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Deciphering the cis-regulatory elements for XYR1 and CRE1 regulators in Trichoderma reesei


In this work, we report the in silico identification of the cis-regulatory elements for XYR1and CRE1 proteins in the filamentous fungus Trichoderma reesei, two regulators thatplay a central role in the expression of cellulase genes. Using four datasets ofcondition-dependent genes from RNA-seq and RT-qPCR experiments, we performedunsupervised motif discovery and found two short motifs resembling the proposedbinding consensus for XYR1 and CRE1. Using these motifs, we analysed the presenceand arrangement of putative cis-regulatory elements recognized by both regulators andfound that shortly spaced sites were more associated with XYR1- and CRE1-dependent promoters than single, high-score sites. Furthermore, the approach usedhere allowed the identification of the previously reported XYR1-binding sites from cel7aand xyn1 promoters, and we also mapped the potential target sequence for thisregulator at the cel6a promoter that has been suggested but not identified previously.Additionally, seven other promoters (for cel7b, cel61a, cel61b, cel3c, cel3d, xyn3 andswo genes) presented a putative XYR1-binding site, and strong sites for CRE1 werefound at the xyr1 and cel7b promoters. Using the cis-regulatory architectures nearlydefined for XYR1 and CRE1, we performed genome-wide identification of potentialtargets for direct regulation by both proteins and important differences on theirfunctional regulons were elucidated. Finally, we performed binding site mapping on thepromoters of differentially expressed genes found in T. reesei mutant strains lackingxyr1 or cre1 and found that indirect regulation plays a key role on their signallingpathways. Taken together, the data provided here shades new light on themechanisms for signal integration mediated by XYR1 and CRE1 at cellulasepromoters. (AU)

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