DegenSeq

Fungi are a relatively understudied and incredibly versatile group of organisms with enormous value and potential for covering the rising human demands. The filamentous fungus Trichoderma reesei is used for the biotechnical production of carbohydrate-active enzymes, in particular cellulases. These enzymes are essential for many other manufacturing industries, for example the food, feed, textile and paper industry. Through a process of random mutagenesis and following screening, researchers have generated strains of T. reesei, which have enhanced cellulase production capacities. However, spontaneous strain degeneration, a phenomenon during which an organism progressively and irreversibly loses its production capacity, does negatively influence cellulase production by T. reesei. It was reported that also other biotechnological production organisms are affected by this phenomenon. This means that this phenomenon can at least result in economic losses or - in worse case - it poses a threat for the secure availability of certain products. On the one hand, the project leader and her co-workers have recently identified the contribution of epigenetic regulatory mechanisms playing a role in this phenomenon, and also the involvement of long non-coding RNAs in the regulation of cellulase expression. On the other hand, technological breakthroughs, notably long-read sequencing techniques, have revolutionized the fields of epigenomics and transcriptomics and opened new research avenues in non-model organisms like T. reesei. Therefore, the current research study will i) investigate the changes in the epigenetic landscape associated with loss of cellulase expression in T. reesei and ii) reveal the long non-coding RNA repertoire and its putative role in cellulase expression in T. reesei using long-read sequencing techniques for both purposes. Third, the modification of the cellulase expression capacities by a combination of genetic and epigenetic strain engineering strategies is planned.