Evolutionary convergence of the lignin degradation mechanism

In a "paleogenetic" study published in the journal PNAS, the Biotechnology for Lignocellulosic Biomass group of the Centro de Investigaciones Biológicas has shown that the more efficient molecular tools in nature to degrade lignin, a key aspect for recycling of carbon in terrestrial ecosystems, have appeared several times during the evolution of ligninolytic fungi.

To reach this conclusion Ayuso-Fernández et al. reconstructed the sequences of the ancestors of the current ligninolytic peroxidases in the order Poliporales, which groups the most active lignin-degrading fungi, to the most recent common ancestor. Additionally, they addressed their resurrection through heterologous expression and biochemical characterization, including the comparison of their molecular structures and the study of their action on model substrates. In this way, a correlation has been established between the independent appearance of a superficial catalytic tryptophan capable of interacting with bulky molecules, and the ability to oxidize lignin (mostly non-phenolic) in two distant lines within the evolution of fungal peroxidases analyzed.

The resurrection of these ancestral proteins provides more detailed information to a study previously published in Science in 2012, with the participation of the group at CIB, where it was established that the appearance of the first fungi capable of degrading lignin, thanks to the presence of ligninolytic peroxidases, coincided with the end of the formation of coal deposits in the Late Carboniferous.

These ancestral proteins have a great biotechnological potential and could serve as a starting point for the rational design and the directed evolution of enzymes in vitro. In the laboratory, the selective pressure of interest could be applied (greater stability at pH or temperature, for example) and obtain biocatalysts of interest in the lignocellulosic biomass industry.

This study has been funded by the European Union under the project H2020-BBI-PPP-2015-720297.

References:
Evolutionary convergence in lignin degrading enzymes. I. Ayuso-Fernández, F.J. Ruiz-Dueñas, A.T. Martínez (2018) Proc. Natl. Acad.Sci. USA. https://doi.org/10.1073/pnas.1802555115
The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. D. Floudas, M. Binder, R. Riley, K. Barry, R.A. Blanchette, B. Henrissat, A.T. Martínez, R. Otillar, J.W. Spatafora, J.S. Yadav, A. Aerts, I. Benoit, A. Boyd, A. Carlson, A. Copeland, P.M. Coutinho, R.P. de Vries, P. Ferreira, K. Findley, B. Foster, J. Gaskell, D. Glotzer, P. Górecki, J. Heitman, C. Hesse, C. Hori, K. Igarashi, J.A. Jurgens, N. Kallen, P. Kersten, A. Kohler, U. Kües, T.K.A. Kumar, A. Kuo, K. LaButti, L.F. Larrondo, E. Lindquist, A. Ling, V. Lombard, S. Lucas, T. Lundell, R. Martin, D. J. McLaughlin, I. Morgenstern, E. Morin, C. Murat, M. Nolan, R.A. Ohm, A. Patyshakuliyeva, A. Rokas, F.J. Ruiz-Dueñas, G. Sabat, A. Salamov, M. Samejima, J. Schmutz, J.C. Slot, F. St.John, J. Stenlid, H. Sun, S. Sun, K. Syed, A. Tsang, A. Wiebenga, D. Young, A. Pisabarro, D.C. Eastwood, F. Martin, D. Cullen, I. V. Grigoriev, D.S. Hibbett. Science 336:1715-1719, 2012.

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