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BackgroundTrichoderma reesei is one of the major producers of enzymes for the conversion of plant biomass to sustainable fuels and chemicals. Crude plant biomass can induce the production of CAZymes in T. reesei, but there is limited understanding of how the transcriptional response to crude plant biomass is regulated. In addition, it is unknown whether induction on untreated recalcitrant crude plant biomass (with a large diversity of inducers) can be sustained for longer. We investigated the transcriptomic response of T. reesei to the two industrial feedstocks, corn stover (CS) and soybean hulls (SBH), over time (4 h, 24 h and 48 h), and its regulatory basis using transcription factor deletion mutants (Δxyr1 and Δara1). We also investigated whether deletion of a xylulokinase gene (Δxki1) from the pentose catabolic pathway that converts potential inducers could lead to increased CAZyme gene expression.ResultsBy analyzing the transcriptomic responses using clustering as well as differential and cumulative expression of plant biomass degrading CAZymes, we found that corn stover induced a broader range and higher expression of CAZymes in T. reesei, while SBH induced more pectinolytic and mannanolytic transcripts. XYR1 was the major TF regulating CS utilization, likely due to the significant amount of d-xylose in this substrate. In contrast, ARA1 had a stronger effect on SBH utilization, which correlates with a higher abundance of l-arabinose in SBH that activates ARA1. Blocking pentose catabolism by deletion of xki1 led to higher expression of CAZyme encoding genes on both substrates at later time points. Surprisingly, this was also observed for Δara1 at later time points. Many of these genes were XYR1 regulated, suggesting that inducers for this regulator accumulated over time on both substrates.ConclusionOur data demonstrates the complexity of the regulatory system related to plant biomass degradation in T. reesei and the effect the feedstock composition has on this. Furthermore, this dataset provides leads to improve the efficiency of a T. reesei enzyme cocktail, such as by the choice of substrate or by deleting xki1 to obtain higher production of plant biomass degrading CAZymes.

The ability of Hypocrea jecorina (Trichoderma reesei) to grow on lactose strongly depends on the formation of an extracellular glycoside hydrolase (GH) family 35 [beta]-galactosidase, encoded by the bga1 gene. Previous studies, using batch or transfer cultures of pregrown cells, had shown that bga1 is induced by lactose and D-galactose, but to a lesser extent by galactitol. To test whether the induction level is influenced by the different growth rates attainable on these carbon sources, bga1 expression was compared in carbon-limited chemostat cultivations at defined dilution (= specific growth) rates. The data showed that bga1 expression by lactose, D-galactose and galactitol positively correlated with the dilution rate, and that galactitol and D-galactose induced the highest activities of [beta]-galactosidase at comparable growth rates. To know more about the actual inducer for [beta]-galactosidase formation, its expression in H. jecorina strains impaired in the first steps of the two D-galactose-degrading pathways was compared. Induction by D-galactose and galactitol was still found in strains deleted in the galactokinase-encoding gene gal1, which is responsible for the first step of the Leloir pathway of D-galactose catabolism. However, in a strain deleted in the aldose/D-xylose reductase gene xyl1, which performs the reduction of D-galactose to galactitol in a recently identified second pathway, induction by D-galactose, but not by galactitol, was impaired. On the other hand, induction by D-galactose and galactitol was not affected in an L-arabinitol 4-dehydrogenase (lad1)-deleted strain which is impaired in the subsequent step of galactitol degradation. These results indicate that galactitol is the actual inducer of Bga1 formation during growth on D-galactose in H. jecorina.

Lactose (1,4-O-[beta]-D-galactopyranosyl-D-glucose) is a soluble and economic carbon source for the industrial production of cellulases or recombinant proteins by Hypocrea jecorina (anamorph Trichoderma reesei). The mechanism by which lactose induces cellulase formation is not understood. Recent data showed that the galactokinase step is essential for cellulase induction by lactose, but growth on D-galactose alone does not induce cellulases. Consequently, the hypothesis was tested that D-galactose may be an inducer only at a low growth rate, which is typically observed when growing on lactose. Carbon-limited chemostat cultivations of H. jecorina were therefore performed at different dilution rates with D-galactose, lactose, galactitol and D-glucose. Cellulase gene expression was monitored by using a strain carrying a fusion between the cbh2 (encoding cellobiohydrolase 2, Cel6A) promoter region and the Aspergillus niger glucose oxidase gene and by identification of the two major cellobiohydrolases Cel7A and Cel6A. The results show that D-galactose indeed induces cbh2 gene transcription and leads to Cel7A and Cel6A accumulation at a low (D=0.015 [h.sup.-1]) but not at higher dilution rates. At the same dilution rate, growth on D-glucose did not lead to cbh2 promoter activation or Cel6A formation but a basal level, lower than that observed on D-galactose, was detected for the carbon-catabolite-derepressible Cel7A. Lactose induced significantly higher cellulase levels at 0.015 [h.sup.-1] than D-galactose and induced cellulases even at growth rates up to 0.042 [h.sup.-1]. Results of chemostats with an equimolar mixture of D-galactose and D-glucose essentially mimicked the behaviour on D-galactose alone, whereas an equimolar mixture of D-galactose and galactitol, the first intermediate of a recently described second pathway of D-galactose catabolism, led to cellulase induction at D=0.030 [h.sup.-1]. It is concluded that D-galactose indeed induces cellulases at low growth rate and that the operation of the alternative pathway further increases this induction. However, under those conditions lactose is still a superior inducer for which the mechanism remains to be clarified.

A study was conducted to investigate the global carbon metabolism of Hypocera jecorina per se and to compare it to genetically modified strains obtained after classical mutagenesis or DNA-mediated transformation. The data obtained demonstrate that the wild-type isolates and transformed strains had the highest variation in growth patterns on individual carbon sources and cellulase mutants were relatively similar to their parental strains.