title: Re-annotation of the CAZy genes of Trichoderma reesei and transcription in the presence of lignocellulosic substrates.
abstract: BACKGROUND
  Trichoderma 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.
  
  
  RESULTS
  In 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.
  
  
  CONCLUSIONS
  In 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.
authors.affiliation: VTT Technical Research Centre of Finland, Tietotie 2, Espoo, FI-02044, VTT, Finland. mari.hakkinen@vtt.fi
authors.forename: Mari
authors.initials: M
authors.lastname: Häkkinen
authors.forename: Mikko
authors.initials: M
authors.lastname: Arvas
authors.forename: Merja
authors.initials: M
authors.lastname: Oja
authors.forename: Nina
authors.initials: N
authors.lastname: Aro
authors.forename: Merja
authors.initials: M
authors.lastname: Penttilä
authors.forename: Markku
authors.initials: M
authors.lastname: Saloheimo
authors.forename: Tiina M
authors.initials: TM
authors.lastname: Pakula
mesh_terms: D018533:Biomass; D044602:Cellulases / Q000145:classification / Q000235:genetics; D016208:Databases, Factual; D020869:Gene Expression Profiling; D016681:Genome, Fungal; D006026:Glycoside Hydrolases / Q000235:genetics / Q000378:metabolism; D008031:Lignin / Q000378:metabolism*; D010802:Phylogeny; D011133:Polysaccharide-Lyases / Q000235:genetics / Q000378:metabolism; D013379:Substrate Specificity; D014242:Trichoderma / Q000235:genetics*
chemical_list: C036909:lignocellulose; D008031:Lignin; D044602:Cellulases; D006026:Glycoside Hydrolases; D011133:Polysaccharide-Lyases