Comparative transcriptome analysis reveals different strategies for degradation of steam-exploded sugarcane bagasse by Aspergillus niger and Trichoderma reesei

Abstract

BackgroundSecond generation (2G) ethanol is produced by breaking down lignocellulosic biomass into fermentable sugars. In Brazil, sugarcane bagasse has been proposed as the lignocellulosic residue for this biofuel production. The enzymatic cocktails for the degradation of biomass-derived polysaccharides are mostly produced by fungi, such as Aspergillus niger and Trichoderma reesei. However, it is not yet fully understood how these microorganisms degrade plant biomass. In order to identify transcriptomic changes during steam-exploded bagasse (SEB) breakdown, we conducted a RNA-seq comparative transcriptome profiling of both fungi growing on SEB as carbon source.ResultsParticular attention was focused on CAZymes, sugar transporters, transcription factors (TFs) and other proteins related to lignocellulose degradation. Although genes coding for the main enzymes involved in biomass deconstruction were expressed by both fungal strains since the beginning of the growth in SEB, significant differences were found in their expression profiles. The expression of these enzymes is mainly regulated at the transcription level, and A. niger and T. reesei also showed differences in TFs content and in their expression. Several sugar transporters that were induced in both fungal strains could be new players on biomass degradation besides their role in sugar uptake. Interestingly, our findings revealed that in both strains several genes that code for proteins of unknown function and pro-oxidant, antioxidant, and detoxification enzymes were induced during growth in SEB as carbon source, but their specific roles on lignocellulose degradation remain to be elucidated.ConclusionsThis is the first report of a time-course experiment monitoring the degradation of pretreated bagasse by two important fungi using the RNA-seq technology. It was possible to identify a set of genes that might be applied in several biotechnology fields. The data suggest that these two microorganisms employ different strategies for biomass breakdown. This knowledge can be exploited for the rational design of enzymatic cocktails and 2G ethanol production improvement.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3857-5) contains supplementary material, which is available to authorized users.

Evolutionary adaptation of Aspergillus niger for increased ferulic acid tolerance

“…The function of the induced LPMOs have not been characterized, however, it has been shown that LPMOs from AA9 catalyze oxidative cleavage of b-(1-4)-xylosyl bonds in xylan and b-(1-4)-glucosyl bonds in cellulose (Frommhagen et al 2015(Frommhagen et al , 2017Brenelli et al 2018). Both induced LPMOs have been predicted to act on cellulose (Borin et al 2017) and one of them (NRRL3_3929) has been suggested to be regulated by AraR (Gruben et al 2017). The transcriptional profile of the FAE encoding genes correlated with previous observations (de Vries et al 2002;Dilokpimol et al 2017).…”

In silico Proteomic Analysis Provides Insights Into Phylogenomics and Plant Biomass Deconstruction Potentials of the Tremelalles

“…STs distribution have been correlated with fungal capability to utilize carbon sources with greater numbers of STs typically observed among metabolically versatile fungi capable of using broader range of substrates (Cornell et al, 2007). In addition to sugar transduction, certain STs also regulate the expression of CAZYmes such as cellulase and xylanases (Zhang et al, 2013;Huang et al, 2015) and have therefore been considered veritable targets for strain improvement in various biotechnological applications (Borin et al, 2017).…”

Succession of physiological stages hallmarks the transcriptomic response of the fungus Aspergillus niger to lignocellulose

“…Subsequent degradation of lignocellulose components can be expected to reflect the evolved fungal biochemical capacity [27,43]. Fungal production of CAZymes and signalling responses to different sources of complex carbohydrates have been documented extensively, often capturing a snapshot of events at one or a selected few moments, such as when the CAZyme expression was peaking, in the cultivation time [28][29][30][31][32][33][34][43][44][45][46]. Knowledge on the wider, and potentially time-staged, physiological responses and degradative strategies of A. niger is however still very limited.…”