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

Laure Ries,Stéphane Delmas,Sunir Malla,Martin J Blythe,David B Archer,Steven T Pullan

doi:10.1186/1471-2164-14-541

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.

Highlights

A major part of second generation biofuel production is the enzymatic saccharification of lignocellulosic biomass into fermentable sugars
The overall aim of this study was to investigate the strategy that Trichoderma reesei employs to degrade complex lignocellulosic polysaccharides and compare this to the mechanism used by Aspergillus niger in order to provide novel insights which may prompt the development of new approaches for the production of 2G biofuels
Transcriptomes were sequenced from replicated independent cultures under 3 different sets of conditions: 1) after growth from conidia for 48 h in the presence of glucose as sole carbon source, a monosaccharide which represses expression of many genes involved in plant cell wall degradation, 2) 24 h after transfer of washed mycelia from 1) into media containing ground wheat straw as the sole carbon source to monitor the induction of genes involved in polysaccharide deconstruction and 3) 5 h after addition of glucose to the straw cultures from 2) to determine genes responsive to carbon catabolite repression

Summary

Introduction

A major part of second generation biofuel production is the enzymatic saccharification of lignocellulosic biomass into fermentable sugars. The overall aim of this study was to investigate the strategy that Trichoderma reesei employs to degrade complex lignocellulosic polysaccharides and compare this to the mechanism used by Aspergillus niger in order to provide novel insights which may prompt the development of new approaches for the production of 2G biofuels. Trichoderma spp. and Aspergillus spp. have many industrial applications due to their production of very high levels of secreted enzymes [1,3,8] This has led to the development of a wide selection of genetic tools in T. reesei, including random and targeted mutagenesis to create cellulase hyper-producing mutants [9,10], to elucidate regulatory mechanisms of pathways concerning the metabolism of simple sugars [11,12] and to target the T. reesei secretion system in order to produce higher protein yields through engineering more efficient and thermostable enzymes [2,9,13,14,15,16,17]. This is similar to the total number (ca. 280) of carbohydrate-degrading enzymes in A. niger

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