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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize
BMC Genomics, Volume 13, No. 1, Article 444, Year 2012
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Description
Background: Softwood is the predominant form of land plant biomass in the Northern hemisphere, and is among the most recalcitrant biomass resources to bioprocess technologies. The white rot fungus, Phanerochaete carnosa, has been isolated almost exclusively from softwoods, while most other known white-rot species, including Phanerochaete chrysosporium, were mainly isolated from hardwoods. Accordingly, it is anticipated that P. carnosa encodes a distinct set of enzymes and proteins that promote softwood decomposition. To elucidate the genetic basis of softwood bioconversion by a white-rot fungus, the present study reports the P. carnosa genome sequence and its comparative analysis with the previously reported P. chrysosporium genome.Results:P. carnosa encodes a complete set of lignocellulose-active enzymes. Comparative genomic analysis revealed that P. carnosa is enriched with genes encoding manganese peroxidase, and that the most divergent glycoside hydrolase families were predicted to encode hemicellulases and glycoprotein degrading enzymes. Most remarkably, P. carnosa possesses one of the largest P450 contingents (266 P450s) among the sequenced and annotated wood-rotting basidiomycetes, nearly double that of P. chrysosporium. Along with metabolic pathway modeling, comparative growth studies on model compounds and chemical analyses of decomposed wood components showed greater tolerance of P. carnosa to various substrates including coniferous heartwood.Conclusions: The P. carnosa genome is enriched with genes that encode P450 monooxygenases that can participate in extractives degradation, and manganese peroxidases involved in lignin degradation. The significant expansion of P450s in P. carnosa, along with differences in carbohydrate- and lignin-degrading enzymes, could be correlated to the utilization of heartwood and sapwood preparations from both coniferous and hardwood species. © 2012 Suzuki et al.; licensee BioMed Central Ltd.
Authors & Co-Authors
Syed, Khajamohiddin
United States, Cincinnati
University of Cincinnati College of Medicine
Salamov, Asaf A.
United States, Berkeley
U.s. Department of Energy Joint Genome Institute
Hori, Chiaki
Japan, Tokyo
The University of Tokyo
Aerts, Andrea L.
United States, Berkeley
U.s. Department of Energy Joint Genome Institute
Henrissat, Bernard
France, Marseille
Laboratoire Architecture et Fonction Des Macromolécules Biologiques
Wiebenga, Ad
Netherlands, Utrecht
Westerdijk Fungal Biodiversity Institute - Knaw
VanKuyk, Patricia A.
Netherlands, Utrecht
Westerdijk Fungal Biodiversity Institute - Knaw
Barry, Kerrie W.
United States, Berkeley
U.s. Department of Energy Joint Genome Institute
Lindquist, Erika A.
United States, Berkeley
U.s. Department of Energy Joint Genome Institute
LaButti, Kurt M.
United States, Berkeley
U.s. Department of Energy Joint Genome Institute
Lapidus, Alla L.
United States, Berkeley
U.s. Department of Energy Joint Genome Institute
Lucas, Susan L.
United States, Berkeley
U.s. Department of Energy Joint Genome Institute
Coutinho, Pedro M.
France, Marseille
Laboratoire Architecture et Fonction Des Macromolécules Biologiques
Abou-Zaid, Mamdouh M.
Canada, Sault Ste Marie
Great Lakes Forestry Centre
de Vries, Ronald P.
Netherlands, Utrecht
Westerdijk Fungal Biodiversity Institute - Knaw
Yadav, Jagjit Singh
United States, Cincinnati
University of Cincinnati College of Medicine
Grigoriev, Igor V.
United States, Berkeley
U.s. Department of Energy Joint Genome Institute
Master, Emma R.
Canada, Toronto
University of Toronto
Statistics
Citations: 105
Authors: 18
Affiliations: 7
Identifiers
Doi:
10.1186/1471-2164-13-444
ISSN:
14712164
Research Areas
Cancer
Genetics And Genomics
Noncommunicable Diseases