Cross-kingdom comparative genomics reveal the metabolic potential of fungi for lignin turnover in deadwood

Kijpornyongpan, Teeratas; Kuatsjah, Eugene; Komp, Evan; Evans, James E.; Ruiz-Dueñas, Francisco Javier; Salvachúa, Davinia

doi:10.1038/s41559-025-02785-6

Title: Cross-kingdom comparative genomics reveal the metabolic potential of fungi for lignin turnover in deadwood

Journal Article · Wed Jul 09 00:00:00 UTC 2025 · Nature Ecology and Evolution

DOI: https://doi.org/10.1038/s41559-025-02785-6 · OSTI ID:2574775

Kijpornyongpan, Teeratas ^[1]; Kuatsjah, Eugene ^[2]; Komp, Evan ^[1]; Evans, James E. ^[3];

^[4];

^[1]

National Renewable Energy Laboratory (NREL), Golden, CO (United States)
National Renewable Energy Laboratory (NREL), Golden, CO (United States); Agency for Science, Technology and Research (A*STAR) (Singapore)
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
Consejo Superior de Investigaciones Cientificas (CSIC), Madrid (Spain). Centro de Investigaciones Biológicas Margarita Salas (CIB)

Deadwood is a major carbon source in forests, and yet the fate of this carbon remains a gap in our understanding of global carbon cycling. Lignin, the most recalcitrant biopolymer in wood, is mainly decayed through extracellular enzymatic and chemical processes initiated by white-rot fungi. However, the intracellular conversion of lignin decay products has been overlooked in the fungal kingdom. Here we integrate comparative genomic and phylogenetic analyses to understand the distribution and evolution of enzymes responsible for modifying lignin-related aromatic compounds-such as decarboxylases, hydroxylases, dioxygenases and other downstream ring-cleavage enzymes-that funnel carbon to central metabolism across the bacterial and the fungal kingdoms. We demonstrate that specific fungal lineages conserve these enzyme families, and that the abilities to enzymatically depolymerize lignin and catabolize lignin-related aromatic compounds are not necessarily coupled. Our analyses also reveal an expanded substrate specificity of aromatic ring-cleavage enzymes during fungal evolution, as well as a clade of extracellular enzymes among them, broadening the spatial range of these biochemical capabilities. Together, our results highlight a large diversity of fungal enzymes and hosts that warrant further investigation for inclusion into carbon cycling models and biotechnological applications for the conversion of aromatic compounds.

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Research Organization:: National Renewable Energy Laboratory (NREL), Golden, CO (United States); Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC05-76RL01830; AC36-08GO28308

OSTI ID:: 2574775

Report Number(s):: NREL/JA--2800-93659; PNNL-SA--212707

Journal Information:: Nature Ecology and Evolution, Journal Name: Nature Ecology and Evolution Journal Issue: 9 Vol. 9; ISSN 2397-334X

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
aromatic
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evolution
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lignin
phylogenetics

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