Strain degeneration in Trichoderma reesei is triggered by high protein productivity and influenced by DNA methylation

Thiago Mello-de-Sousa 1 Christian Derntl 2 Robert Mach 2 Debbie Yaver 3 Astrid Mach-Aigner 1
1Institute of Chemical, Environmental and Biological Engineering, Christian Doppler Laboratory for Optimized Expression of Carbohydrate-Active Enzymes, TU Wien, Vienna, Austria
2Institute of Chemical, Environmental and Biological Engineering, TU Wien, Vienna, Austria
3., Novozymes Inc., Davis, California, USA

Since when QM6a, the wild-type T. reesei strain, was isolated during the Second World War, it has been used in strain development programs in order to isolate engineered derivatives for cellulase production. Nevertheless, higher productivity often comes with a cost. Hyper-productive strains (cel+) occasionally lose protein productivity after extended enzyme production fermentation and acquire a cellulase negative (cel-) phenotype. In this study we developed a lab-scale method based on extended cultivations to monitor the occurrence of the (cel-) phenotype and to evaluate the reversibility of the degeneration process. An exploratory investigation was performed with four T. reesei strains with different enzyme production capacities (QM6a QM6a-OExyr1 M4 M10). We observed that the occurrence of the (cel-) phenotype is triggered by endoplasmic reticulum stress and influenced by (1) productivity and (2) how adapted the production host is in order to deal with intense protein production. The higher the production and the slower the unfolded protein response, the higher is the frequency of the (cel-) phenotype occurrence. The loss of productivity of the (cel-) phenotype is partially related to reduced chromatin accessibility and strong down-regulation of the gene encoding the Xylanase regulator 1 (Xyr1). Moreover, the linkage of the degeneration process to DNA methylation was assumed based on hydralazine treatment. The induced DNA hypomethylation applied to strains M4 and M10 attenuates the process of degeneration and partially recovers the (cel+) phenotype in (cel-) isolates.