Systems analysis of cellulase production

The ascomycete fungus Trichoderma reesei (anamorph: Hypocrea jecorina) is widely used in industry as a source of cellulases and hemicellulases for the hydrolysis of plant cell wall polysaccharides. In past decades, (hemi)cellulases have already received considerable attention because of their applications in food, feed, textile, pulp and paper industries. Today, these enzymes are employed for the production of renewable biofuels and other fine chemicals from plant biomass. Second generation biofuels derived from agricultural crop residues, grasses, wood and municipal solid waste would have important advantages over first generation biofuels produced from food crops as feedstock since they do not directly or indirectly compete with food production. Lignocellulosic biomass is however notoriously difficult to convert into fermentable sugars and one of the major obstacles that must be overcome are the high costs for hydrolyzing the insoluble and crystalline cellulose by cellulases. To make biofuel production cost-effective a number of technological breakthroughs in the area of enzymes, pre-treatment and fermentation are needed. New studies to understand and improve cellulase efficiency and productivity are therefore at the forefront of biomass research. Academic and industrial research programs have over the past decades produced different T. reesei strains by random mutagenesis whose production of cellulases exceeds 100 grams per liter. In contrasts, reports on successful strain improvement by direct targeted genetic engineering are rare and cellulase yields of these strains cannot compete with the producer strains generated by classical mutagenesis. Molecular manipulations would, however, make strain development more straightforward and would also eliminate undesired deleterious mutations which accumulate during random mutagenesis programs. An important step towards understanding cellulase regulation and improving production was the publication of the completed genome sequence of T. reesei in 2008. The genome sequence paved the way for the development of genome-wide tools including next-generation DNA sequencing technologies for whole genome comparisons of improved producer strains to their ancestors. However, genome sequencing and comparison alone is not sufficient to interpret the observed genomic changes in terms of cellulase production and identify key factors for cellulase production. For a correct interpretation of the mutagenic events additional transcriptomic and phenotypic information is required. Understanding the changes in the genomes and transcriptomes that accompanied the improvement of cellulase production is a straightforward means to detect key factors involved in cellulase regulation and production and thereby identifying bottlenecks for cellulase overproduction. The obtained information can in turn be used to create more efficient cellulase producing strains through targeted molecular genetic manipulation rather than through random mutagenesis that leads to collateral and deleterious genomic damages.