Trichoderma reesei Cellulase in the Monoculture and the Mixed Culture with Aspergillus niger: From Transcripts to Proteins.

The mixed culture of Trichoderma reesei and Aspergillus niger enhanced cellulase production, optimized cellulase composition, and improved enzymatic hydrolysis efficiency. In our multi-omics study, we found that the transcriptional changes in cellulase components in the mixed culture, compared to the monoculture, did not align with the corresponding changes at the protein level. However, the reason why cellulase proteins exhibited different variations from their corresponding transcripts remains unclear. Here, we systematically analyzed cellulase production in the mixed culture at both the transcriptional and protein levels, using the monoculture of T. reesei as a control, to elucidate the underlying mechanism. In the mixed culture, the transcription of most cellulase genes generally increased, with some exceptions, such as egl5, which decreased. This suggests the complexity of signaling pathways and regulatory networks. The cellulase gene expression profiles and the protein profiles were inconsistent. Only cbh2, eg2, and egl5 proteins exhibited noticeable increase in abundance compared to the monoculture. We compared the composition of cellulase in the T. reesei monoculture with that in the mixed culture of T. reesei and A. niger and found that the patterns differed much less than at the transcriptional level. Compared to the T. reesei monoculture, the cellulase from the mixed culture had a higher proportion of CBH II (cbh2), which is crucial for the synergistic degradation capacity of cellulase during enzymatic hydrolysis. The various physiological responses to the mixed culture-including signaling pathways, unfolded protein response (UPR), endoplasmic reticulum-associated degradation (ERAD), apoptosis, autophagy, translocation, secretion, and proteolysis-played distinct roles in determining the fate of each cellulase component. The mechanism by which the mixed culture affected cellulase production in T. reesei is elucidated and elaborated. These findings shed light on a systems engineering approach of T. reesei for cellulase production.