Systems biological approaches towards understanding cellulase production by Trichoderma reesei

Abstract

Recent progress and improvement in "-omics" technologies has made it possible to study the physiology of organisms by integrated and genome-wide approaches. This bears the advantage that the global response, rather than isolated pathways and circuits within an organism, can be investigated ("systems biology"). The sequencing of the genome of Trichoderma reesei (teleomorph Hypocrea jecorina), a fungus that serves as a major producer of biomass-degrading enzymes for the use of renewable lignocellulosic material towards production of biofuels and biorefineries, has offered the possibility to study this organism and its enzyme production on a genome wide scale. In this review, I will highlight the use of genomics, transcriptomics, proteomics and metabolomics towards an improved and novel understanding of the biochemical processes that involve in the massive overproduction of secreted proteins.

Fig. 1

CAZys, indicated by GH-number, that are amplified in Trichoderma. Numbers on the vertical axes of the plots indicate number of gene paralogues. Abbreviations: J, T. reesei; V, T. virens; T, T. atroviride; A, Aspergillus nidulans; N, Aspergillus niger; G, Gibberella zeae; M, Magnaporthe grisea; P, Podospora anserina; B, Botryodiplodia fuckeliana; S, Sclerotium sclerotiorum; E, Neurospora crassa; O, Rhizopus nigricans; D, Batrachochytrium dendrobatidis. Data were compiled from Martinez et al. (2008), Eastwood et al. (2011), Goodwin et al. (2011), and Kubicek et al. (2011, 2012).

Fig. 2

Genomic synteny of areas containing cellulase clusters, as determined by REEF. Synteny data were retrieved from the synteny browser at http://genome.jgi-psf.org/Trire2/Trire2.home.html, using the genome of T. atroviride as a comparison. Interrupted bars indicate lack of synteny. The different degrees of fillings of the bars (from black to grey) indicate occurrence of the respective areas on different scaffolds in T. atroviride. Numbers indicate the respective position on the scaffold in Mbp's. Areas containing cellulase genes are indicated by red boxes.

Fig. 3

Pedigree of H. jecorina mutant strains whose genome has been sequenced. The parent strain, whose genome sequence is already available is boxed; the cellulase negative mutants are located within the blue box.

Fig. 4

Extracellular CAZymes identified by proteomic approaches by Jun et al., 2011 (A), Herpoël-Gimbert et al., 2009 (B) and Adav et al., 2011 (C). Black boxes indicate that the protein was detected, numbers are the protein IDs in the T. reesei genome database. Note that the endoglucanase marked with an * is actually a cellulose monooxygenase.