Transcriptome-wide survey of gene expression changes and alternative splicing in Trichophyton rubrum in response to undecanoic acid

Abstract

While fatty acids are known to be toxic to dermatophytes, key physiological aspects of the Trichophyton rubrum response to undecanoic acid (UDA), a medium chain saturated fatty acid (C11:0), are not well understood. Thus, we analysed RNA-seq data from T. rubrum exposed to sub-lethal doses of UDA for 3 and 12 h. Three putative pathways were primarily involved in UDA detoxification: lipid metabolism and cellular membrane composition, oxidative stress, and pathogenesis. Biochemical assays showed cell membrane impairment, reductions in ergosterol content, and an increase in keratinolytic activity following UDA exposure. Moreover, we assessed differential exon usage and intron retention following UDA exposure. A key enzyme supplying guanine nucleotides to cells, inosine monophosphate dehydrogenase (IMPDH), showed high levels of intron 2 retention. Additionally, phosphoglucomutase (PGM), which is involved in the glycogen synthesis and degradation as well as cell wall biosynthesis, exhibited a significant difference in exon 4 usage following UDA exposure. Owing to the roles of these enzymes in fungal cells, both have emerged as promising antifungal targets. We showed that intron 2 retention in impdh and exon 4 skipping in pgm might be related to an adaptive strategy to combat fatty acid toxicity. Thus, the general effect of UDA fungal toxicity involves changes to fungal metabolism and mechanisms for regulating pre-mRNA processing events.

Major challenges and perspectives in the diagnostics and treatment of dermatophyte infections

“…Moreover, RNA sequence analysis performed to determine the expression of T. rubrum genes treated with undecylenic acid also showed positive regulation of several genes encoding antioxidant enzymes Mendes et al 2018). In response to undecylenic acid, besides increased catalase activity, enzymes such as superoxide dismutase, peroxidase, glutathione transferase and glutathione peroxidase were expressed as well, which led to enzymatic oxidative detoxification of fungal cells (Mendes et al 2018). The ability of dermatophytes to increase the secretion of exoenzymes can be associated with the pathogenicity of these fungi and their response to cellular stress, and thus with the mechanisms of detoxification (Brasch et al 1991;Gnat et al 2018c).…”

“…Increased expression of catalase genes can provide a compensatory mechanism to maintain a constant level of this enzyme inside the cell, thus protecting it from the adverse effects of the drug. Moreover, RNA sequence analysis performed to determine the expression of T. rubrum genes treated with undecylenic acid also showed positive regulation of several genes encoding antioxidant enzymes Mendes et al 2018). In response to undecylenic acid, besides increased catalase activity, enzymes such as superoxide dismutase, peroxidase, glutathione transferase and glutathione peroxidase were expressed as well, which led to enzymatic oxidative detoxification of fungal cells (Mendes et al 2018).…”

HacA Governs Virulence Traits and Adaptive Stress Responses in Trichophyton rubrum

“…This uncorrelated data might be due to a metabolic rearrangement as an attempt to use this complex protein substrate. Previous work reported that T. rubrum under undecanoic acid exposure presented a decrease in keratin growth and an increase in keratinolytic activity, which might be a consequence of changes in enzymes by posttranslation modifications (Mendes et al, 2018).…”

Dermatophyte Resistance to Antifungal Drugs: Mechanisms and Prospectus

“…In particular, it is still challenging to utilize gene targeting to study gene function in most species of this group of fungi; thus, transcriptomics have been applied to better understand the molecular mechanisms involved in drug-stress responses and adaptation. For example, T. interdigitale and T. rubrum respond to sub-lethal doses of several antifungal compounds by modulating the expression of genes related to various processes, such as protein transport, drug efflux, lipid metabolism, signal transduction, translation, post-translational modifications, and oxidative stress, depending on the drug and time of exposure ( Paião et al, 2007 ; Yu et al, 2007a ; Zhang et al, 2007 , 2009 ; Peres et al, 2010b ; Persinoti et al, 2014 ; Mendes et al, 2018 ). Specifically, a gene encoding a transposable element was shown to be up-regulated in T. interdigitale after exposure to several drugs ( Paião et al, 2007 ; Peres et al, 2010b ).…”

“…However, the regulatory mechanisms involved in stress responses are complex. Recently, a refined use of pre-mRNA processing events has been reported in T. rubrum in response to undecanoic acid (UDA), regulating the expression of genes encoding phosphoglucomutase, which is involved in gluconeogenesis and in cell wall biosynthesis, along with inosine monophosphate dehydrogenase, a key enzyme supplying guanine nucleotides to cells ( Mendes et al, 2018 ). These mechanisms, along with others, collectively help the cells to counteract the toxicity of drugs and cope with stress.…”