GSE163357
StuA-Regulated Processes in the Dermatophyte T. rubrum: Transcription Profile, Cell-Cell Adhesion, and Immunomodulation
Purpose: We aimed to gain more aspects about Stua-regulated processes in T. rubrum by assessing the global gene expression after its growth on keratin or glucose sources. Methods: T. rubrum strain CBS118892 and the null mutant strain ?stuA  were inoculated into 100 mL Sabouraud dextrose broth, and incubated under agitation at 28 °C for 96 h. Mycelia were aseptically transferred into 100 mL minimal medium (MM) at pH 5.0 containing 70 mM nitrate and 50 mM glucose (control) or 0.5% (w/v) bovine keratin (test condition) as an  alternative carbon source. The cultures were incubated under agitation at 28 °C for 24 h, 48 h, or 96 h. Equal amounts of RNA from three independent biological replicates of keratin or glucose cultures were sequenced with a NextSeq 500  sequencer. Paired-end reads of 150 bp in size were generated. Raw data obtained were processed for quality control by FastQC tool and trimmed with Trimmomatic to remove adapters and Illumina-specific sequences. Trimmed paired-end reads from each sample were aligned to the T. rubrum reference genome. Gene-level read counts were quantified with STAR's '-quantModeGeneCounts' parameter. Differential expression was analyzed with the DESeq2 bioconductor package. A Benjamini-Hochberg correction adjusted the P threshold and was applied to reveal statistically significant changes in gene expression levels. It was set to 0.05,  and a cut off threshold of ±1.5 log2-fold change was set to reveal statistically significant changes in expression levels, and referred  as differentially expressed genes (DEG). DEGs  were functionally categorized with the Gene Ontology (GO) terms assigned by the Blast2GO algorithm. Ultimately, the most representative categories for each experimental condition were identified by enrichment analysis using the BayGO algorithm . Results: Our data showed the involvement of Stua in biological processes related to carbon central metabolism and glycerol catabolism, ROS metabolism, and cell wall construction. The deep changes in carbohydrate metabolism might be responsible for significant alteration in cell wall pattern and consequently in cell to cell interaction and adhesion as we also demonstrated in this study. The mutant strain presented an impairment in biofilm production and promoted an increase in pro-inflammatory cytokine secretion. Moreover, we displayed a StuA-dependent regulation on catalase genes. Conclusions: In conclusion,  our data demonstrated the multitude of regulatory targets in TrStuA with a critical role in central metabolism that ultimately may be responsible to trigger a cascade of secondary effects with strong impacts on fungal physiology and virulence traits. Overall design: We proceeded an RNA-Seq analysis of T. rubrum  stuA knock-out strain to consider changes in global gene expression promoted by the presence of keratin or glucose medium in comparison to wild type.