Comparative analysis of the Trichoderma reesei transcriptome during growth on the cellulase inducing substrates wheat straw and lactose

Abstract

Background: Renewable lignocellulosic biomass is an advantageous resource for the production of second generation biofuels and other biorefinery products. In Middle Europe, wheat straw is one of the most abundant low-cost sources of lignocellulosic biomass. For its efficient use, an efficient mix of cellulases and hemicellulases is required. In this paper, we investigated how cellulase production by T. reesei on wheat straw compares to that on lactose, the only soluble and also cheap inducing carbon source for enzyme production.

Results: We have examined and compared the transcriptome of T. reesei growing on wheat straw and lactose as carbon sources under otherwise similar conditions. Gene expression on wheat straw exceeded that on lactose, and 1619 genes were found to be only induced on wheat straw but not on lactose. They comprised 30% of the CAZome, but were also enriched in genes associated with phospholipid metabolism, DNA synthesis and repair, iron homeostatis and autophagy. Two thirds of the CAZome was expressed both on wheat straw as well as on lactose, but 60% of it at least >2-fold higher on the former. Major wheat straw specific genes comprised xylanases, chitinases and mannosidases. Interestingly, the latter two CAZyme families were significantly higher expressed in a strain in which xyr1 encoding the major regulator of cellulase and hemicellulase biosynthesis is non-functional.

Conclusions: Our data reveal several major differences in the transcriptome between wheat straw and lactose which may be related to the higher enzyme formation on the former and their further investigation could lead to the development of methods for increasing enzyme production on lactose.

Figure 1

Growth profiles of T. reesei QM 9414 on different substrates. The biomass dry weight per liter was directly measured gravimetrically for glucose (squares) and lactose (diamonds) or calculated from the intracellular protein content for wheat straw (triangles) on the basis of 0.35 g intracellular protein per g dry biomass. Error bars show the respective standard deviation of three biological replicates.

Figure 2

Hierarchical cluster analysis of expression of genes related to iron homeostasis. Glc, glucose; Lac, lactose; WS, wheat straw. Data are shown as a heat map, and the color code of respective expression values (dark blue: 0; dark red: 16; numbers indicate the log₂ of the mean expression level, n = 2). Numbers and names indicate the respective Trire2: number and putative gene function. The letters at the major branches specify the transcript groups, as defined in the text.

Figure 3

At least >2-fold upregulated genes encoding putative secreted proteins during growth of T. reesei on wheat straw and lactose. Different transcript groups (for explanation see text) are: transcript group A, blue; transcript group B, red; transcript group C, green; transcript group D, yellow; and transcript group E, white. Esterases and lipases include both carbohydrate esterases as well as lipases.

Figure 4

Hierarchical cluster analysis of glycosyl hydrolase gene expression. Data are shown as a heat map, and the color code of respective expression values (dark blue: 0; dark red: 16; numbers indicate the log₂ of the mean expression level, n = 2). Roman numbers and (in certain cases) lower case letters specify clades characterized by consistent expression patterns.

Figure 5

Results of qPCR analyses of those chitinases, galactanases and mannanases that were upregulated on either lactose, wheat straw or both carbon sources. The expression of the lactose samples and wheat straw samples, taken at the indicated time points (see legend) is related to that of an 8 h sample from a QM 9414 glucose culture and normalized on tef1. Error bars show the standard deviation of two independent experiments.

Figure 6

Changes in gene expression of autophagy related T. reesei genes on glucose, lactose and wheat straw: blue bars show the expression of lactose (Lac) cultures relative to glucose (Glc) cultures, red bars show the expression of wheat straw (Wheat) cultures relative to glucose (Glc) cultures, and green bars show the expression of wheat straw (Wheat) cultures relative to lactose (Lac) cultures. Values represent the mean of three biological replicates, error bars show the standard deviation.