAD+, respectively.

Conclusions

An NADP+ dependent FDH from L. buchneri NRRL B-30929 was cloned, expressed and identified with its unusual characteristics. The LbFDH can be a promising candidate for NADPH regeneration through biocatalysis requiring acidic conditions and high temperatures.

Keywords

Acidic formate dehydrogenase Biochemical and kinetic characterization Highly NADP+ dependent formate dehydrogenase Lactobacillus buchneri NRRL B-30929 Solvent stable Thermostability 

Notes

Acknowledgements

This work was supported by Research Fund of the Yildiz Technical University (Project Number: FDK-2018-3331) and special thanks to Dr. Siqing Liu from USDA ARS for providing chromosomal DNA of Lactobacillus buchneri NRRL B-30929.

Supporting information

Supplementary Fig. 1—MALDI-TOF MS analysis of His6-LbFDH

Supplementary Fig. 2—The Differential Scanning Calorimetry (DSC) result of LbFDH

Supplementary Fig. 3—Effect of metal ions on the activity of recombinant LbFDH.

Supplementary Fig. 4—Organic solvent stability of LbFDH in 20% DMSO and acetonitrile for 6 h.

Supplementary Fig. 5—Effect of different storage temperatures on the stability of LbFDH.

Supplementary Fig. 6 a, b, c, d—Michaelis–Menten curves for NAD+ and NADP+ dependent reaction of LbFDH.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

10529_2018_2568_MOESM1_ESM.docx (955 kb)
Supplementary material 1 (DOCX 933 kb)

References

  1. Alekseeva A, Savin S, Tishkov V (2011) NAD+ dependent formate dehydrogenase from plants. Acta Nat 4:38–54Google Scholar
  2. Andreadeli A, Platis D, Tishkov V, Popov V, Labrou NE (2008) Structure-guided alteration of coenzyme specificity of formate dehydrogenase by saturation mutagenesis to enable efficient utilization of NADP+. FEBS J 275:3859–3869CrossRefPubMedGoogle Scholar
  3. Bommarius AS, Karau A (2005) Deactivation of formate dehydrogenase (FDH) in solution and at gas-liquid interfaces. Biotechnol Prog 21:1663–1672CrossRefPubMedGoogle Scholar
  4. Davis BG, Celik A, Davies GJ, Ruane KM (2009) Novel enzyme. US patent 20130029378 A1Google Scholar
  5. Ding HT, Liu DF, Li ZL, Du YQ, Xu XH, Zhao YH (2011) Characterization of a thermally stable and organic solvent-adaptative NAD+-dependent formate dehydrogenase from Bacillus sp. F1. J Appl Microbiol 111:1075–1085CrossRefPubMedGoogle Scholar
  6. Fogal S, Beneventi E, Cendron L, Bergantino E (2015) Structural basis for double cofactor specificity in a new formate dehydrogenase from the acidobacterium Granulicella mallensis MP5ACTX8. Appl Microbiol Biotechnol 99:9541–9554CrossRefPubMedGoogle Scholar
  7. Galkin A, Kulakova L, Tishkov V, Esaki N, Soda K (1995) Cloning of formate dehydrogenase gene from a methanolutilizing bacterium Mycobacterium vaccae N10. Appl Microbiol Biotechnol 44:479–483CrossRefPubMedGoogle Scholar
  8. Gao X, Ni K, Zhao C, Ren Y, Wei D (2014) Enhancement of the activity of enzyme immobilized onpolydopamine-coated iron oxide nanoparticles by rational orientation of formate dehydrogenase. J Biotechnol 188:36–41CrossRefPubMedGoogle Scholar
  9. Gul-Karaguler N, Sessions RB, Clarke AR, Holbrook J (2001) A single mutation in the NAD-specific formate dehydrogenase from Candida methylica allows the enzyme to use NADP. Biotechnol Lett 23:283–287CrossRefGoogle Scholar
  10. Hatrongjit R, Packdibamrung K (2010) A novel NADP+dependent formate dehydrogenase from Burkholderia stabilis 15516: screening, purification and characterization. Enzyme Microb Technol 46:557–561CrossRefGoogle Scholar
  11. Hoelsch K, Sührer I, Heusel M, Weuster-Botz D (2013) Engineering of formate dehydrogenase: synergistic effect of mutations affecting cofactor specificity and chemical stability. Appl Microbiol Biotechnol 97:2473–2481CrossRefPubMedGoogle Scholar
  12. Hussain H, Chong NF (2016) Combined overlap extension PCR method for improved site directed mutagenesis. Biomed Res Int 2016:8041532CrossRefPubMedPubMedCentralGoogle Scholar
  13. Klibanov A (2001) Improving enzymes by using them in organic solvents. Nature 409:241–246CrossRefPubMedGoogle Scholar
  14. Lamzin VS, Dauter Z, Popov VO, Harutyunyan EH, Wilson KS (1994) High resolution structures of holo and apo formate dehydrogenase. J Mol Biol 236:759–785CrossRefPubMedGoogle Scholar
  15. Maurer SC, Schulze H, Schmid RD, Urlacher V (2003) Immobilisation of P450BM-3 and an NADP+ cofactor recycling system: towards a technical application of heme-containing monooxygenases in fine chemical synthesis. Adv Synth Catal 345:802–810CrossRefGoogle Scholar
  16. Özgün GP, Ordu EB, Tütüncü HE, Yelboğa E, Sessions RB, Karagüler NG (2016) Site saturation mutagenesis applications on Candida methylica formate dehydrogenase. Scientifica ID 4902450:1–7Google Scholar
  17. Papadopoulos JS, Agarwala R (2007) COBALT: constraint-based alignment tool for multiple protein sequences. Bioinformatics 23:1073–1079CrossRefPubMedGoogle Scholar
  18. Popov VO, Lamzin VS (1994) NAD(+)-dependent formate dehydrogenase. Biochem 301:625–643CrossRefGoogle Scholar
  19. Schirwitz K, Schmidt A, Lamzin VS (2007) High-resolution structures of formate dehydrogenase from Candida boidinii. Protein Sci 16:1146–1156CrossRefPubMedPubMedCentralGoogle Scholar
  20. Serov AE, Popova AS, Fedorchuk VV, Tishkov VI (2002) Engineering of coenzyme specificity of formate dehydrogenase from Saccharomyces cerevisiae. Biochem J 367:841–847CrossRefPubMedPubMedCentralGoogle Scholar
  21. Shabalin IG, Polyakov KM, Tishkov VI, Popov VO (2009) Atomic resolution crystal structure of NAD (+) dependent formate dehydrogenase from bacterium moraxella sp. C-1. Acta Nat 1:89–93Google Scholar
  22. Studier FW (2005) Protein production by auto-induction in high density shaking cultures. Protein Expr Purif 41:207–234CrossRefPubMedGoogle Scholar
  23. Tishkov VI, Popov VO (2004) Catalytic mechanism and application of formate dehydrogenase. Biochem (Moscow) 69:1252–1267CrossRefGoogle Scholar
  24. Tishkov VI, Popov VO (2006) Protein engineering of formate dehydrogenase. Biomol Eng 23:89–110CrossRefPubMedGoogle Scholar
  25. Wu W, Zhu D, Hua L (2009) Site-saturation mutagenesis of formate dehydrogenase from Candida bodinii creating effective NADP(+)-dependent FDH enzymes. J Mol Catal B Enzym 61:157–161CrossRefGoogle Scholar
  26. Yu X, Niks D, Mulchandani A, Hille R (2017) Efficient reduction of CO2 by the molybdenum-containing formate dehydrogenase from Cupriavidus necator (Ralstonia eutropha). J Biol Chem 292(41):16872–16879CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media B.V., part of Springer Nature 2018

Authors and Affiliations

  • Saadet Alpdağtaş
    • 1
    • 2
  • Sevil Yücel
    • 2
  • Handan Açelya Kapkaç
    • 3
  • Siqing Liu
    • 4
  • Barış Binay
    • 5
  1. 1.Department of Biology, Faculty of ScienceVan Yuzuncu Yil UniversityVanTurkey
  2. 2.Department of Bioengineering, Faculty of Chemistry and MetallurgyYildiz Technical UniversityIstanbulTurkey
  3. 3.Department of BiologyAnadolu UniversityEskişehirTurkey
  4. 4.U.S. Department of Agriculture, Renewable Product Technology Research UnitNational Centre for Agricultural Utilization ResearchPeoriaUSA
  5. 5.Department of BioengineeringGebze Technical UniversityKocaeliTurkey

Personalised recommendations