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

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Borin, Gustavo Pagotto ; Sanchez, Camila Cristina ; de Santana, Eliane Silva ; Zanini, Guilherme Keppe ; Correa dos Santos, Renato Augusto ; Pontes, Angelica de Oliveira ; de Souza, Aline Tieppo ; Tavares Soares Dal'Mas, Roberta Maria Menegaldo ; Riano-Pachon, Diego Mauricio ; Goldman, Gustavo Henrique ; de Castro Oliveira, Juliana Velasco

• Document type: Journal article
• Source: BMC Genomics; v. 18, JUN 30 2017.
• Web of Science Citations: 22

Abstract

Background: Second 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. Results: Particular 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. Conclusions: This 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. (AU)

• FAPESP's process: 14/11733-1 - Characterization of transporters from Pseudozyma brasiliensis
• Grantee: Eliane Silva de Santana
• Support type: Scholarships in Brazil - Scientific Initiation
• FAPESP's process: 13/09541-4 - Genomic studies of global gene expression of Aspergillus niger grown on sugarcane bagasse and stem
• Grantee: Camila Cristina Sanchez
• Support type: Scholarships in Brazil - Master
• FAPESP's process: 14/11766-7 - Characterization of novel transcription factors of Trichoderma reesei involved in the degradation of lignocellulosic biomass
• Grantee: Juliana Velasco de Castro Oliveira
• Support type: Program for Research on Bioenergy (BIOEN) - Regular Program Grants
• FAPESP's process: 11/08945-9 - Comparative genomic studies of global gene expression in filamentous fungi grown on bagasse and sugarcane culm
• Grantee: Juliana Velasco de Castro Oliveira
• Support type: Regular Research Grants
• FAPESP's process: 14/15799-7 - Genomic analysis of the xylanolytic yeast Pseudozyma brasiliensis
• Grantee: Renato Augusto Corrêa dos Santos
• Support type: Scholarships in Brazil - Master
• FAPESP's process: 15/08222-8 - Analysis of transcriptional co-regulation and identification of genes of biotechnological interest in Trichoderma reesei
• Grantee: Gustavo Pagotto Borin
• Support type: Scholarships in Brazil - Doctorate