<scp>ARA</scp>1 regulates not only <scp>l</scp>‐arabinose but also <scp>d</scp>‐galactose catabolism in <i>Trichoderma reesei</i>

The fungal kingdom is too large to be discovered exclusively by classical genetics. The access to omics data opens a new opportunity to study the diversity within the fungal kingdom and how adaptation to new environments shapes fungal metabolism. Genomes are the foundation of modern science but their quality is crucial when analysing omics data. In this study, we demonstrate how one gold-standard genome can improve functional prediction across closely related species to be able to identify key enzymes, reactions and pathways with the focus on primary carbon metabolism.Based on this approach we identified alternative genes encoding various steps of the different sugar catabolic pathways, and as such provided leads for functional studies into this topic. We also revealed significant diversity with respect to genome content, although this did not always correlate to the ability of the species to use the corresponding sugar as a carbon source.

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“…2012), Ensembl Fungi Biomart release 38 (Kinsella et al. 2011), (Benocci et al. 2018) and the AspGD database (Cerqueira et al.…”

Section: Methodsmentioning

confidence: 99%

The gold-standard genome of Aspergillus niger NRRL 3 enables a detailed view of the diversity of sugar catabolism in fungi

Pontes

Brandl

McDonnell

et al. 2018

Studies in Mycology

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“…In the last few years, several advances have been achieved in different research fields and contributed to a better understanding of the physiology and key features behind the T. reesei hypercellulolytic capacity. Such advances include the development of new tools for genetic manipulation (Derntl et al, 2015 ; Liu et al, 2015 ), transcriptomic and proteomic studies using lignocellulosic residues (Dos Santos Castro et al, 2014 ; Borin et al, 2015 , 2017 ; Daly et al, 2017 ; Ellilä et al, 2017 ; Cologna et al, 2018 ), the discovery of new transcription factors (TFs) and regulatory elements (Derntl et al, 2016 , 2017 ; Stappler et al, 2017 ; Zheng et al, 2017b ; Benocci et al, 2018 ), promoter characterization (Zheng et al, 2017a ; Kiesenhofer et al, 2018 ) and structural studies of cellulases (Li et al, 2015 ; Bodenheimer and Meilleur, 2016 ; Eibinger et al, 2016 ; Ma et al, 2017 ; Borisova et al, 2018 ).…”

Section: Introductionmentioning

confidence: 99%

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

Borin

Carazzolle

Santos

et al. 2018

Front. Bioeng. Biotechnol.

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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, ~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, β-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.

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“…Beside these, a number of other transcription factors have been characterized including ARA1, which is involved in the utilization of d -galactose and l -arabinose and regulates different CAZymes in response to d -galactose (Benocci et al, 2018 ). The xylanase regulator SxlR seems to be a repressor for GH11 family xylanases as an overexpression in RUT-C30 resulted in a reduced and a deletion in an increased xylanase activity (Liu et al, 2017 ).…”

Section: Engineering Of Promotersmentioning

confidence: 99%

The Promoter Toolbox for Recombinant Gene Expression in Trichoderma reesei

Fitz

Wanka

Schink

2018

Front. Bioeng. Biotechnol.

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The ascomycete Trichoderma reesei is one of the main fungal producers of cellulases and xylanases based on its high production capacity. Its enzymes are applied in food, feed, and textile industry or in lignocellulose hydrolysis in biofuel and biorefinery industry. Over the last years, the demand to expand the molecular toolbox for T. reesei to facilitate genetic engineering and improve the production of heterologous proteins grew. An important instrument to modify the expression of key genes are promoters to initiate and control their transcription. To date, the most commonly used promoter for T. reesei is the strong inducible promoter of the main cellobiohydrolase cel7a. Beside this one, there is a number of alternative inducible promoters derived from other cellulase- and xylanase encoding genes and a few constitutive promoters. With the advances in genomics and transcriptomics the identification of new constitutive and tunable promoters with different expression strength was simplified. In this review, we will discuss new developments in the field of promoters and compare their advantages and disadvantages. Synthetic expression systems constitute a new option to control gene expression and build up complex gene circuits. Therefore, we will address common structural features of promoters and describe options for promoter engineering and synthetic design of promoters. The availability of well-characterized gene expression control tools is essential for the analysis of gene function, detection of bottlenecks in gene networks and yield increase for biotechnology applications.

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ARA1 regulates not only l‐arabinose but also d‐galactose catabolism in Trichoderma reesei

Cited by 25 publications

References 55 publications

The gold-standard genome of Aspergillus niger NRRL 3 enables a detailed view of the diversity of sugar catabolism in fungi

The gold-standard genome of Aspergillus niger NRRL 3 enables a detailed view of the diversity of sugar catabolism in fungi

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

The Promoter Toolbox for Recombinant Gene Expression in Trichoderma reesei

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