Abstract
BackgroundTrichoderma reesei is a soft rot Ascomycota fungus utilised for industrial production of secreted enzymes, especially lignocellulose degrading enzymes. About 30 carbohydrate active enzymes (CAZymes) of T. reesei have been biochemically characterised. Genome sequencing has revealed a large number of novel candidates for CAZymes, thus increasing the potential for identification of enzymes with novel activities and properties. Plenty of data exists on the carbon source dependent regulation of the characterised hydrolytic genes. However, information on the expression of the novel CAZyme genes, especially on complex biomass material, is very limited.ResultsIn this study, the CAZyme gene content of the T. reesei genome was updated and the annotations of the genes refined using both computational and manual approaches. Phylogenetic analysis was done to assist the annotation and to identify functionally diversified CAZymes. The analyses identified 201 glycoside hydrolase genes, 22 carbohydrate esterase genes and five polysaccharide lyase genes. Updated or novel functional predictions were assigned to 44 genes, and the phylogenetic analysis indicated further functional diversification within enzyme families or groups of enzymes. GH3 β-glucosidases, GH27 α-galactosidases and GH18 chitinases were especially functionally diverse. The expression of the lignocellulose degrading enzyme system of T. reesei was studied by cultivating the fungus in the presence of different inducing substrates and by subjecting the cultures to transcriptional profiling. The substrates included both defined and complex lignocellulose related materials, such as pretreated bagasse, wheat straw, spruce, xylan, Avicel cellulose and sophorose. The analysis revealed co-regulated groups of CAZyme genes, such as genes induced in all the conditions studied and also genes induced preferentially by a certain set of substrates.ConclusionsIn this study, the CAZyme content of the T. reesei genome was updated, the discrepancies between the different genome versions and published literature were removed and the annotation of many of the genes was refined. Expression analysis of the genes gave information on the enzyme activities potentially induced by the presence of the different substrates. Comparison of the expression profiles of the CAZyme genes under the different conditions identified co-regulated groups of genes, suggesting common regulatory mechanisms for the gene groups.
Highlights
Trichoderma reesei is a soft rot Ascomycota fungus utilised for industrial production of secreted enzymes, especially lignocellulose degrading enzymes
In order to verify whether the selection of candidate genes for Carbohydrate active enzyme (CAZyme) was supported by protein sequences from other fungi, the protein homology clusters described in [49] and updated to include 49 fungal species [50], were mapped to the Carbohydrate active enzyme database (CAZy) database
The results suggest that several regulatory mechanisms, depending on the inducers present, may act on the CAZyme gene promoters simultaneously, and in some cases in an additive manner
Summary
Trichoderma reesei is a soft rot Ascomycota fungus utilised for industrial production of secreted enzymes, especially lignocellulose degrading enzymes. Natural resources are diminishing while the demand for commodities, energy and food increases This sets a requirement to find solutions for efficient utilisation of renewable biological material in production of energy and chemicals. The most abundant terrestrial renewable organic resource is lignocellulose that can be derived from industrial side-streams, municipal waste, or by-products of agriculture and forestry, and can be used as a raw material in biorefinery applications (for reviews, see [1] and [2]). It consists of cellulose, hemicellulose and lignin. Since the cost of enzymes is still a major limitation in the utilisation of biomass, improvement of the enzyme production systems and use of optimal mixtures of synergistic enzymes, as well as the choice of raw material and pretreatment method, are of importance in setting up a cost effective biorefinery process [4]
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