CLR1 and CLR2 are light dependent regulators of xylanase and pectinase genes in Trichoderma reesei.

Regulation of plant cell wall degradation is of utmost importance for understanding the carbon cycle in nature, but also to improve industrial processes aimed at enzyme production for next generation biofuels. Thereby, the transcription factor networks in different fungi show conservation as well as striking differences, particularly between Trichoderma reesei and Neurospora crassa. Here, we aimed to gain insight into the function of the transcription factors CLR1 and CLR2 in T. reesei, which are crucial for cellulase gene expression in N. crassa. We studied impacts on gene regulation with cellulose, xylan, pectin and chitin, growth on 95 different carbon sources as well as an involvement in regulation of secondary metabolism or development. We found that CLR1 is present in the genome of T. reesei and other Trichoderma spp., albeit with considerably lower homology compared to other ascomycetes. CLR1 and CLR2 regulate pectinase transcript levels upon growth on pectin, no major function was detected on chitin. CLR1 and CLR2 form a positive feedback cycle on xylan and were found to be responsible for balancing co-regulation of xylanase genes in light and darkness with distinct and in part opposite regulatory effects of up to 8fold difference. Our data suggest that CLR1 and CLR2 have evolved differently in T. reesei compared to other fungi. We propose a model in which their main function is in adjustment of regulation of xylanase gene expression to different light conditions and to balance transcript levels of genes involved in plant cell wall degradation according to their individual relevance for this process.