Does Genomic Imprinting Affect Hydrolase Expression in Trichoderma reesei?

Strain degradation is an often-observed phenomenon in eukaryotic microorganisms and spans from the loss of pathogenicity to the degeneration of production strains used in biotechnology. Nonetheless such phenomenon hampers various basic research approaches as well as biotechnological applications, it is only poorly understood. One possible explanation for such phenomenon could be genetic imprinting. In the proposed study it is intended to investigate epigenetic effects on the expression of two closely related regulons (cellulase and xylanase) in the industrially important ascomycete Trichoderma reesei. The study will focus on strain- and growth condition- dependent differences in expression of both regulons. It will include wild type, production, and degenerated production strains as well as inducing and repressing conditions for both regulons. Enzymes resulting from the expression of both regulons are key players in the second-generation biofuel production. Both during strain improvement attempts as well as in biofuel production processes strain degeneration can be observed. The project will aid in a better understanding of such degeneration processes consequently leading to avoiding strategies.

To date, enzymes play an important role in many types of industry (such as food and feed, textile, pulp and paper), however, their significance might still increase considering rising attempts for a careful usage of non-renewable resources. Securing the supply with enzymes in best case as cost-efficient as possible is consequently a move forward towards sustainable products and production processes. The saprotrophic fungus Trichoderma reesei naturally produces enzymes that decompose plant matter. Consequently, this fungus is used for industrial production of these enzymes. Unfortunately, the used production strains sometimes suddenly loose their productivity right during the production process, and sometimes this happens slowly, however, always unpredictably and without obvious reasons. The observation of such a spontaneous degeneration is not limited to T. reesei, but applies to a number of microbial production organisms, and therefore must be considered as a drawback for all affected biotechnological processes. In the present research project it became clear that cis epigenetic mechanisms are the reason for the occurrence of non-producing strains. These mechanisms embrace the presence of more tightly packed DNA (so-called condensed chromatin) and related to this, chemical modifications on small proteins about which the DNA is wrapped (so-called histones). Next to this, methylation of DNA turned out to play a crucial role in the degeneration phenomenon. In this context, the reversion of non-producing strains into producing strains could be achieved during the research work, even though the degeneration was thought to be irreversible until then. Finally, the alterations in physiology and gene expression of the fungal cell that are implicated by the occurrence of degenerated strains could be associated with proteins that mediate shifts in the epigenetic landscape of these strains. Based on the gained knowledge such mediators and their targets should be identified in a follow-up project (a recently established Christian Doppler-laboratory). According engineering and targeted modification of these mediators and targets is assumed to result in stable production strains.