Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
권호 표지
DOI QR코드

DOI QR Code

Discovery of a Novel Cellobiose Dehydrogenase from Cellulomonas palmilytica EW123 and Its Sugar Acids Production

  • Ake-kavitch Siriatcharanon (Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT)) ;
  • Sawannee Sutheeworapong (Division of Bioinformatics and Systems Biology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT)) ;
  • Sirilak Baramee (Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi (KMUTT)) ;
  • Rattiya Waeonukul (Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT)) ;
  • Patthra Pason (Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT)) ;
  • Akihiko Kosugi (Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS)) ;
  • Ayaka Uke (Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS)) ;
  • Khanok Ratanakhanokchai (Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT)) ;
  • Chakrit Tachaapaikoon (Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT))
  • Received : 2023.07.05
  • Accepted : 2023.09.20
  • Published : 2024.02.28
Download PDF
⟨ Previous Next ⟩

Abstract

Cellobiose dehydrogenases (CDHs) are a group of enzymes belonging to the hemoflavoenzyme group, which are mostly found in fungi. They play an important role in the production of acid sugar. In this research, CDH annotated from the actinobacterium Cellulomonas palmilytica EW123 (CpCDH) was cloned and characterized. The CpCDH exhibited a domain architecture resembling class-I CDH found in Basidiomycota. The cytochrome c and flavin-containing dehydrogenase domains in CpCDH showed an extra-long evolutionary distance compared to fungal CDH. The amino acid sequence of CpCDH revealed conservative catalytic amino acids and a distinct flavin adenine dinucleotide region specific to CDH, setting it apart from closely related sequences. The physicochemical properties of CpCDH displayed optimal pH conditions similar to those of CDHs but differed in terms of optimal temperature. The CpCDH displayed excellent enzymatic activity at low temperatures (below 30℃), unlike other CDHs. Moreover, CpCDH showed the highest substrate specificity for disaccharides such as cellobiose and lactose, which contain a glucose molecule at the non-reducing end. The catalytic efficiency of CpCDH for cellobiose and lactose were 2.05 × 105 and 9.06 × 104 (M-1 s-1), respectively. The result from the Fourier-transform infrared spectroscopy (FT-IR) spectra confirmed the presence of cellobionic and lactobionic acids as the oxidative products of CpCDH. This study establishes CpCDH as a novel and attractive bacterial CDH, representing the first report of its kind in the Cellulomonas genus.

Keywords

Acknowledgement

We would like to thank and gratefully acknowledge the financial support given by Petchra Pra Jom Klao Ph.D. Research Scholarship year 2018, King Mongkut's University of Technology Thonburi, Thailand, under financial supported number 32/2561. In addition, this research project is supported by King Mongkut's University of Technology Thonburi under "KMUTT Research Center of Excellent Project (Grant number 7601.24/4054)".

References

  1. Cavener DR. 1992. GMC oxidoreductases. A newly defined family of homologous proteins with diverse catalytic activities. J. Mol. Biol. 223: 811-814.
  2. Hernandez-Ortega A, Ferreira P, Martinez AT. 2012. Fungal aryl-alcohol oxidase: a peroxide-producing flavoenzyme involved in lignin degradation. Appl. Microbiol. Biotechnol. 93: 1395-1410.
  3. Tan TC, Spadiut O, Wongnate T, Sucharitakul J, Krondorfer I, Sygmund C, et al. 2013. The 1.6 A crystal structure of pyranose dehydrogenase from Agaricus meleagris rationalizes substrate specificity and reveals a flavin intermediate. PLoS One 8: e53567.
  4. Wongnate T, Chaiyen P. 2013. The substrate oxidation mechanism of pyranose 2-oxidase and other related enzymes in the glucose-methanol-choline superfamily. FEBS J. 280: 3009-3027.
  5. Sutzl L, Foley G, Gillam EMJ, Boden M, Haltrich D. 2019. The GMC superfamily of oxidoreductases revisited: analysis and evolution of fungal GMC oxidoreductases. Biotechnol. Biofuels 12: 118.
  6. Phillips CM, Beeson WT, Cate JH, Marletta MA. 2011. Cellobiose dehydrogenase and a copper-dependent polysaccharide monooxygenase potentiate cellulose degradation by Neurospora crassa. ACS Chem. Biol. 6: 1399-1406.
  7. Isaksen T, Westereng B, Aachmann FL, Agger JW, Kracher D, Kittl R, et al. 2014. A C4-oxidizing lytic polysaccharide monooxygenase cleaving both cellulose and cello-oligosaccharides. J. Biol. Chem. 289: 2632-2642.
  8. Eibinger M, Ganner T, Bubner P, Rosker S, Kracher D, Haltrich D, et al. 2014. Cellulose surface degradation by a lytic polysaccharide monooxygenase and its effect on cellulase hydrolytic efficiency. J. Biol. Chem. 289: 35929-35938.
  9. Csarman F, Wohlschlager L, Ludwig R. 2020. Cellobiose dehydrogenase. Enzymes 47: 457-489.
  10. Zamocky M, Ludwig R, Peterbauer C, Hallberg BM, Divne C, Nicholls P, et al. 2006. Cellobiose dehydrogenase--a flavocytochrome from wood-degrading, phytopathogenic and saprotrophic fungi. Curr. Protein Pept. Sci. 7: 255-280.
  11. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B. 2009. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res. 37: D233-238.
  12. Igarashi K, Samejima M, Eriksson KE. 1998. Cellobiose dehydrogenase enhances Phanerochaete chrysosporium cellobiohydrolase I activity by relieving product inhibition. Eur. J. Biochem. 253: 101-106.
  13. Ander P, Mishra C, Farrell RL, Eriksson K-EL. 1990. Redox reactions in lignin degradation: interactions between laccase, different peroxidases and cellobiose: quinone oxidoreductase. J. Biotechnol. 13: 189-198.
  14. Sulej J, Osinska-Jaroszuk M, Jaszek M, Graz M, Kutkowska J, Pawlik A, et al. 2019. Antimicrobial and antioxidative potential of free and immobilised cellobiose dehydrogenase isolated from wood degrading fungi. Fungal Biol. 123: 875-886.
  15. Fischer C, Krause A, Kleinschmidt T. 2014. Optimization of production, purification and lyophilisation of cellobiose dehydrogenase by Sclerotium rolfsii. BMC Biotechnol. 14: 97.
  16. Oh YR, Song JK, Eom GT. 2022. Efficient production of cellobionic acid using whole-cell biocatalyst of genetically modified Pseudomonas taetrolens. Bioprocess Biosyst. Eng. 45: 1057-1064.
  17. Kiryu T, Kiso T, Nakano H, Murakami H. 2015. Lactobionic and cellobionic acid production profiles of the resting cells of acetic acid bacteria. Biosci. Biotechnol. Biochem. 79: 1712-1718.
  18. Siriatcharanon AK, Sutheeworapong S, Waeonukul R, Pason P, Uke A, Kosugi A, et al. 2022. Cellulomonas palmilyticum sp. nov., from earthworm soil biofertilizer with the potential to degrade oil palm empty fruit bunch. Int. J. Syst. Evol. Microbiol. 72. doi:10.1099/ijsem.0.005494.
  19. Taylor EC. 1982. Role of aerobic microbial populations in cellulose digestion by desert millipedes. Appl. Environ. Microbiol. 44: 281-291.
  20. Ye J, Coulouris G, Zaretskaya I, Cutcutache I, Rozen S, Madden TL. 2012. Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics 13: 134.
  21. Wittig I, Braun HP, Schagger H. 2006. Blue native PAGE. Nat. Protoc. 1: 418-428.
  22. Bey M, Berrin JG, Poidevin L, Sigoillot JC. 2011. Heterologous expression of Pycnoporus cinnabarinus cellobiose dehydrogenase in Pichia pastoris and involvement in saccharification processes. Microb Cell Fact. 10: 113.
  23. Hall T A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41: 95-98.
  24. Tamura K, Stecher G, Kumar S. 2021. MEGA11: molecular evolutionary genetics analysis version 11. Mol. Biol. Evol. 38: 3022-3027.
  25. Bjellqvist B, Hughes GJ, Pasquali C, Paquet N, Ravier F, Sanchez JC, et al. 1993. The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences. Electrophoresis 14: 1023-1031.
  26. Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A. 2003. ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res. 31: 3784-3788.
  27. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, et al. 2011. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7: 539.
  28. Wang S, Li W, Liu S, Xu J. 2016. RaptorX-Property: a web server for protein structure property prediction. Nucleic Acids Res. 44: W430-W435.
  29. Karapetyan KN, Fedorova TV, Vasil'chenko LG, Ludwig R, Haltrich D, Rabinovich ML. 2006. Properties of neutral cellobiose dehydrogenase from the ascomycete Chaetomium sp. INBI 2-26(-) and comparison with basidiomycetous cellobiose dehydrogenases. J. Biotechnol. 121: 34-48.
  30. Baminger U, Subramaniam SS, Renganathan V, Haltrich D. 2001. Purification and characterization of cellobiose dehydrogenase from the plant pathogen Sclerotium (Athelia) rolfsii. Appl. Environ. Microbiol. 67: 1766-1774.
  31. Zamocky M, Hallberg M, Ludwig R, Divne C, Haltrich D. 2004. Ancestral gene fusion in cellobiose dehydrogenases reflects a specific evolution of GMC oxidoreductases in fungi. Gene 338: 1-14.
  32. Kozlowski LP. 2017. Proteome-pI: proteome isoelectric point database. Nucleic Acids Res. 45: D1112-D1116.
  33. Bjellqvist B, Basse B, Olsen E, Celis JE. 1994. Reference points for comparisons of two-dimensional maps of proteins from different human cell types defined in a pH scale where isoelectric points correlate with polypeptide compositions. Electrophoresis 15: 529-539.
  34. Harreither W, Sygmund C, Dunhofen E, Vicuna R, Haltrich D, Ludwig R. 2009. Cellobiose dehydrogenase from the ligninolytic basidiomycete Ceriporiopsis subvermispora. Appl. Environ. Microbiol. 75: 2750-2757.
  35. Hallberg BM, Henriksson G, Pettersson G, Divne C. 2002. Crystal structure of the flavoprotein domain of the extracellular flavocytochrome cellobiose dehydrogenase. J. Mol. Biol. 315: 421-434.
  36. Hallberg BM, Henriksson G, Pettersson G, Vasella A, Divne C. 2003. Mechanism of the reductive half-reaction in cellobiose dehydrogenase. J. Biol. Chem. 278: 7160-7166.
  37. Sygmund C, Santner P, Krondorfer I, Peterbauer CK, Alcalde M, Nyanhongo GS, et al. 2013. Semi-rational engineering of cellobiose dehydrogenase for improved hydrogen peroxide production. Microb Cell Fact. 12: 38.
  38. Tan TC, Kracher D, Gandini R, Sygmund C, Kittl R, Haltrich D, et al. 2015. Structural basis for cellobiose dehydrogenase action during oxidative cellulose degradation. Nat. Commun. 6: 7542.
  39. Ludwig R, Harreither W, Tasca F, Gorton L. 2010. Cellobiose dehydrogenase: a versatile catalyst for electrochemical applications. Chemphyschem 11: 2674-2697.
  40. Scheiblbrandner S, Ludwig R. 2020. Cellobiose dehydrogenase: bioelectrochemical insights and applications. Bioelectrochemistry 131: 107345.
  41. Rotsaert FA, Li B, Renganathan V, Gold MH. 2001. Site-directed mutagenesis of the heme axial ligands in the hemoflavoenzyme cellobiose dehydrogenase. Arch. Biochem. Biophys. 390: 206-214.
  42. Bertini I, Cavallaro G, Rosato A. 2007. Evolution of mitochondrial-type cytochrome c domains and of the protein machinery for their assembly. J. Inorg. Biochem. 101: 1798-1811.
  43. Schou C, Christensen MH, Schulein M. 1998. Characterization of a cellobiose dehydrogenase from Humicola insolens. Biochem. J. 330: 565-571.
  44. Roy BP, Dumonceaux T, Koukoulas AA, Archibald FS. 1996. Purification and characterization of cellobiose dehydrogenases from the white rot fungus Trametes versicolor. Appl. Environ. Microbiol. 62: 4417-4427.
  45. Harreither W, Sygmund C, Augustin M, Narciso M, Rabinovich ML, Gorton L, et al. 2011. Catalytic properties and classification of cellobiose dehydrogenases from ascomycetes. Appl. Environ. Microbiol. 77: 1804-1815.
  46. Desriani, Ferri S, Sode K. 2010. Amino acid substitution at the substrate-binding subsite alters the specificity of the Phanerochaete chrysosporium cellobiose dehydrogenase. Biochem. Biophys. Res. Commun. 391: 1246-1250.
  47. Ludwig R, Salamon A, Varga J, Zamocky M, Peterbauer CK, Kulbe KD, et al. 2004. Characterisation of cellobiose dehydrogenases from the white-rot fungi Trametes pubescens and Trametes villosa. Appl. Microbiol. Biotechnol. 64: 213-222.
  48. Henriksson G, Sild V, Szabo IJ, Pettersson G, Johansson G. 1998. Substrate specificity of cellobiose dehydrogenase from Phanerochaete chrysosporium. Biochim. Biophys. Acta 1383: 48-54.
  49. Hudson KL, Bartlett GJ, Diehl RC, Agirre J, Gallagher T, Kiessling LL, et al. 2015. Carbohydrate-aromatic interactions in proteins. J. Am. Chem. Soc. 137: 15152-15160.
  50. Waterhouse A, Bertoni M, Bienert S, Studer G, Tauriello G, Gumienny R, et al. 2018. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 46(W1): W296-W303.
  51. Fiser A. 2010. Template-based protein structure modeling. Methods Mol. Biol. 673: 73-94.
  52. Kryshtafovych A, Schwede T, Topf M, Fidelis K, Moult J. 2019. Critical assessment of methods of protein structure prediction (CASP)-Round XIII. Proteins 87: 1011-1020.