Transcriptomic and genetic analysis reveals a Zn2Cys6 transcription factor necessary for conidiation in submerged culture in Thermothelomyces thermophilus [RNA-seq 2]
Filamentous fungi are important producers of enzymes and secondary metabolites in the biotech industry. A relatively new but highly promising fungus for industrial production is Thermothelomyces thermophilus, which is closely related to the model fungus Neurospora crassa. Nevertheless, to fully exploit the potential of T. thermophilus, a deeper understanding of its biology is necessary. A critical aspect of the filamentous fungal life cycle is the production of asexual spores (conidia), regulated by various stimuli, including nutrient availability. Under certain submerged fermentation conditions, several filamentous fungi produce conidia, which can be detrimental to product expression. In this study, we utilized RNA-seq to map transcriptomic changes during conidia production under submerged conditions in T. thermophilus. We found that the essential genes for conidiation in Aspergillus sp. and N. crassa, fluG and fluffy (fl), are not essential for conidiation in T. thermophilus. However, we identified a transcription factor, res1, whose deletion resulted in a complete loss of conidia production under fermentation conditions. This deletion also led to increased biomass production without increasing enzyme secretion. Notably, the deletion of res1 did not affect spore production on solid media. Differential gene expression analysis between the wild type and the res1 deletion mutant revealed that res1 regulates a broad range of cellular and metabolic processes, including MAPK and spore production pathways. Overexpression of res1 caused a severe growth defect and early conidia production compared to the wild type. Using ChIP-seq, we identified 35 potential target genes of res1, including known conidiation-related genes such as acon3, MAPK genes, and transcription factors like cpc1, as well as genes with unknown functions. Overall, we identified res1 to be obligatory for submerged conidia production and lay the foundation for further work on the T. thermophilus conidiation pathway and its applications. Overall design: We grew WT, ?res1 and ?res1 PH2A::res1-V5 (res1 overexpression) in submerged conditions in pre-culture medium as biological triplicates and took samples for RNAseq at 6, 7.5 and 9  hours post inoculation.