JGI Decodes Wood & Toxic Waste-Degrading Fungus Genome

The United States Department of Energy (DOE) Joint Genome Institute (JGI) announces today the publication of a high-quality draft genome sequence of the white rot fungus, Phanerochaete chrysosporium. These are the only known microbes capable of efficiently degrading the recalcitrant aromatic plant polymer lignin, one of the most abundant natural materials on earth. White rot fungi such as Phanerochaete chrysosporium play a pivotal role in the carbon cycle–the circulation of carbon from the atmosphere into organisms and back again. They also have demonstrated the ability to remediate explosive contaminants, pesticides and toxic waste with similar chemical structures to lignin. The sequence findings are summarized in the May 2nd on-line edition of the journal Nature Biotechnology.

“Phanerochaete chrysosporium is the first basidiomycete fungus to be sequenced, providing a glimpse into the genetic diversity of fungi,” says Dan Rokhsar, head of the JGI Computational Genomics Department. “It’s the first of a trio of fungal genomes we’ll be tackling that have their own unique constellation of degradative enzymes. The availability of these genomes will spur industrial and bioremediative uses for these organisms.”

Basidiomycetes are represented by important agricultural species including the familiar edible white button mushroom, Agaricus bisporus, and such plant pathogens as smuts and rusts. They also comprise certain opportunistic human pathogens that can be problematic especially in immune-compromised individuals. The basidiomycetes are believed to have diverged from the ascomycetes, a classification that includes Saccharomyces cerevisiae (brewer’s yeast) and Neurospora (bread mold), over 500 million years ago, and to be more than a billion years removed from plants and animals.

“Sequencing the white rot genome is the first step toward understanding a very complex chemical process,” says Randy Berka, research fellow from Novozymes Biotech in Davis, Calif., and one of the authors on the paper. “This organism is capable of doing some unique and complicated biochemistry. But with the genetic blueprint in hand, we can begin to understand the choreography of how white rot fungi degrade lignin and assess the implications for the pulp and paper industry and for bioremediation applications. Having free access to the complete manifest that the genome provides will enable researchers to realize industrial and societal benefits sooner.”

White rots are filamentous, or threadlike, wood decay fungi commonly found inhabiting forest detritus and fallen trees. The name derives from the bleached skeletal appearance of the crystalline cellulose left by selective degradation of lignin caused by these fungi. P. chrysosporium has the uncanny ability to consume the lignin and leave the cellulose of the wood virtually untouched–a major asset in paper production. White rot fungi catalyze the initial decomposition of lignin by secreting an array of enzymes known as oxidases and peroxidases.

“By elucidating the repertoire of genes, the P. chrysosporium genome database now established provides an experimental framework to more fully understand this fundamental process,” says Dan Cullen, research scientist with the USDA Forest Products Lab in Madison, Wisconsin, and another author on the paper.

“The oxidative enzyme systems of P. chrysosporium not only degrade lignin but also transform an impressive array of xenobiotics,” says Cullen. Xenobiotics are man-made compounds, for instance, the broad spectrum of organopollutants that include PCBs (polychlorinated biphenyls), PCP (pentachlorophenol), and various PAHs (polycyclic aromatic hydrocarbons). In numerous laboratory and field trials Phanerochaete has been shown to degrade these compounds for the remediation of contaminated soils and effluents.

“These enzymes hold much promise in the modification of wood and textile fibers and in converting low-grade materials into fuels and chemicals,” Cullen continues. “Of particular interest to the pulp and paper industry are such enzyme systems that offer environmentally friendly approaches to bleaching. The white rot genome also provides a foundation for clarifying the genetics and physiology of fungal colonization of wood.

“This information is key to improving bioprocesses such as biomechanical pulping where fungal pretreatment of wood chips substantially reduces energy consumption in mechanical pulping,” says Cullen. “Further, the information gives us insight into the destructive decay of wood ’in service’ and may ultimately pave the way for developing effective and environmentally benign preservatives.”

JGI used the shotgun sequencing approach to attain over ten times coverage across the 30-million-base pair genome of P. chrysosporium. “By employing a predictive modeling strategy for gene finding, the annotation team identified 11,777 genes in the genome,” says Diego Martinez, a JGI biomedical scientist and lead author on the paper. “Rich with enzymatic activity, the P. chrysosporium genome harbors the genetic information to encode more than 240 theoretical carbohydrate-active enzymes.”

The other authors of the Nature Biotechnology article include Luis F. Larrondo of the Millenium Institute for Fundamental and Applied Biology, Pontifica Universidad Católica de Chile; Nik Putnam, Jarrod Chapman, Maarten D. Sollewijn Gelpke , Katherine Huang and J. Chris Detter of JGI; Kevin G Helfenbein of the Invertebrate Zoology, American Museum of Natural History, New York City; Preethi Ramaiya of Novozymes Biotech; Frank Larimer of Oak Ridge National Laboratory; Pedro M. Coutinho and Bernard Henrissat of the Architecture et Fonction des Macromolécules Biologiques, and Universités d’Aix-Marseille, France. The annotated genome, with the various highlighted genes and genetic motifs, is available on an interactive web portal at http://www.jgi.doe.gov/whiterot/.

The Joint Genome Institute (JGI), located in Walnut Creek, California, was established in 1997 by three of the DOE national laboratories managed by the University of California: Lawrence Berkeley National Laboratory and Lawrence Livermore National Laboratory in California and Los Alamos National Laboratory in New Mexico. In addition to its microbial sequencing projects, JGI has whole-genome sequencing programs that include vertebrates, fungi, and plants. Funding for the JGI is predominantly from the Office of Biological and Environmental Research in DOE’s Office of Science.

For More Information, Contact:
David Gilbert
Joint Genome Institute
(925) 296-5643
DEGilbert@lbl.gov