Beyond similarity: Unveiling the distinctive transcriptional regulatory roles of ARA1 in plant biomass utilization by Myceliophthora thermophila and related fungi

Saprobic fungi have important biotechnological applications, particularly in biorefinery processes in which their hydrolytic enzymes (CAZymes) convert the biomass into valuable products such as biofuels and biochemicals. Myceliophthora thermophila is a thermophilic fungus, which makes it an attractive source of enzymes for biorefinery. However, the regulatory system that controls the production of CAZymes in this species is only partially understood. This study focuses on understanding the role of ARA1 in M. thermophila, investigating its function beyond conventional L-arabinose/D-galactose utilization, by using deletion and overexpression strains for detailed transcriptomic and phenotypic analyses. The comparison with other fungi provides insights into ARA1's diverse functions within Sordariomycete fungi. Our results indicate that ARA1 is a key regulator in M. thermophila, as it controls the utilization of L-arabinose, D-galactose, xylan, cellulose and pectin, exhibiting a broader role compared to its orthologs in other Sordariomycetes. Moreover, co-regulation between XYR1 and ARA1, with significant overlap in target genes, was observed for the first time in M. thermophila. Constitutive overexpression of ara1 is identified as a promising approach for enhancing hydrolytic performance during M. thermophila growth on complex and recalcitrant substrates but is strongly dependent on the right promoter. In conclusion, our study identifies M. thermophila ARA1 as a key regulator in plant biomass utilization, although additional regulators, e.g., CLR1 and CLR2, remain to be investigated to fully elucidate the regulatory network governing this process. The observed diversity in the role of ARA1 among Sordariomycetes highlights the flexibility of transcriptional networks involved in biomass degradation and offers leads for improving biotechnological processes.