The Post-genomic Era of Trichoderma reesei: What's Next? Vijai Kumar Gupta, Andrei Stecca Steindorff, Renato Graciano de Paula, Rafael Silva-Rocha, Astrid R. Mach-Aigner, Robert L. Mach, Roberto N. Silva  Trends in Biotechnology  Volume 34, Issue 12, Pages 970-982 (December 2016) DOI: 10.1016/j.tibtech.2016.06.003 Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 1 Comparative T. reesei Genome Characteristics to Five Well-studied Biomass Degraders and to S. cerevisiae. (A) Phylogenetic tree representation based on ITS 1 and 2 of 6 fungi representing classes Sordariomycetes (T. reesei AF510497; N. crassa JX981479), Eurotiomycetes (A. niger FJ011542; A. nidulans KP131592; P. chrysogenum KF417579), and Saccharomycetes (S. cerevisiae KU311155). (B) Genome size and repeat content. (C) Number of predicted genes/proteins. (D) Protein counts of transcription factors, transporters, and CAZymes. The data in this figure are visual representations of information from Mycocosm [76] or Ensembl Fungi [77]. Abbreviations: CAZymes, carbohydrate active enzymes. Trends in Biotechnology 2016 34, 970-982DOI: (10.1016/j.tibtech.2016.06.003) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 2 Overview of Global Regulation of Cellulase Expression in T. reesei. This figure shows the processes that are expected to be involved in regulating lignocelluosic enzymes in T. reesei. The main enzymes involved with lignocellulosic material mobilization are endoglucanases (EGs), cellobiohydrolases (CBHs), and β-glucosidases. These enzymes act synergistically to break down biomass. EGs hydrolyze cellulose bonds internally, while CBHs cleave cellobiose units from the ends of the polysaccharide chains. The released cellobiose units (disaccharide) are finally hydrolyzed by β-glucosidases, releasing glucose. Swollenins rapidly induce the extension of plant cell walls by weakening the noncovalent interactions that help to maintain their integrity. Polysaccharide monooxygenases (PMOs) are newly thought to play a role in this process. Cellobiose dehydrogenase (CDH) is a potential electron donor for PMOs. EGs and PMOs cleave internally cellulose chains releasing chain ends that are targeted by CBHs. The expression of all degrading enzymes is controlled by the main transcription factors (TFs): XYR1, ACE1, ACE2, ACE3, CRE1, and the HAP2/3/5 complex. Additionally, a putative protein methyltransferase LAE1 and VELVET were shown to be important in cellulase gene expression. Under conditions of high glucose, T. reesei cannot induce the expression of cellulases, and the TF CRE1 mediates this carbon catabolite repression. New insights to be investigated as potential areas of research for enhancing enzyme secretion are indicated by dotted arrows. At this point, TFs still not characterized might activate or repress (directly or indirectly) the master TFs involved with cellulase expression. Moreover, these TFs may regulate the expression of major facilitator superfamily (MFS) and ATP-binding cassette (ABC) transporters that in turn are responsible for sugar uptake in response to different carbon sources. Trends in Biotechnology 2016 34, 970-982DOI: (10.1016/j.tibtech.2016.06.003) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure I Distribution of CAZyome Orthologs from Six Fungi. Each block on this diagram represents one intersection of all 63 possibilities when grouping six sets, and the number inside the block is the number of proteins shared among the species indicated by the letters in the box. The central dark blue block shows 114 proteins shared by all fungus represented by the letters A, B, C, D, E, and F. The red blocks represent the unique proteins for each species. The intermediate blocks represent proteins shared by 2–5 species (light blue, five species; green, four species; yellow, three species; orange, two species). The data in this figure are visual representations of information from the Carbohydrate-Active enZYmes database (http://www.cazy.org/) [80]. Trends in Biotechnology 2016 34, 970-982DOI: (10.1016/j.tibtech.2016.06.003) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure II Unique CAZymes from T. reesei. CAZy classes of the 71 proteins identified as unique to T. reesei: glycoside hydrolases (GH), glycosyltransferases (GT), carbohydrate esterases (CE), polysaccharide lyases (PL), auxiliary activities (AA), and carbohydrate-binding modules (CBM). Glycoside hydrolases represent 51% of all of the unique proteins. The diversity of these proteins is shown with their respective counts in parentheses. Abbreviations: EXPN, expansin. Trends in Biotechnology 2016 34, 970-982DOI: (10.1016/j.tibtech.2016.06.003) Copyright © 2016 Elsevier Ltd Terms and Conditions