Deciphering the phenol degradation metabolic pathway in Scedosporium apiospermum HDO1

The filamentous fungus Scedosporium apiospermum is a microorganism capable of phenol degradation. Phenol is a petroleum-derived pollutant and a compound widely used in several industries. As a result of its widespread use, phenol is commonly discarded and accumulated in soils and water bodies. In this study, overexpressed and repressed genes that produce enzymes involved in phenol metabolism were identified in S. apiospermum HDO1 when the fungus grows in the presence of phenol. The fungus was grown with either glucose (control) or phenol as the sole carbon source to achieve this. RNA from the mycelium was extracted and sequenced using the Illumina Hiseq-4000 platform, with paired-end libraries. Eighteen genes coding for enzymes related to catechol ortho-cleavage, catechol meta-cleavage, and hydroquinone pathways were annotated from the assembled transcriptome. In the differential gene expression analysis, 11 genes coding for phenol 2-monooxygenase, catechol 1,2-dioxygenase, 3-oxoadipate enol lactonase, hydroxyquinol 1,2-dioxygenase, and aldehyde dehydrogenase were overexpressed. In contrast, one gene coding for protocatechuate 3,4-dioxygenase was repressed. We show for the first time that phenol degradation in S. apiospermum occurs through one of the catechol routes, the catechol-ortho ring cleavage pathway, and through the hydroquinone A pathway. These findings are important because they improve the understanding of how eukaryotic microorganisms with the potential for bioremediation degrade organic pollutants such as phenol.IMPORTANCEIn recent years, bioremediation has emerged as one of the solutions to eliminate pollutants from the environment. Scedosporium apiospermum is one of the fungi capable of tolerating and degrading common pollutants such as phenol. This ability is of great interest as it highlights its potential for use, but also as an important eukaryotic model in contaminant metabolism. S. apiospermum has been widely studied for its clinical significance, but little is yet known about its role in natural environments and its capacity for removing organic pollutants. Using previously published biochemical data together with our differential gene expression results, we validated and completed the proposed phenol metabolic pathways.