Abstract
Lignocellulosic biomass is rich in lignins, which represent a bottomless natural source of aromatic compounds. Due to the high chemical complexity of these aromatic polymers, their biological fractionation remains challenging for biorefinery. The production of aromatics from the biological valorization of lignins requires the action of ligninolytic peroxidases and laccases produced by fungi and bacteria. Therefore, identification of efficient ligninolytic enzymes with high stability represents a promising route for lignins biorefining. Our strategy consists in exploiting the enzymatic potential of the thermophilic bacterium Thermobacillus xylanilyticus to produce robust and thermostable ligninolytic enzymes. In this context, a gene encoding a putative catalase-peroxidase was identified from the bacterial genome. The present work describes the production of the recombinant protein, its biochemical characterization, and ligninolytic potential. Our results show that the catalase-peroxidase from T. xylanilyticus is thermostable and exhibits catalase-peroxidase and manganese peroxidase activities. The electrochemical characterization using intermittent pulse amperometry showed the ability of the enzyme to oxidize small aromatic compounds derived from lignins. This promising methodology allows the fast screening of the catalase-peroxidase activity towards small phenolic molecules, suggesting its potential role in lignin transformation.
Key points
• Production and characterization of a new thermostable bacterial catalase-peroxidase
• The enzyme is able to oxidize many phenolic monomers derived from lignins
• Intermittent pulse amperometry is promising to screen ligninolytic enzyme
Graphical abstract
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Data availability
All data generated or analyzed during this study are included in this publish article and its supplementary information files.
References
Abdellaoui S, Bekhouche M, Noiriel A, Henkens R, Bonaventura C, Blum LJ, Doumèche B (2013a) Rapid electrochemical screening of NAD-dependent dehydrogenases in a 96-well format. Chem Comm 49:5781. https://doi.org/10.1039/c3cc42065e
Abdellaoui S, Noiriel A, Henkens R, Bonaventura C, Blum LJ, Doumeche B (2013b) A 96-well electrochemical method for the screening of enzymatic activities. Anal Chem 85:3690–3697. https://doi.org/10.1021/ac303777r
Adav SS, Li AA, Manavalan A, Punt P, Sze SK (2010) Quantitative iTRAQ secretome analysis of Aspergillus niger reveals novel hydrolytic enzymes. J Proteome Res 9:3932–3940. https://doi.org/10.1021/pr100148j
Ahmad M, Roberts JN, Hardiman EM, Singh R, Eltis LD, Bugg TD (2011) Identification of DypB from Rhodococcus jostii RHA1 as a lignin peroxidase. Biochemistry 50:5096–5107. https://doi.org/10.1021/bi101892z
Asgher M, Ramzan M, Bilal M (2016) Purification and characterization of manganese peroxidases from native and mutant Trametes versicolor IBL-04. Chinese J Catal 37:561–570. https://doi.org/10.1016/S1872-2067(15)61044-0
Asina FNU, Brzonova I, Kozliak E, Kubátová A, Ji Y (2017) Microbial treatment of industrial lignin: successes, problems and challenges. Renew Sust Energ Rev 77:1179–1205. https://doi.org/10.1016/j.rser.2017.03.098
Aymard C, Bonaventura C, Henkens R, Mousty C, Hecquet L, Charmantray F, Blum LJ, Doumèche B (2017) High-throughput electrochemical screening assay for free and immobilized oxidases: electrochemiluminescence and intermittent pulse amperometry. Chem Electro Chem 4:957–966. https://doi.org/10.1002/celc.201600647
Aymard CMG, Halma M, Comte A, Mousty C, Prevot V, Hecquet L, Charmantray F, Blum LJ, Doumeche B (2018) Innovative electrochemical screening allows transketolase inhibitors to be identified. Anal Chem 90:9241–9248. https://doi.org/10.1021/acs.analchem.8b01752
Bradford MM (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. https://doi.org/10.1016/0003-2697(76)90527-3
Brown ME, Walker MC, Nakashige TG, Iavarone AT, Chang MC (2011) Discovery and characterization of heme enzymes from unsequenced bacteria: application to microbial lignin degradation. J Am Chem Soc 133:18006–18009. https://doi.org/10.1021/ja203972q
Brown ME, Barros T, Chang MC (2012) Identification and characterization of a multifunctional dye peroxidase from a lignin-reactive bacterium. ACS Chem Biol 7:2074–2081. https://doi.org/10.1021/cb300383y
Bugg TD, Rahmanpour R (2015) Enzymatic conversion of lignin into renewable chemicals. Curr Opin Chem Biol 29:10–17. https://doi.org/10.1016/j.cbpa.2015.06.009
Bugg TDH, Williamson JJ, Rashid GMM (2020) Bacterial enzymes for lignin depolymerisation: new biocatalysts for generation of renewable chemicals from biomass. Curr Opin Chem Biol 55:26–33. https://doi.org/10.1016/j.cbpa.2019.11.007
Chang A, Jeske L, Ulbrich S, Hofmann J, Koblitz J, Schomburg I, Neumann-Schaal M, Jahn D, Schomburg D (2020) BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res 49:D498–D508. https://doi.org/10.1093/nar/gkaa1025
Chauhan PS (2020) Role of various bacterial enzymes in complete depolymerization of lignin: a review. Biocatal Agric Biotechnol 23:101498. https://doi.org/10.1016/j.bcab.2020.101498
Christian V, Shrivastava R, Shukla D, Modi H, Vyas BRM (2005) Mediator role of veratryl alcohol in the lignin peroxidase-catalyzed oxidative decolorization of Remazol brilliant blue R. Enzyme Microb Technol 36:327–332. https://doi.org/10.1016/j.enzmictec.2004.09.006
Dashtban M, Schraft H, Syed AT, Qin W (2010) Fungal biodegradation and enzymatic modification of lignin. Int J Biochem Mol Biol 1:36–50
Davis JR, Goodwin LA, Woyke T, Teshima H, Bruce D, Detter C, Tapia R, Han S, Han J, Pitluck S, Nolan M, Mikhailova N, Land ML, Sello JK (2012) Genome sequence of Amycolatopsis sp. strain ATCC 39116, a plant biomass-degrading actinomycete. J Bacteriol 194:2396–2397. https://doi.org/10.1128/JB.00186-12
Deangelis KM, Sharma D, Varney R, Simmons B, Isern NG, Markilllie LM, Nicora C, Norbeck AD, Taylor RC, Aldrich JT, Robinson EW (2013) Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1. Front Microbiol 4:280. https://doi.org/10.3389/fmicb.2013.00280
Debeche T, Cummings N, Connerton I, Debeire P, O’donohue MJ (2000) Genetic and biochemical characterization of a highly thermostable α-L-arabinofuranosidase from Thermobacillus xylanilyticus. Appl Environ Microbiol 66:1734–1736. https://doi.org/10.1128/aem.66.4.1734-1736.2000
Dupoiron S, Lameloise M-L, Pommet M, Bennaceur O, Lewandowski R, Allais F, Teixeira ARS, Rémond C, Rakotoarivonina H (2017) A novel and integrative process: from enzymatic fractionation of wheat bran with a hemicellulasic cocktail to the recovery of ferulic acid by weak anion exchange resin. Ind Crops Prod 105:148–155. https://doi.org/10.1016/j.indcrop.2017.05.004
Ghiladi RA, Knudsen GM, Medzihradszky KF, Ortiz De Montellano PR (2005) The Met-Tyr-Trp cross-link in Mycobacterium tuberculosis catalase-peroxidase (KatG): autocatalytic formation and effect on enzyme catalysis and spectroscopic properties. J Biol Chem 280:22651–22663. https://doi.org/10.1074/jbc.M502486200
Gonzalez PS, Agostini E, Milrad SR (2008) Comparison of the removal of 2,4-dichlorophenol and phenol from polluted water, by peroxidases from tomato hairy roots, and protective effect of polyethylene glycol. Chemosphere 70:982–989. https://doi.org/10.1016/j.chemosphere.2007.08.025
Granja-Travez RS, Wilkinson RC, Persinoti GF, Squina FM, Fulop V, Bugg TDH (2018) Structural and functional characterisation of multi-copper oxidase CueO from lignin-degrading bacterium Ochrobactrum sp. reveal its activity towards lignin model compounds and lignosulfonate. FEBS J 285:1684–1700. https://doi.org/10.1111/febs.14437
Hofrichter M (2002) Review: lignin conversion by manganese peroxidase (MnP). Enzyme Microb Technol 30:454–466. https://doi.org/10.1016/S0141-0229(01)00528-2
Janusz G, Pawlik A, Sulej J, Swiderska-Burek U, Jarosz-Wilkolazka A, Paszczynski A (2017) Lignin degradation: microorganisms, enzymes involved, genomes analysis and evolution. FEMS Microbiol Rev 41:941–962. https://doi.org/10.1093/femsre/fux049
Kamimura N, Takahashi K, Mori K, Araki T, Fujita M, Higuchi Y, Masai E (2017) Bacterial catabolism of lignin-derived aromatics: new findings in a recent decade: update on bacterial lignin catabolism. Environ Microbiol Rep 9:679–705. https://doi.org/10.1111/1758-2229.12597
Kamimura N, Sakamoto S, Mitsuda N, Masai E, Kajita S (2019) Advances in microbial lignin degradation and its applications. Curr Opin Biotechnol 56:179–186. https://doi.org/10.1016/j.copbio.2018.11.011
Kumar M, Verma S, Gazara RK, Kumar M, Pandey A, Verma PK, Thakur IS (2018) Genomic and proteomic analysis of lignin degrading and polyhydroxyalkanoate accumulating beta-proteobacterium Pandoraea sp. ISTKB Biotechnol Biofuels 11:154. https://doi.org/10.1186/s13068-018-1148-2
Kuzmič P (1996) Program DYNAFIT for the analysis of enzyme kinetic data: application to HIV proteinase. Anal Biochem 237:260–273. https://doi.org/10.1006/abio.1996.0238
Levasseur A, Drula E, Lombard V, Coutinho P, Henrissat B (2013) Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes. Biotechnol Biofuels. https://doi.org/10.1186/1754-6834-6-41
Lončar N, Colpa DI, Fraaije MW (2016) Exploring the biocatalytic potential of a DyP-type peroxidase by profiling the substrate acceptance of Thermobifida fusca DyP peroxidase. Tetrahedron 72:7276–7281. https://doi.org/10.1016/j.tet.2015.12.078
Ma R, Xu Y, Zhang X (2015) Catalytic oxidation of biorefinery lignin to value-added chemicals to support sustainable biofuel production. Chemsuschem 8:24–51. https://doi.org/10.1002/cssc.201402503
Majumdar S, Lukk T, Solbiati JO, Bauer S, Nair SK, Cronan JE, Gerlt JA (2014) Roles of small laccases from Streptomyces in lignin degradation. Biochemistry 53:4047–4058. https://doi.org/10.1021/bi500285t
Martínez A, Speranza M, Ruiz-Dueñas F, Ferreira P, Camarero S, Guillén F, Martínez M, Gutiérrez A, Del Río J (2005) Biodegradation of lignocellulosics: microbial, chemical, and enzymatic aspects of the fungal attack of lignin. Int Microbiol 8(3):195–204
Min K, Gong G, Woo HM, Kim Y, Um Y (2015) A dye-decolorizing peroxidase from Bacillus subtilis exhibiting substrate-dependent optimum temperature for dyes and beta-ether lignin dimer. Sci Rep 5:8245. https://doi.org/10.1038/srep08245
Ndontsa EN, Moore RL, Goodwin DC (2012) Stimulation of KatG catalase activity by peroxidatic electron donors. Arch Biochem Biophys 525:215–222. https://doi.org/10.1016/j.abb.2012.06.003
Nelson DP, Kiesow LA (1972) Enthalpy of decomposition of hydrogen peroxide by catalase at 25°C (with molar extinction coefficients of H2O2 solutions in the UV). Anal Biochem 49:474–478. https://doi.org/10.1016/0003-2697(72)90451-4
Ninomiya R, Zhu B, Kojima T, Iwasaki Y, Nakano H (2014) Role of disulfide bond isomerase DsbC, calcium ions, and hemin in cell-free protein synthesis of active manganese peroxidase isolated from Phanerochaete chrysosporium. J Biosci Bioeng 117:652–657. https://doi.org/10.1016/j.jbiosc.2013.11.003
Palmieri G, Cennamo G, Sannia G (2005) Remazol brilliant blue R decolourisation by the fungus Pleurotus ostreatus and its oxidative enzymatic system. Enzyme Microb Technol 36:17–24. https://doi.org/10.1016/j.enzmictec.2004.03.026
Paul S, Dutta A (2018) Challenges and opportunities of lignocellulosic biomass for anaerobic digestion. Resour Conserv Recycl 130:164–174. https://doi.org/10.1016/j.resconrec.2017.12.005
Petruccioli M, Frasconi M, Quaratino D, Covino S, Favero G, Mazzei F, Federici F, D’annibale A (2009) Kinetic and redox properties of MnP II, a major manganese peroxidase isoenzyme from Panus tigrinus CBS 577.79. J Biol Inorg Chem 14:1153–1163. https://doi.org/10.1007/s00775-009-0559-8
Piermarini S, Micheli L, Ammida NH, Palleschi G, Moscone D (2007) Electrochemical immunosensor array using a 96-well screen-printed microplate for aflatoxin B1 detection. Biosens Bioelectron 22:1434–1440. https://doi.org/10.1016/j.bios.2006.06.029
Pollegioni L, Tonin F, Rosini E (2015) Lignin-degrading enzymes. FEBS J 282:1190–1213. https://doi.org/10.1111/febs.13224
Quiroga M, Guerrero C, Botella M, Barceló A, Amaya I, Medina M, Alonso F, De Forchetti S, Tigier H, Valpuesta V (2000) A tomato peroxidase involved in the synthesis of lignin and suberin. Plant Physiol 122(4). https://doi.org/10.1104/pp.122.4.1119
Ragauskas AJ, Beckham GT, Biddy MJ, Chandra R, Chen F, Davis MF, Davison BH, Dixon RA, Gilna P, Keller M, Langan P, Naskar AK, Saddler JN, Tschaplinski TJ, Tuskan GA, Wyman CE (2014) Lignin valorization: improving lignin processing in the biorefinery. Science 344:1246843. https://doi.org/10.1126/science.1246843
Rahmanpour R, Rea D, Jamshidi S, Fulop V, Bugg TD (2016) Structure of Thermobifida fusca DyP-type peroxidase and activity towards Kraft lignin and lignin model compounds. Arch Biochem Biophys 594:54–60. https://doi.org/10.1016/j.abb.2016.02.019
Rakotoarivonina H, Hermant B, Monthe N, Remond C (2012) The hemicellulolytic enzyme arsenal of Thermobacillus xylanilyticus depends on the composition of biomass used for growth. Microb Cell Fact 11:159. https://doi.org/10.1186/1475-2859-11-159
Rakotoarivonina H, Hermant B, Aubry N, Rabenoelina F, Baillieul F, Remond C (2014) Dynamic study of how the bacterial breakdown of plant cell walls allows the reconstitution of efficient hemicellulasic cocktails. Bioresour Technol 170:331–341. https://doi.org/10.1016/j.biortech.2014.07.097
Rakotoarivonina H, Revol PV, Aubry N, Remond C (2016) The use of thermostable bacterial hemicellulases improves the conversion of lignocellulosic biomass to valuable molecules. Appl Microbiol Biotechnol 100:7577–7590. https://doi.org/10.1007/s00253-016-7562-0
Rakotoarivonina H, Loux V, Doliwa C, Martin V, Rémond C, Thrash JC (2022) Draft genome sequence of the lignocellulolytic and thermophilic bacterium Thermobacillus xylanilyticus XE. Microbiol Resour Announc 11:e00934-e1021. https://doi.org/10.1128/mra.00934-21
Rakotoarivonina H, Hermant B, Chabbert B, Touzel J, Remond C (2011) A thermostable feruloyl-esterase from the hemicellulolytic bacterium Thermobacillus xylanilyticus releases phenolic acids from non-pretreated plant cell walls. Appl Microbiol Biotechnol 541–552.https://doi.org/10.1007/s00253-011-3103z
Samain E, Debeire P, Touzel JP (1997) High level production of a cellulase-free xylanase in glucose-limited fed batch cultures of a thermophilic Bacillus strain. J Biotechnol 58:71–78. https://doi.org/10.1016/S0168-1656(97)00140-5
Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. CSHL Press, Plainview
Sawatdeenarunat C, Surendra KC, Takara D, Oechsner H, Khanal SK (2015) Anaerobic digestion of lignocellulosic biomass: challenges and opportunities. Bioresour Technol 178:178–186. https://doi.org/10.1016/j.biortech.2014.09.103
Singh R, Wiseman B, Deemagarn T, Jha V, Switala J, Loewen PC (2008) Comparative study of catalase-peroxidases (KatGs). Arch Biochem Biophys 471:207–214. https://doi.org/10.1016/j.abb.2007.12.008
Singh A, Singh A, Grover S, Pandey B, Kumari A, Grover A (2018) Wild-type catalase peroxidase vs G279D mutant type: molecular basis of isoniazid drug resistance in Mycobacterium tuberculosis. Gene 641:226–234. https://doi.org/10.1016/j.gene.2017.10.047
Strassberger Z, Tanase S, Rothenberg G (2014) The pros and cons of lignin valorisation in an integrated biorefinery. RSC Adv 4:25310–25318. https://doi.org/10.1039/c4ra04747h
Stravoravdis S, Shipway JR, Goodell B (2021) How do shipworms eat wood? screening shipworm gill symbiont genomes for lignin-modifying enzymes. Front Microbiol 12.https://doi.org/10.3389/fmicb.2021.665001
Tien M, Kirk TK (1988) Lignin peroxidase of Phanerochaete chrysosporium. Meth Enzymol 161:238–249. https://doi.org/10.1016/0076-6879(88)61025-1
Touzel JP, Donohue M, Debeire P, Samain E, Breton C (2000) Thermobacillus xylanilyticus gen. nov., sp. nov., a new aerobic thermophilic xylan-degrading bacterium isolated from farm soil. Int J Syst Evol 50:315–320. https://doi.org/10.1099/00207713-50-1-315
Tsegaye B, Balomajumder C, Roy P (2019) Microbial delignification and hydrolysis of lignocellulosic biomass to enhance biofuel production: an overview and future prospect. Bull Natl Res Cent 43.https://doi.org/10.1186/s42269-019-0094-x
Vardon DR, Franden MA, Johnson CW, Karp EM, Guarnieri MT, Linger JG, Salm MJ, Strathmann TJ, Beckham GT (2015) Adipic acid production from lignin. Energy Environ Sci 8:617–628. https://doi.org/10.1039/c4ee03230f
Vásquez-Garay F, Carrillo-Varela I, Vidal C, Reyes-Contreras P, Faccini M, Teixeira Mendonça R (2021) A review on the lignin biopolymer and its integration in the elaboration of sustainable materials. Sustainability 13:2697. https://doi.org/10.3390/su13052697
Vega-Garcia V, Diaz-Vilchis A, Saucedo-Vazquez JP, Solano-Peralta A, Rudino-Pinera E, Hansberg W (2018) Structure, kinetics, molecular and redox properties of a cytosolic and developmentally regulated fungal catalase-peroxidase. Arch Biochem Biophys 640:17–26. https://doi.org/10.1016/j.abb.2017.12.021
Wariishi H, Valli K, Gold M (1992) Manganese (II) oxidation by manganese peroxidase from the basidiomycete Phanerochaete chrysosporium. Kinetic mechanism and role of chelators. J Biol Chem 267(33):23688–23695
Xu H, Guo MY, Gao YH, Bai XH, Zhou XW (2017) Expression and characteristics of manganese peroxidase from Ganoderma lucidum in Pichia pastoris and its application in the degradation of four dyes and phenol. BMC Biotechnol 17:19. https://doi.org/10.1186/s12896-017-0338-5
Zamocky M, Furtmuller PG, Bellei M, Battistuzzi G, Stadlmann J, Vlasits J, Obinger C (2009) Intracellular catalase/peroxidase from the phytopathogenic rice blast fungus Magnaporthe grisea: expression analysis and biochemical characterization of the recombinant protein. Biochem J 418:443–451. https://doi.org/10.1042/BJ20081478
Zamocky M, Droghetti E, Bellei M, Gasselhuber B, Pabst M, Furtmuller PG, Battistuzzi G, Smulevich G, Obinger C (2012) Eukaryotic extracellular catalase-peroxidase from Magnaporthe grisea - biophysical/chemical characterization of the first representative from a novel phytopathogenic KatG group. Biochimie 94:673–683. https://doi.org/10.1016/j.biochi.2011.09.020
Zhao X, Yu H, Yu S, Wang F, Sacchettini JC, Magliozzo RS (2006) Hydrogen peroxide-mediated isoniazid activation catalyzed by Mycobacterium tuberculosis catalase−peroxidase (KatG) and Its S315T mutant. Biochemistry 45:4131–4140. https://doi.org/10.1021/bi051967o
Funding
The authors are grateful to the Reims Champagne Ardenne University and Foundation for the funding of FI’s PhD thesis. The authors also thank the Grand Reims, the French Region Grand Est, and the European Regional Development Fund (ERDF) for CQ PhD thesis and for the financial support of the Chaire AFERE.
Author information
Authors and Affiliations
Contributions
FI, OM, DB, and RH conceived and designed the research. FI and CQ conducted the experiments. FI, AS, RC, OM, DB and RH analyzed the data. All the authors contributed to the manuscript preparation, read, and approved the final manuscript.
Corresponding author
Ethics declarations
Ethics approval
This article does not contain any studies with human participants or animals performed by any of the authors.
Competing interests
The authors declare no competing interests.
Additional information
Publisher’s Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary information
Below is the link to the electronic supplementary material.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Fall, I., Czerwiec, Q., Abdellaoui, S. et al. A thermostable bacterial catalase-peroxidase oxidizes phenolic compounds derived from lignins. Appl Microbiol Biotechnol 107, 201–217 (2023). https://doi.org/10.1007/s00253-022-12263-9
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00253-022-12263-9