Sequencing of Fungus Genome Opens Opportunities for Improvements in Biofuels Enzymes

5 May 2008

Microscope image of T. reesei hyphae with vesicle membranes stained red and cell wall chitin in blue. Click to enlarge. Courtesy of Mari Valkonen, VTT Finland.

The genome analysis of the fungus Trichoderma reesei, notorious for the deterioration of fatigues and tents in the South Pacific theater of WWII, highlights opportunities for further improvements in enzymes customized for biofuels production. The results were published online 4 May in Nature Biotechnology by an international team of government, academic, and industry researchers led by the US Department of Energy Joint Genome Institute (DOE JGI) and Los Alamos National Laboratory (LANL).

The progenitor strain of T. reesei has yielded variants for broad industrial applications and is known today as an abundant source of enzymes, particularly cellulases and hemicellulases, currently being explored to catalyze the deconstruction of plant cell walls as a first step towards the production of biofuels from lignocellulose.

The information generated from the genome of T. reesei provides us with a roadmap for accelerating research to optimize fungal strains for reducing the current prohibitively high cost of converting lignocellulose to fermentable sugars. Improved industrial enzyme ‘cocktails’ from T. reseei and other fungi will enable more economical conversion of biomass from such feedstocks as the perennial grasses Miscanthus and switchgrass, wood from fast-growing trees like poplar, agricultural crop residues, and municipal waste, into next-generation biofuels. Through these incremental advances, we hope to eventually supplant the gasoline-dependent transportation sector of our economy with a more carbon-neutral strategy.

—Eddy Rubin, DOE JGI Director and one of the paper’s senior authors

The research team compared the 34-million-nucleotide genome of T. reesei with 13 previously characterized fungi and discovered something counterintuitive. Despite its reputation as an avid plant polysaccharide degrader, T. reesei, was found to have the smallest inventory of genes powering its robust degradation machinery.

We were aware of T. reesei’s reputation as a producer of massive quantities of degrading enzymes, however we were surprised by how few enzyme types it produces, which suggested to us that its protein secretion system is exceptionally efficient. While little appears to have changed in the secretion machinery since divergence with a common ancestor with yeast there are some intriguing differences in the way T. reesei processes some protein bonds important for cellulase production.

—Diego Martinez, lead author

In their comparative analysis of T. reesei with other fungi, the team observed clustering of carbohydrate-active enzyme genes, which suggested a specific biological role: polysaccharide degradation.

While plant tissues are not likely the main source of nutrients for T. reesei, upon detection of cellulose and hemicellulose it seems that the organization of these degrading genes may be the key to a rapid response.

—Diego Martinez

Resources

• Diego Martinez, et. al. (2008) Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina), Nature Biotechnology Published online: 4 May 2008 | DOI: 10.1038/nbt1403