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Lytic xylan oxidases from wood-decay fungi unlock biomass degradation

Nature Chemical Biology volume 14, pages 306–310 (2018)Cite this article

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Abstract

Wood biomass is the most abundant feedstock envisioned for the development of modern biorefineries. However, the cost-effective conversion of this form of biomass into commodity products is limited by its resistance to enzymatic degradation. Here we describe a new family of fungal lytic polysaccharide monooxygenases (LPMOs) prevalent among white-rot and brown-rot basidiomycetes that is active on xylans—a recalcitrant polysaccharide abundant in wood biomass. Two AA14 LPMO members from the white-rot fungus Pycnoporus coccineus substantially increase the efficiency of wood saccharification through oxidative cleavage of highly refractory xylan-coated cellulose fibers. The discovery of this unique enzyme activity advances our knowledge on the degradation of woody biomass in nature and offers an innovative solution for improving enzyme cocktails for biorefinery applications.

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Figure 1: Phylogeny of the AA14 family of LPMOs.
Figure 2: Structure of AA14 LPMO and organization of the copper active site.
Figure 3: Contribution of PcAA14 enzymes to the saccharification of biomass.
Figure 4: Enzymatic activity of PcAA14 LPMOs.

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Protein Data Bank

References

  1. Field, C.B., Behrenfeld, M.J., Randerson, J.T. & Falkowski, P. Primary production of the biosphere: integrating terrestrial and oceanic components. Science 281, 237–240 (1998).

    CAS  PubMed  Google Scholar 

  2. Himmel, M.E. et al. Biomass recalcitrance: engineering plants and enzymes for biofuels production. Science 315, 804–807 (2007).

    Article  CAS  PubMed  Google Scholar 

  3. Biely, P., Singh, S. & Puchart, V. Towards enzymatic breakdown of complex plant xylan structures: state of the art. Biotechnol. Adv. 34, 1260–1274 (2016).

    Article  CAS  PubMed  Google Scholar 

  4. Simmons, T.J. et al. Folding of xylan onto cellulose fibrils in plant cell walls revealed by solid-state NMR. Nat. Commun. 7, 13902 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Loqué, D., Scheller, H.V. & Pauly, M. Engineering of plant cell walls for enhanced biofuel production. Curr. Opin. Plant Biol. 25, 151–161 (2015).

    Article  PubMed  Google Scholar 

  6. Hibbett, D.S. & Donoghue, M.J. Analysis of character correlations among wood decay mechanisms, mating systems, and substrate ranges in homobasidiomycetes. Syst. Biol. 50, 215–242 (2001).

    Article  CAS  PubMed  Google Scholar 

  7. Lombard, V., Golaconda Ramulu, H., Drula, E., Coutinho, P.M. & Henrissat, B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 42, D490–D495 (2014).

    Article  CAS  PubMed  Google Scholar 

  8. Riley, R. et al. Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi. Proc. Natl. Acad. Sci. USA 111, 9923–9928 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Vaaje-Kolstad, G. et al. An oxidative enzyme boosting the enzymatic conversion of recalcitrant polysaccharides. Science 330, 219–222 (2010).

    Article  CAS  PubMed  Google Scholar 

  10. Quinlan, R.J. et al. Insights into the oxidative degradation of cellulose by a copper metalloenzyme that exploits biomass components. Proc. Natl. Acad. Sci. USA 108, 15079–15084 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Kracher, D. et al. Extracellular electron transfer systems fuel cellulose oxidative degradation. Science 352, 1098–1101 (2016).

    Article  CAS  PubMed  Google Scholar 

  12. Johansen, K.S. Discovery and industrial applications of lytic polysaccharide mono-oxygenases. Biochem. Soc. Trans. 44, 143–149 (2016).

    Article  CAS  PubMed  Google Scholar 

  13. Hemsworth, G.R., Henrissat, B., Davies, G.J. & Walton, P.H. Discovery and characterization of a new family of lytic polysaccharide monooxygenases. Nat. Chem. Biol. 10, 122–126 (2014).

    Article  CAS  PubMed  Google Scholar 

  14. Vu, V.V., Beeson, W.T., Span, E.A., Farquhar, E.R. & Marletta, M.A. A family of starch-active polysaccharide monooxygenases. Proc. Natl. Acad. Sci. USA 111, 13822–13827 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Lo Leggio, L. et al. Structure and boosting activity of a starch-degrading lytic polysaccharide monooxygenase. Nat. Commun. 6, 5961 (2015).

    Article  CAS  PubMed  Google Scholar 

  16. Couturier, M. et al. Enhanced degradation of softwood versus hardwood by the white-rot fungus Pycnoporus coccineus. Biotechnol. Biofuels 8, 216 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  17. Frandsen, K.E. et al. The molecular basis of polysaccharide cleavage by lytic polysaccharide monooxygenases. Nat. Chem. Biol. 12, 298–303 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Peisach, J. & Blumberg, W.E. Structural implications derived from the analysis of electron paramagnetic resonance spectra of natural and artificial copper proteins. Arch. Biochem. Biophys. 165, 691–708 (1974).

    Article  CAS  PubMed  Google Scholar 

  19. Garajova, S. et al. Single-domain flavoenzymes trigger lytic polysaccharide monooxygenases for oxidative degradation of cellulose. Sci. Rep. 6, 28276 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Bennati-Granier, C. et al. Substrate specificity and regioselectivity of fungal AA9 lytic polysaccharide monooxygenases secreted by Podospora anserina. Biotechnol. Biofuels 8, 90 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  21. Herpoël-Gimbert, I. et al. Comparative secretome analyses of two Trichoderma reesei RUT-C30 and CL847 hypersecretory strains. Biotechnol. Biofuels 1, 18 (2008).

    Article  PubMed  PubMed Central  Google Scholar 

  22. Westereng, B. et al. Enzymatic cellulose oxidation is linked to lignin by long-range electron transfer. Sci. Rep. 5, 18561 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Villares, A. et al. Lytic polysaccharide monooxygenases disrupt the cellulose fibers structure. Sci. Rep. 7, 40262 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Frommhagen, M. et al. Discovery of the combined oxidative cleavage of plant xylan and cellulose by a new fungal polysaccharide monooxygenase. Biotechnol. Biofuels 8, 101 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  25. Fanuel, M. et al. The Podospora anserina lytic polysaccharide monooxygenase PaLPMO9H catalyzes oxidative cleavage of diverse plant cell wall matrix glycans. Biotechnol. Biofuels 10, 63 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  26. McCartney, L. et al. Differential recognition of plant cell walls by microbial xylan-specific carbohydrate-binding modules. Proc. Natl. Acad. Sci. USA 103, 4765–4770 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Nieduszynski, I. & Marchessault, R.H. Structure of β-D-(1→4′)xylan hydrate. Nature 232, 46–47 (1971).

    Article  CAS  PubMed  Google Scholar 

  28. Miyauchi, S. et al. Visual comparative omics of fungi for plant biomass Deconstruction. Front. Microbiol. 7, 1335 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  29. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).

    Article  CAS  PubMed  Google Scholar 

  30. Edgar, R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Katoh, K. & Standley, D.M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Talavera, G. & Castresana, J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 56, 564–577 (2007).

    Article  CAS  PubMed  Google Scholar 

  33. Price, M.N., Dehal, P.S. & Arkin, A.P. FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One 5, e9490 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  34. Huson, D.H. & Scornavacca, C. Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Syst. Biol. 61, 1061–1067 (2012).

    Article  PubMed  Google Scholar 

  35. Vos, R.A., Caravas, J., Hartmann, K., Jensen, M.A. & Miller, C. BIO:Phylo-phyloinformatic analysis using perl. BMC Bioinformatics 12, 63 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  36. Haon, M. et al. Recombinant protein production facility for fungal biomass-degrading enzymes using the yeast Pichia pastoris. Front. Microbiol. 6, 1002 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  37. Kittl, R., Kracher, D., Burgstaller, D., Haltrich, D. & Ludwig, R. Production of four Neurospora crassa lytic polysaccharide monooxygenases in Pichia pastoris monitored by a fluorimetric assay. Biotechnol. Biofuels 5, 79 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Englyst, H.N. & Cummings, J.H. Improved method for measurement of dietary fiber as non-starch polysaccharides in plant foods. J. Assoc. Off. Anal. Chem. 71, 808–814 (1988).

    CAS  PubMed  Google Scholar 

  39. Westbye, P., Svanberg, C. & Gatenholm, P. The effect of molecular composition of xylan extracted from birch on its assembly onto bleached softwood kraft pulp. Holzforschung 60, 143–148 (2006).

    Article  CAS  Google Scholar 

  40. Larsson, P.T., Wickholm, K. & Iversen, T. A CP/MAS 13C NMR investigation of molecular ordering in celluloses. Carbohydr. Res. 302, 19–25 (1997).

    Article  CAS  Google Scholar 

  41. Kabsch, W. XDS. Acta Crystallogr. D Biol. Crystallogr. 66, 125–132 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Winn, M.D. et al. Overview of the CCP4 suite and current developments. Acta Crystallogr. D Biol. Crystallogr. 67, 235–242 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Cowtan, K. The Buccaneer software for automated model building. 1. Tracing protein chains. Acta Crystallogr. D Biol. Crystallogr. 62, 1002–1011 (2006).

    Article  PubMed  Google Scholar 

  44. Emsley, P., Lohkamp, B., Scott, W.G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Murshudov, G.N., Vagin, A.A. & Dodson, E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 53, 240–255 (1997).

    Article  CAS  PubMed  Google Scholar 

  46. Chen, V.B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D Biol. Crystallogr. 66, 12–21 (2010).

    CAS  PubMed  Google Scholar 

  47. Berman, H., Henrick, K. & Nakamura, H. Announcing the worldwide Protein Data Bank. Nat. Struct. Biol. 10, 980 (2003).

    Article  CAS  PubMed  Google Scholar 

  48. Stoll, S. & Schweiger, A. EasySpin, a comprehensive software package for spectral simulation and analysis in EPR. J. Magn. Reson. 178, 42–55 (2006).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank the European Synchrotron Radiation Facility (Grenoble), and the synchrotron Soleil (Gif-sur-Yvette) for beamtime allocation and assistance. We thank S. Tapin (Centre Technique du Papier, France) for providing cellulose fibers, E. Bonnin and J. Vigouroux for compositional analyses, G. Toriz and P. Gatenholm (Chalmers University of Technology, Sweden) for providing purified wood xylan, L. Foucat and X. Falourd for their valued assistance with treatments of the NMR data, E. Perrin for the excellent technical support for TEM images, B. Seantier for the access and assistance to AFM facilities, D. Hartmann and E. Bertrand for their help with enzyme production in bioreactor, D. Gillet (Mahtani Chitosan, India) for providing chitin, and D. Navarro and G. Anasontzis for insightful discussions. M.C. was funded by a Marie Curie International Outgoing Fellowship within the 7th European Community Framework Program (328162). S.L., M.-N.R. and J.-G.B. were funded by the Microbio-E A*MIDEX project (ANR-11-IDEX-0001-02). This work was supported in part by the CNRS and the French Infrastructure for Integrated Structural Biology (FRISBI) ANR-10-INSB-05-01. N.L. and B.H. were supported by Agence Française de l'Environnement et de la Maîtrise de l'Energie (1201C102). P.H.W., G.J.D. and L.C. thank the UK Biotechnology and Biological Sciences Research Council (BB/L001926/1 and BB/L021633/1) for funding. G.J.D. is the Royal Society Ken Murray Research Professor.

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Author notes

  1. Marie Couturier and Simon Ladevèze: These authors contributed equally to this work.

Authors and Affiliations

  1. INRA, Aix Marseille University, Biodiversité et Biotechnologie Fongiques (BBF), Marseille, France

    Marie Couturier, Simon Ladevèze, Kristian E Frandsen, Aurore Labourel, Isabelle Herpoël-Gimbert, Sacha Grisel, Mireille Haon, Marie-Noëlle Rosso & Jean-Guy Berrin

  2. Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille University, Marseille, France

    Gerlind Sulzenbacher, Nicolas Lenfant & Bernard Henrissat

  3. INRA, USC1408 Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille, France

    Gerlind Sulzenbacher & Bernard Henrissat

  4. Department of Chemistry, University of York, York, UK

    Luisa Ciano, Gideon J Davies & Paul H Walton

  5. INRA, Unité de Recherche Biopolymères Interactions Assemblages (BIA), Nantes, France

    Mathieu Fanuel, Céline Moreau, Ana Villares, Bernard Cathala, Hélène Rogniaux & David Ropartz

  6. IMBE Aix Marseille University, IRD CNRS UAPV, Faculté de Pharmacie, Marseille, France

    Florence Chaspoul

  7. Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia

    Bernard Henrissat

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  1. Marie Couturier
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Contributions

M.C. identified the new enzymes and performed biochemical characterization. M.-N.R. was in charge of transcriptomic and proteomic analyses. M.C., S.L., S.G., I.H.-G. and M.H. performed production of proteins in flasks and bioreactors. F.C. performed ICP-MS analysis. S.L. and S.G. performed synergy assays with xylanase and protein crystallization. S.L. and G.S. solved the crystal structure of PcAA14B. B.H. and N.L. performed bioinformatic analyses. M.C., S.L., S.G. performed HPAEC analyses. M.F., D.R. and H.R. identified oxidized products using mass spectrometry. M.C., S.G. and I.H.-G. performed saccharification assays. A.V., C.M. and B.C. carried out microscopy and NMR analyses. L.C. performed the EPR study under the direction of P.H.W. and G.J.D. J.-G.B. supervised the work and organized the data. The manuscript was written by J.-G.B. with contributions from B.H. and P.H.W. All authors made comments on the manuscript and approved the final version. Figures were prepared by J.-G.B., K.E.F., A.L., N.L., S.L., L.C., M.F., S.G. and I.H.-G.

Corresponding author

Correspondence to Jean-Guy Berrin.

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Supplementary information

Supplementary Text and Figures

Supplementary Tables 1–4 and Supplementary Figures 1–13 (PDF 3061 kb)

Life Sciences Reporting Summary (PDF 129 kb)

Supplementary Data Set 1

Number of AA14 genes in fungal genomes (XLSX 27 kb)

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Couturier, M., Ladevèze, S., Sulzenbacher, G. et al. Lytic xylan oxidases from wood-decay fungi unlock biomass degradation. Nat Chem Biol 14, 306–310 (2018). https://doi.org/10.1038/nchembio.2558

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