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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

Gene Co-expression Network Reveals Potential New Genes Related to Sugarcane Bagasse Degradation in Trichoderma reesei RUT-30

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Author(s):
Bonin, Gustavo Pagotto [1, 2] ; Carazzolle, Marcelo Falsarella [3] ; Correa dos Santos, Renato Augusto [4] ; Riano-Pachon, Diego Mauricio [5] ; de Castro Oliveira, Juliana Velasco [1, 2]
Total Authors: 5
Affiliation:
[1] CNPEM, Lab Nacl Ciencia & Tecnol Bioetanol CTBE, Campinas, SP - Brazil
[2] Univ Estadual Campinas, Inst Biol, Programa Posgrad Genet & Biol Mol, UNICAMP, Campinas, SP - Brazil
[3] Univ Estadual Campinas, UNICAMP, Inst Biol, LGE, Dept Genet Evolucao Microbiol & Imunol, Campinas, SP - Brazil
[4] Univ Sao Paulo, Fac Ciencias Farmaceut Ribeirao Preto, Ribeirao Preto - Brazil
[5] Univ Sao Paulo, Ctr Energia Nucl Agr, Pracicaba - Brazil
Total Affiliations: 5
Document type: Journal article
Source: FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY; v. 6, OCT 22 2018.
Web of Science Citations: 1
Abstract

The biomass-degrading fungus Trichoderma reesei has been considered a model for cellulose degradation, and it is the primary source of the industrial enzymatic cocktails used in second-generation (2G) ethanol production. However, although various studies and advances have been conducted to understand the cellulolytic system and the transcriptional regulation of T. reesei, the whole set of genes related to lignocellulose degradation has not been completely elucidated. In this study, we inferred a weighted gene co-expression network analysis based on the transcriptome dataset of the T. reesei RUT-C30 strain aiming to identify new target genes involved in sugarcane bagasse breakdown. In total, similar to 70% of all the differentially expressed genes were found in 28 highly connected gene modules. Several cellulases, sugar transporters, and hypothetical proteins coding genes upregulated in bagasse were grouped into the same modules. Among them, a single module contained the most representative core of cellulolytic enzymes (cellobiohydrolase, endoglucanase, beta-glucosidase, and lytic polysaccharide monooxygenase). In addition, functional analysis using Gene Ontology (GO) revealed various classes of hydrolytic activity, cellulase activity, carbohydrate binding and cation:sugar symporter activity enriched in these modules. Several modules also showed GO enrichment for transcription factor activity, indicating the presence of transcriptional regulators along with the genes involved in cellulose breakdown and sugar transport as well as other genes encoding proteins with unknown functions. Highly connected genes (hubs) were also identified within each module, such as predicted transcription factors and genes encoding hypothetical proteins. In addition, various hubs contained at least one DNA binding site for the master activator Xyr1 according to our in silico analysis. The prediction of Xyr1 binding sites and the co-expression with genes encoding carbohydrate active enzymes and sugar transporters suggest a putative role of these hubs in bagasse cell wall deconstruction. Our results demonstrate a vast range of new promising targets that merit additional studies to improve the cellulolytic potential of T. reesei strains and to decrease the production costs of 2G ethanol. (AU)

FAPESP's process: 17/18987-7 - Construction of mutant Trichoderma reesei strains and analysis of regulatory elements aiming to identify and characterize new genes with biotechnological potential for lignocellulose deconstruction
Grantee:Gustavo Pagotto Borin
Support type: Scholarships abroad - Research Internship - Doctorate
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: 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