Network of proteins, enzymes and genes linked to biomass degradation shared by Trichoderma species

Abstract

Understanding relationships between genes responsible for enzymatic hydrolysis of cellulose and synergistic reactions is fundamental for improving biomass biodegradation technologies. To reveal synergistic reactions, the transcriptome, exoproteome, and enzymatic activities of extracts from Trichoderma harzianum, Trichoderma reesei and Trichoderma atroviride under biodegradation conditions were examined. This work revealed co-regulatory networks across carbohydrate-active enzyme (CAZy) genes and secreted proteins in extracts. A set of 80 proteins and respective genes that might correspond to a common system for biodegradation from the studied species were evaluated to elucidate new co-regulated genes. Differences such as one unique base pair between fungal genomes might influence enzyme-substrate binding sites and alter fungal gene expression responses, explaining the enzymatic activities specific to each species observed in the corresponding extracts. These differences are also responsible for the different architectures observed in the co-expression networks.

“Integrative Genomic Analysis for the Bioprospection of Regulators and Accessory Enzymes Associated with Cellulose Degradation in a Filamentous Fungus (Trichoderma harzianum)”

“…Analyzing the level of expression of certain genes under certain conditions is an important step in understanding how transcription is affected in a specific biological condition [17, 35]; however, there is not always a direct relationship between what is being highly expressed and the proteins that are important in the extracellular medium. Thus, in this work, in addition to studying the most expressed genes that we found in the genomic regions, we also searched for those with a confirmed presence in the fungus secretome CEL degradation conditions.…”

“…Coregulation networks provide insights into how genes correlate and interact with each other [35, 42, 43]. We identified 36 genes directly associated with the CLR2 regulatory factor; these genes may be important in the regulation process of this factor, which is linked to the expression of cellulases in other filamentous fungi.…”

“…The expression levels of ThIOC3844 were analyzed using RNA-Seq data ( PRJNA336221 ) obtained from a previous study in which the transcripts were obtained following growth of the fungus on two different carbon sources, CEL and GLU [35]. The reads from the RNA-Seq library were mapped against the ThIOC3844 genes using the CLC Genomics Workbench (https://www.qiagenbioinformatics.com/products/clc-genomics-workbench/) [58].…”

“…The gene regulatory networks were assembled from the reference mapped RNA-Seq data using each set of biological triplicates for the CEL and GLU conditions [35]. The interaction between the genes was obtained by calculating Pearson’s correlation for each pair of genes.…”

Identificação de alvos de fosforilação de MAPK em <i>Trichoderma reesei</i> através de fosfoproteômica durante a produção de celulases

“…Além disso, outras proteínas de T. reesei também estão envolvidas no processo de degradação de celulose, sendo elas a solenina (swo1) e expansinas/família 45 endoglicanase-like (EEL1, EEL2 e EEL3), as quais auxiliam no acesso das enzimas celulolíticas à cadeia polissacarídica; e lipopolissacarídeo mono-oxigenases (LPMOs), cuja ação é compreendida pelo metabolismo oxidativo dependente de íons metálicos bivalentes (BISCHOF; RAMONI; SEIBOTH, 2016;GUPTA et al, 2016;HERPOEL-GIMBERT et al, 2008). A ação sinérgica de todas essas proteínas e este sistema enzimático permitem que a holocelulose seja hidrolisada de modo eficiente pelo respectivo fungo filamentoso (BERLIN, 2013;GUPTA et al, 2016;HORTA et al, 2018).…”