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The hygromycin B phosphotransferase gene from <i>Escherichia coli</i> and the pyrithiamine resistance gene from <i>Aspergillus oryzae</i> are two dominant selectable marker genes widely used to genetically manipulate several fungal species. Despite the recent development of CRISPR/Cas9 and marker-free systems, in vitro molecular tools to study <i>Aspergillus</i> <i>fumigatus</i>, which is a saprophytic fungus causing life-threatening diseases in immunocompromised hosts, still rely extensively on the use of dominant selectable markers. The limited number of drug selectable markers is already a critical aspect, but the possibility that their introduction into a microorganism could induce enhanced virulence or undesired effects on metabolic behavior constitutes another problem. In this context, here, we demonstrate that the use of <i>ptrA</i> in <i>A. fumigatus</i> leads to the secretion of a compound that allows the recovery of thiamine auxotrophy. In this study, we developed a simple modification of the two commonly used dominant markers in which the development of resistance can be controlled by the xylose-inducible promoter <i>PxylP</i> from <i>Penicillium chrysogenum</i>. This strategy provides an easy solution to avoid undesired side effects, since the marker expression can be readily silenced when not required.