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Unraveling the code of a common mushroom leads to less expensive biofuels


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Fuzzy Fungi (Schizophyllum commune) 1

A recent effort to sequence the genomes of white rot fungi has provided researchers insights into the workings of plant enzymes that could help accelerate the development of industrial enzymes used to break down plant materials for biofuels. Two researchers from Pacific Northwest National Laboratory, Scott Baker and Jon Magnuson, were instrumental in the study, results of which were published in the July, 2010, issue of Nature Biotechnology. Baker was part of the team that successfully proposed and initiated the project in collaboration with the U.S. Department of Energy Joint Genome Institute while Magnuson participated in the annotation and analysis of the genome sequence.

Why it matters:

To manufacture biofuels from biomass, plant cell walls must be broken down—especially lignin—which is more difficult to break down than cellulose. Currently, the enzymes used to degrade biomass are so expensive that cost is one of the bottlenecks in bringing biologically derived fuels to the market. Fungi are a rich source of enzymes that break down plant cell walls and Schizophyllum commune, the fungus studied in this research, is particularly good at breaking down lignin. Information about S. commune gained through this research has provided valuable insights into how lignin is broken down.


S. commune is a wood-rotting fungus that has been used often in studies on bioremediation and degrading ligno-cellulosic materials. In this study, the DOE Joint Genome Institute (JGI) sequences the genome of S. commune and provides computationally derived models of gene sequences contained within the genome. In the next step, the research team manually analyzes the catalog of gene models in an effort to develop a high-level snapshot of the metabolic and enzymatic processes encoded within the genome. In other words, they attempt to determine what S. commune does, which genes are present, how they work together, and what the organism is capable of doing. There are 13,181 predicted gene models in S. commune so it takes time and a large team of researchers to analyze all of the genes. Different researchers take on different areas; identifying biomass-degrading enzymes, for example, is one of many areas. In this study, researchers studying enzymes catalogued the secreted enzymes that play a role in degrading the cellulose and lignin fibers of plants. This research will help them identify and understand the enzymes that allow fungi to degrade complex plant materials—especially lignin. Scientists from around the world have been working on this project to unravel the genomic sequence of this important and common fungus for the past four years.

What's next:

The genome sequencing of white rot fungi fits into a larger project dedicated to enhancing our understanding of the myriad of biological processes that are associated with fungi and with DOE mission areas in bioremediation, carbon cycling and bioenergy.

Acknowledgements: The Joint Genome Institute is funded by the U.S. Department of Energy's Office of Biological and Environmental Research. The PNNL research team was funded by the Office of Energy Efficiency and Renewable Energy's Biomass Program.

Research team: The research team for this work includes: Robin A. Ohm, Utrecht University, The Netherlands; Jan F. de Jong, Utrecht University, The Netherlands; Luis G. Lugones, Utrecht University, The Netherlands; Andrea Aerts, DOE Joint Genome Institute; Erika Kothe, Friedrich Schiller University, Germany; Jason E. Stajich, University of California, Riverside; Ronald P. de Vries, Utrecht University and CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands; Eric Record, INRA, UMR1163, Biotechnologie des Champignons Filamenteux, France, and Universites Aix-Marseille; Anthony Levasseur, INRA, UMR1163, Biotechnologie des Champignons Filamenteux, France, and Universites Aix-Marseille; Scott E. Baker, DOE Joint Genome Institute and Pacific Northwest National Laboratory; Kirk A. Bartholomew, Sacred Heart University, Ct., USA; Pedro M. Coutinho, Univ. Aix-Marseille, France; Susann Erdmann, Friedrich Schiller University, Germany; Thomas J. Fowler, Southern Illinois University Edwardsville; Allen C. Gathman; Southeast Missouri State University; Vincent Lombard, Univ. Aix-Marseille, France; Bernard Henrissat, Univ. Aix-Marseille, France; Nicole Knabe, DOE Joint Genome Institute; Ursula Kües, Büsgen-Institute, University of Göttingen, Germany; Walt W. Lilly, Southeast Missouri State University; Erika Lindquist, DOE Joint Genome Institute; Susan Lucas, DOE Joint Genome Institute; Jon K. Magnuson, Pacific Northwest National Laboratory; François Piumi, INRA, UMR1163, Biotechnologie des Champignons Filamenteux, France and Universites Aix-Marseille; Marjatta Raudaskoski, University of Turku, Finland; Asaf Salamov, DOE Joint Genome Institute; Jeremy Schmutz, DOE Joint Genome Institute; Francis W.M.R. Schwarze, Swiss Federal Laboratories for Materials Testing and Research, Switzerland; Patricia A. vanKuyk, Leiden University, The Netherlands; Stephen Horton, Union College, Schenectady, New York; Igor V. Grigoriev, DOE Joint Genome Institute; Han A.B. Wösten, Utrecht University, The Netherlands.

1)Schizophyllum commune, or white rot fungi. Photo courtesy of Doug Bowman,


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