Genome-wide transcriptional response of Trichoderma reesei to lignocellulose using RNA sequencing and comparison with Aspergillus niger

Abstract

BackgroundA major part of second generation biofuel production is the enzymatic saccharification of lignocellulosic biomass into fermentable sugars. Many fungi produce enzymes that can saccarify lignocellulose and cocktails from several fungi, including well-studied species such as Trichoderma reesei and Aspergillus niger, are available commercially for this process. Such commercially-available enzyme cocktails are not necessarily representative of the array of enzymes used by the fungi themselves when faced with a complex lignocellulosic material. The global induction of genes in response to exposure of T. reesei to wheat straw was explored using RNA-seq and compared to published RNA-seq data and model of how A. niger senses and responds to wheat straw.ResultsIn T. reesei, levels of transcript that encode known and predicted cell-wall degrading enzymes were very high after 24 h exposure to straw (approximately 13% of the total mRNA) but were less than recorded in A. niger (approximately 19% of the total mRNA). Closer analysis revealed that enzymes from the same glycoside hydrolase families but different carbohydrate esterase and polysaccharide lyase families were up-regulated in both organisms. Accessory proteins which have been hypothesised to possibly have a role in enhancing carbohydrate deconstruction in A. niger were also uncovered in T. reesei and categories of enzymes induced were in general similar to those in A. niger. Similarly to A. niger, antisense transcripts are present in T. reesei and their expression is regulated by the growth condition.ConclusionsT. reesei uses a similar array of enzymes, for the deconstruction of a solid lignocellulosic substrate, to A. niger. This suggests a conserved strategy towards lignocellulose degradation in both saprobic fungi. This study provides a basis for further analysis and characterisation of genes shown to be highly induced in the presence of a lignocellulosic substrate. The data will help to elucidate the mechanism of solid substrate recognition and subsequent degradation by T. reesei and provide information which could prove useful for efficient production of second generation biofuels.

Transcriptomic Profile of Lignocellulose Degradation from Trametes versicolor on Poplar Wood

“…The "GO slim" option was employed to reduce the number of functional classes. Gene ontology slim annotation results were then used as queries against the AgBase database to classify genes into to the three main categories (molecular function, biological process, and cellular component) and to be further assigned to secondary categories (Ries et al 2013).…”

Optimizing Cellulase Production from Municipal Solid Waste (MSW) using Solid State Fermentation (SSF)

“…Procedures for storing and cultivating T. reesei and A. niger were as previously described by Ries et al [23].…”

Transcriptional Regulation and Responses in Filamentous Fungi Exposed to Lignocellulose

“…HSIPs include proteins such as hydrophobins and other proteins with similar functional properties. Genes that encoded HSIPs, were induced in A. niger in response to wheat straw [31], willow [68] and sugar cane bagasse [69] and in T. reesei in response to wheat straw [135]. The induction of HSIPs suggests a possible role for HSIPs in improving the efficiency of saccharification of lignocellulose.…”

“…Swollenins were also shown to aid in the amorphogenesis step during the enzymatic hydrolysis of pre-treated biomass [134]. The swollenin gene swo1 was highly induced in T. reesei when cultured with wheat straw [135]. Saloheimo et al [133] showed swo1 in T. reesei was regulated in a similar manner to cellulases with swo1 induced by cellulose, lactose, sophorose and cellobiose.…”