ArticlePloS one2014
Deciphering the cis-regulatory elements for XYR1 and CRE1 regulators in Trichoderma reesei.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 52 citations in OpenAlex.
- Article
- Transcriptomic and metabolic changes in Trichoderma reesei caused by mutation in xylanase regulator 1 (xyr1).Biotechnology for biofuels and bioproducts · 2024Article
- Proteome profiling of enriched membrane-associated proteins unraveled a novel sophorose and cello-oligosaccharide transporter in Trichoderma reesei.Microbial cell factories · 2024Article
- Carbon catabolite repression involves physical interaction of the transcription factor CRE1/CreA and the Tup1-Cyc8 complex in Penicillium oxalicum and Trichoderma reesei.Biotechnology for biofuels · 2021Article
- CreA-mediated repression of gene expression occurs at low monosaccharide levels during fungal plant biomass conversion in a time and substrate dependent manner.Cell surface (Amsterdam, Netherlands) · 2021Article
- Review
- Article
- Co-culture of Vel1-overexpressed Trichoderma asperellum and Bacillus amyloliquefaciens: An eco-friendly strategy to hydrolyze the lignocellulose biomass in soil to enrich the soil fertility, plant growth and disease resistance.Microbial cell factories · 2021Article
- A Novel CreA-Mediated Regulation Mechanism of Cellulase Expression in the Thermophilic FungusInternational journal of molecular sciences · 2019Article
- Article
- The Duality of the MAPK Signaling Pathway in the Control of Metabolic Processes and Cellulase Production in Trichoderma reesei.Scientific reports · 2018Article
- Gene Co-expression Network Reveals Potential New Genes Related to Sugarcane Bagasse Degradation inFrontiers in bioengineering and biotechnology · 2018Article
- A copper-controlled RNA interference system for reversible silencing of target genes inBiotechnology for biofuels · 2018Article
- Identification of two integration sites in favor of transgene expression inBiotechnology for biofuels · 2018Article
- Trichoderma reesei CRE1-mediated Carbon Catabolite Repression in Re-sponse to Sophorose Through RNA Sequencing Analysis.Current genomics · 2016Article
- Recent Progress on Systems and Synthetic Biology Approaches to Engineer Fungi As Microbial Cell Factories.Current genomics · 2016Article
- Fungal-mediated consolidated bioprocessing: the potential of Fusarium oxysporum for the lignocellulosic ethanol industry.AMB Express · 2016Article
- Genome wide analysis of protein production load in Trichoderma reesei.Biotechnology for biofuels · 2016Article
- Understanding the Role of the Master Regulator XYR1 in Trichoderma reesei by Global Transcriptional Analysis.Frontiers in microbiology · 2016Article
- Synergistic and Dose-Controlled Regulation of Cellulase Gene Expression in Penicillium oxalicum.PLoS genetics · 2015Article
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In this work, we report the in silico identification of the cis-regulatory elements for XYR1 and CRE1 proteins in the filamentous fungus Trichoderma reesei, two regulators that play a central role in the expression of cellulase genes. Using four datasets of condition-dependent genes from RNA-seq and RT-qPCR experiments, we performed unsupervised motif discovery and found two short motifs resembling the proposed binding consensus for XYR1 and CRE1. Using these motifs, we analysed the presence and arrangement of putative cis-regulatory elements recognized by both regulators and found that shortly spaced sites were more associated with XYR1- and CRE1-dependent promoters than single, high-score sites. Furthermore, the approach used here allowed the identification of the previously reported XYR1-binding sites from cel7a and xyn1 promoters, and we also mapped the potential target sequence for this regulator at the cel6a promoter that has been suggested but not identified previously. Additionally, seven other promoters (for cel7b, cel61a, cel61b, cel3c, cel3d, xyn3 and swo genes) presented a putative XYR1-binding site, and strong sites for CRE1 were found at the xyr1 and cel7b promoters. Using the cis-regulatory architectures nearly defined for XYR1 and CRE1, we performed genome-wide identification of potential targets for direct regulation by both proteins and important differences on their functional regulons were elucidated. Finally, we performed binding site mapping on the promoters of differentially expressed genes found in T. reesei mutant strains lacking xyr1 or cre1 and found that indirect regulation plays a key role on their signalling pathways. Taken together, the data provided here sheds new light on the mechanisms for signal integration mediated by XYR1 and CRE1 at cellulase promoters.
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