Peroxidase evolution in white-rot fungi follows wood lignin evolution in plants
Abstract
A comparison of sequenced Agaricomycotina genomes suggests that efficient degradation of wood lignin was associated with the appearance of secreted peroxidases with a solvent-exposed catalytic tryptophan. This hypothesis is experimentally demonstrated here by resurrecting ancestral fungal peroxidases, after sequence reconstruction from genomes of extant white-rot Polyporales, and evaluating their oxidative attack on the lignin polymer by state-of-the-art analytical techniques. Rapid stopped-flow estimation of the transient-state constants for the 2 successive one-electron transfers from lignin to the peroxide-activated enzyme (k2appandk3app) showed a progressive increase during peroxidase evolution (up to 50-fold higher values for the rate-limitingk3app). The above agreed with 2-dimensional NMR analyses during steady-state treatments of hardwood lignin, showing that its degradation (estimated from the normalized aromatic signals of lignin units compared with a control) and syringyl-to-guaiacyl ratio increased with the enzyme evolutionary distance from the first peroxidase ancestor. More interestingly, the stopped-flow estimations of electron transfer rates also showed how the most recent peroxidase ancestors that already incorporated the exposed tryptophan into their molecular structure (as well as the extant lignin peroxidase) were comparatively more efficient at oxidizing hardwood (angiosperm) lignin, while the most ancestral “tryptophanless” enzymes were more efficient at abstracting electrons from softwood (conifer) lignin. A time calibrationmore »
- Authors:
-
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, E-28040 Madrid, Spain,
- Instituto de Recursos Naturales y Agrobiología de Sevilla, Consejo Superior de Investigaciones Científicas E-41012 Seville, Spain
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1564415
- Alternate Identifier(s):
- OSTI ID: 1625038
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Published Article
- Journal Name:
- Proceedings of the National Academy of Sciences of the United States of America
- Additional Journal Information:
- Journal Name: Proceedings of the National Academy of Sciences of the United States of America Journal Volume: 116 Journal Issue: 36; Journal ID: ISSN 0027-8424
- Publisher:
- Proceedings of the National Academy of Sciences
- Country of Publication:
- United States
- Language:
- English
- Subject:
- Science & Technology - Other Topics
Citation Formats
Ayuso-Fernández, Iván, Rencoret, Jorge, Gutiérrez, Ana, Ruiz-Dueñas, Francisco Javier, and Martínez, Angel T. Peroxidase evolution in white-rot fungi follows wood lignin evolution in plants. United States: N. p., 2019.
Web. doi:10.1073/pnas.1905040116.
Ayuso-Fernández, Iván, Rencoret, Jorge, Gutiérrez, Ana, Ruiz-Dueñas, Francisco Javier, & Martínez, Angel T. Peroxidase evolution in white-rot fungi follows wood lignin evolution in plants. United States. https://doi.org/10.1073/pnas.1905040116
Ayuso-Fernández, Iván, Rencoret, Jorge, Gutiérrez, Ana, Ruiz-Dueñas, Francisco Javier, and Martínez, Angel T. Mon .
"Peroxidase evolution in white-rot fungi follows wood lignin evolution in plants". United States. https://doi.org/10.1073/pnas.1905040116.
@article{osti_1564415,
title = {Peroxidase evolution in white-rot fungi follows wood lignin evolution in plants},
author = {Ayuso-Fernández, Iván and Rencoret, Jorge and Gutiérrez, Ana and Ruiz-Dueñas, Francisco Javier and Martínez, Angel T.},
abstractNote = {A comparison of sequenced Agaricomycotina genomes suggests that efficient degradation of wood lignin was associated with the appearance of secreted peroxidases with a solvent-exposed catalytic tryptophan. This hypothesis is experimentally demonstrated here by resurrecting ancestral fungal peroxidases, after sequence reconstruction from genomes of extant white-rot Polyporales, and evaluating their oxidative attack on the lignin polymer by state-of-the-art analytical techniques. Rapid stopped-flow estimation of the transient-state constants for the 2 successive one-electron transfers from lignin to the peroxide-activated enzyme (k2appandk3app) showed a progressive increase during peroxidase evolution (up to 50-fold higher values for the rate-limitingk3app). The above agreed with 2-dimensional NMR analyses during steady-state treatments of hardwood lignin, showing that its degradation (estimated from the normalized aromatic signals of lignin units compared with a control) and syringyl-to-guaiacyl ratio increased with the enzyme evolutionary distance from the first peroxidase ancestor. More interestingly, the stopped-flow estimations of electron transfer rates also showed how the most recent peroxidase ancestors that already incorporated the exposed tryptophan into their molecular structure (as well as the extant lignin peroxidase) were comparatively more efficient at oxidizing hardwood (angiosperm) lignin, while the most ancestral “tryptophanless” enzymes were more efficient at abstracting electrons from softwood (conifer) lignin. A time calibration of the ancestry of Polyporales peroxidases localized the appearance of the first peroxidase with a solvent-exposed catalytic tryptophan to 194 ± 70 Mya, coincident with the diversification of angiosperm plants characterized by the appearance of dimethoxylated syringyl lignin units.},
doi = {10.1073/pnas.1905040116},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = 36,
volume = 116,
place = {United States},
year = {2019},
month = {8}
}
https://doi.org/10.1073/pnas.1905040116
Web of Science
Figures / Tables:

Works referenced in this record:
Lignin-degrading peroxidases in Polyporales: an evolutionary survey based on 10 sequenced genomes
journal, November 2013
- Ruiz-Dueñas, Francisco J.; Lundell, Taina; Floudas, Dimitrios
- Mycologia, Vol. 105, Issue 6
Wheat cells accumulate a syringyl-rich lignin during the hypersensitive resistance response
journal, February 2007
- Menden, Barbara; Kohlhoff, Markus; Moerschbacher, Bruno M.
- Phytochemistry, Vol. 68, Issue 4
The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes
journal, June 2012
- Floudas, Dimitrios; Binder, Manfred; Riley, Robert
- Science, Vol. 336, Issue 6089
Enzymatic delignification of plant cell wall: from nature to mill
journal, June 2009
- Martínez, Ángel T.; Ruiz-Dueñas, Francisco J.; Martínez, María Jesús
- Current Opinion in Biotechnology, Vol. 20, Issue 3
The origin and evolution of lignin biosynthesis: Tansley review
journal, June 2010
- Weng, Jing-Ke; Chapple, Clint
- New Phytologist, Vol. 187, Issue 2
Variation of the phenolic hydroxyl group content in wood lignins
journal, September 1991
- Lai, Y. -Z.; Guo, X. -P.
- Wood Science and Technology, Vol. 25, Issue 6
Megaphylogeny resolves global patterns of mushroom evolution
journal, March 2019
- Varga, Torda; Krizsán, Krisztina; Földi, Csenge
- Nature Ecology & Evolution, Vol. 3, Issue 4
Estimating Divergence Times in Large Phylogenetic Trees
journal, October 2007
- Britton, Tom; Anderson, Cajsa Lisa; Jacquet, David
- Systematic Biology, Vol. 56, Issue 5
Increase of Redox Potential during the Evolution of Enzymes Degrading Recalcitrant Lignin
journal, January 2019
- Ayuso-Fernández, Iván; De Lacey, Antonio L.; Cañada, Francisco J.
- Chemistry - A European Journal, Vol. 25, Issue 11
The timescale of early land plant evolution
journal, February 2018
- Morris, Jennifer L.; Puttick, Mark N.; Clark, James W.
- Proceedings of the National Academy of Sciences, Vol. 115, Issue 10
Enzymatic "Combustion": The Microbial Degradation of Lignin
journal, October 1987
- Kirk, T. K.; Farrell, R. L.
- Annual Review of Microbiology, Vol. 41, Issue 1, p. 465-501
Substrate oxidation sites in versatile peroxidase and other basidiomycete peroxidases
journal, January 2009
- Ruiz-Duenas, F. J.; Morales, M.; Garcia, E.
- Journal of Experimental Botany, Vol. 60, Issue 2
Experimental recreation of the evolution of lignin-degrading enzymes from the Jurassic to date
journal, March 2017
- Ayuso-Fernández, Iván; Martínez, Angel T.; Ruiz-Dueñas, Francisco J.
- Biotechnology for Biofuels, Vol. 10, Issue 1
Evolutionary dynamics of host specialization in wood-decay fungi
journal, August 2018
- Krah, Franz-Sebastian; Bässler, Claus; Heibl, Christoph
- BMC Evolutionary Biology, Vol. 18, Issue 1
A Rapid Bootstrap Algorithm for the RAxML Web Servers
journal, October 2008
- Stamatakis, Alexandros; Hoover, Paul; Rougemont, Jacques
- Systematic Biology, Vol. 57, Issue 5
Independent Recruitment of an O -Methyltransferase for Syringyl Lignin Biosynthesis in Selaginella moellendorffii
journal, July 2011
- Weng, Jing-Ke; Akiyama, Takuya; Ralph, John
- The Plant Cell, Vol. 23, Issue 7
Pyrolysis-gas chromatography/Mass spectrometry analysis of phenolic and etherified units in natural and industrial lignins
journal, April 1999
- Camarero, Susana; Bocchini, Paola; Galletti, Guido C.
- Rapid Communications in Mass Spectrometry, Vol. 13, Issue 7
PAML 4: Phylogenetic Analysis by Maximum Likelihood
journal, April 2007
- Yang, Z.
- Molecular Biology and Evolution, Vol. 24, Issue 8
Comparative Genomics of Early-Diverging Mushroom-Forming Fungi Provides Insights into the Origins of Lignocellulose Decay Capabilities
journal, December 2015
- Nagy, László G.; Riley, Robert; Tritt, Andrew
- Molecular Biology and Evolution, Vol. 33, Issue 4
Role of surface tryptophan for peroxidase oxidation of nonphenolic lignin
journal, September 2016
- Sáez-Jiménez, Verónica; Rencoret, Jorge; Rodríguez-Carvajal, Miguel Angel
- Biotechnology for Biofuels, Vol. 9, Issue 1
Evolutionary convergence in lignin-degrading enzymes
journal, June 2018
- Ayuso-Fernández, Iván; Ruiz-Dueñas, Francisco J.; Martínez, Angel T.
- Proceedings of the National Academy of Sciences, Vol. 115, Issue 25
Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi
journal, June 2014
- Riley, Robert; Salamov, Asaf A.; Brown, Daren W.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 27
Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78
journal, May 2004
- Martinez, Diego; Larrondo, Luis F.; Putnam, Nik
- Nature Biotechnology, Vol. 22, Issue 6
Climate, decay, and the death of the coal forests
journal, July 2016
- Hibbett, David; Blanchette, Robert; Kenrick, Paul
- Current Biology, Vol. 26, Issue 13
Lignins: Natural polymers from oxidative coupling of 4-hydroxyphenyl- propanoids
journal, January 2004
- Ralph, John; Lundquist, Knut; Brunow, Gösta
- Phytochemistry Reviews, Vol. 3, Issue 1-2, p. 29-60
Figures / Tables found in this record: