Alternative Splicing in Trichophyton rubrum Occurs in Efflux Pump Transcripts in Response to Antifungal Drugs
Abstract
:1. Introduction
2. Materials and Methods
2.1. Strains and Culture Conditions
2.2. Drug Exposure in a Biofilm Environment
2.3. RNA Extraction and Cdna Synthesis
2.4. In Silico Analyses to Characterize the ABC Transporter Isoforms
2.5. In Silico Analysis of Genic Interaction Network
2.6. Alternative Splicing Validation—Gene Expression Analysis
3. Results
3.1. In Silico Analyses
Characterization of the ABC Transporter Isoforms
3.2. Alternative Splicing in Response to Antifungals Exposure
3.3. Alternative Splicing Evaluation in Response to Antifungal Exposure in the Biofilm Environment
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Nenoff, P.; Krüger, C.; Ginter-Hanselmayer, G.; Tietz, H.J. Mycology—An update. Part 1: Dermatomycoses: Causative agents, epidemiology and pathogenesis. J. Dtsch. Dermatol. Ges. 2014, 12, 188–209. [Google Scholar] [CrossRef]
- Martinez-Rossi, N.M.; Peres, N.T.A.; Bitencourt, T.A.; Martins, M.P.; Rossi, A. State-of-the-Art Dermatophyte Infections: Epidemiology Aspects, Pathophysiology, and Resistance Mechanisms. J. Fungi 2021, 7, 629. [Google Scholar] [CrossRef]
- Persinoti, G.F.; de Aguiar Peres, N.T.; Jacob, T.R.; Rossi, A.; Vêncio, R.Z.; Martinez-Rossi, N.M. RNA-sequencing analysis of Trichophyton rubrum transcriptome in response to sublethal doses of acriflavine. BMC Genom. 2014, 15 (Suppl. S7), S1. [Google Scholar] [CrossRef] [Green Version]
- Martinez-Rossi, N.M.; Bitencourt, T.A.; Peres, N.T.A.; Lang, E.A.S.; Gomes, E.V.; Quaresemin, N.R.; Martins, M.P.; Lopes, L.; Rossi, A. Dermatophyte Resistance to Antifungal Drugs: Mechanisms and Prospectus. Front. Microbiol. 2018, 9, 1108. [Google Scholar] [CrossRef] [Green Version]
- Cowen, L.E.; Sanglard, D.; Howard, S.J.; Rogers, P.D.; Perlin, D.S. Mechanisms of Antifungal Drug Resistance. Cold Spring Harb. Perspect Med. 2014, 5, a019752. [Google Scholar] [CrossRef]
- Sanguinetti, M.; Posteraro, B.; Lass-Flörl, C. Antifungal drug resistance among Candida species: Mechanisms and clinical impact. Mycoses 2015, 58, 2–13. [Google Scholar] [CrossRef]
- Gadzalski, M.; Ciesielska, A.; Stączek, P. Bioinformatic survey of ABC transporters in dermatophytes. Gene 2016, 576, 466–475. [Google Scholar] [CrossRef]
- Martins, M.P.; Rossi, A.; Sanches, P.R.; Martinez-Rossi, N.M. Differential expression of multidrug-resistance genes in Trichophyton rubrum. J. Integr. OMICS 2019, 9, 65–69. [Google Scholar] [CrossRef]
- Yamada, T.; Yaguchi, T.; Salamin, K.; Guenova, E.; Feuermann, M.; Monod, M. MFS1, a Pleiotropic Transporter in Dermatophytes That Plays a Key Role in Their Intrinsic Resistance to Chloramphenicol and Fluconazole. J. Fungi 2021, 7, 542. [Google Scholar] [CrossRef]
- Martins, M.P.; Franceschini, A.C.C.; Jacob, T.R.; Rossi, A.; Martinez-Rossi, N.M. Compensatory expression of multidrug-resistance genes encoding ABC transporters in dermatophytes. J. Med. Microbiol. 2016, 65, 605–610. [Google Scholar] [CrossRef]
- Silva, S.; Rodrigues, C.F.; Araújo, D.; Rodrigues, M.E.; Henriques, M. Candida Species Biofilms’ Antifungal Resistance. J. Fungi 2017, 3, 8. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Castelo-Branco, D.d.S.C.M.; Aguiar, L.d.; Araújo, G.d.S.; Lopes, R.G.P.; Sales, J.d.A.; Pereira-Neto, W.A.; Pinheiro, A.d.Q.; Paixão, G.C.; Cordeiro, R.d.A.; Sidrim, J.J.C. In vitro and ex vivo biofilms of dermatophytes: A new panorama for the study of antifungal drugs. Biofouling 2020, 36, 783–791. [Google Scholar] [CrossRef] [PubMed]
- Robbins, N.; Caplan, T.; Cowen, L.E. Molecular Evolution of Antifungal Drug Resistance. Annu. Rev. Microbiol. 2017, 71, 753–775. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Pereira, R.; Dos Santos Fontenelle, R.O.; de Brito, E.H.S.; de Morais, S.M. Biofilm of Candida albicans: Formation, regulation and resistance. J. Appl. Microbiol. 2021, 131, 11–22. [Google Scholar] [CrossRef] [PubMed]
- Mendes, N.S.; Bitencourt, T.A.; Sanches, P.R.; Silva-Rocha, R.; Martinez-Rossi, N.M.; Rossi, A. Transcriptome-wide survey of gene expression changes and alternative splicing in Trichophyton rubrum in response to undecanoic acid. Sci. Rep. 2018, 8, 2520. [Google Scholar] [CrossRef] [Green Version]
- Neves-da-Rocha, J.; Bitencourt, T.A.; Oliveira, V.M.; Sanches, P.R.; Rossi, A.; Martinez-Rossi, N.M. Alternative Splicing in Heat Shock Protein Transcripts as a Mechanism of Cell Adaptation in Trichophyton rubrum. Cells 2019, 8, 1206. [Google Scholar] [CrossRef] [Green Version]
- Rossi, A.; Martins, M.P.; Bitencourt, T.A.; Peres, N.T.A.; Rocha, C.H.L.; Rocha, F.M.G.; Neves-da-Rocha, J.; Lopes, M.E.R.; Sanches, P.R.; Bortolossi, J.C.; et al. Reassessing the Use of Undecanoic Acid as a Therapeutic Strategy for Treating Fungal Infections. Mycopathologia 2021, 186, 327–340. [Google Scholar] [CrossRef]
- Gomes, E.V.; Bortolossi, J.C.; Sanches, P.R.; Mendes, N.S.; Martinez-Rossi, N.M.; Rossi, A. STE20/PAKA Protein Kinase Gene Releases an Autoinhibitory Domain through Pre-mRNA Alternative Splicing in the Dermatophyte Trichophyton rubrum. Int. J. Mol. Sci. 2018, 19, 3654. [Google Scholar] [CrossRef] [Green Version]
- Coelho, L.M.; Aquino-Ferreira, R.; Maffei, C.M.L.; Martinez-Rossi, N.M. In vitro antifungal drug susceptibilities of dermatophytes microconidia and arthroconidia. J. Antimicrob. Chemother. 2008, 62, 758–761. [Google Scholar] [CrossRef] [Green Version]
- Costa-Orlandi, C.B.; Sardi, J.C.; Santos, C.T.; Fusco-Almeida, A.M.; Mendes-Giannini, M.J. In vitro characterization of Trichophyton rubrum and T. mentagrophytes biofilms. Biofouling 2014, 30, 719–727. [Google Scholar] [CrossRef]
- Bitencourt, T.A.; Neves-da-Rocha, J.; Martins, M.P.; Sanches, P.R.; Lang, E.A.S.; Bortolossi, J.C.; Rossi, A.; Martinez-Rossi, N.M. StuA-Regulated Processes in the Dermatophyte Trichophyton rubrum. Front. Cell. Infect. Microbiol. 2021, 11, 643659. [Google Scholar] [CrossRef] [PubMed]
- Bitencourt, T.A.; Oliveira, F.B.; Sanches, P.R.; Rossi, A.; Martinez-Rossi, N.M. The prp4 kinase gene and related spliceosome factor genes in Trichophyton rubrum respond to nutrients and antifungals. J. Med. Microbiol. 2019, 68, 591–599. [Google Scholar] [CrossRef] [PubMed]
- Liu, W.; Xie, Y.; Ma, J.; Luo, X.; Nie, P.; Zuo, Z.; Lahrmann, U.; Zhao, Q.; Zheng, Y.; Zhao, Y.; et al. IBS: An illustrator for the presentation and visualization of biological sequences. Bioinformatics 2015, 31, 3359–3361. [Google Scholar] [CrossRef] [Green Version]
- Jacob, T.R.; Peres, N.T.; Persinoti, G.F.; Silva, L.G.; Mazucato, M.; Rossi, A.; Martinez-Rossi, N.M. rpb2 is a reliable reference gene for quantitative gene expression analysis in the dermatophyte Trichophyton rubrum. Med. Mycol. 2012, 50, 368–377. [Google Scholar] [CrossRef] [Green Version]
- Livak, K.J.; Schmittgen, T.D. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 2001, 25, 402–408. [Google Scholar] [CrossRef] [PubMed]
- Kean, R.; Delaney, C.; Sherry, L.; Borman, A.; Johnson, E.M.; Richardson, M.D.; Rautemaa-Richardson, R.; Williams, C.; Ramage, G. Transcriptome assembly and profiling of Candida auris reveals novel insights into biofilm-mediated resistance. Msphere 2018, 3, 00334-18. [Google Scholar] [CrossRef] [Green Version]
- Prasad, R.; Rawal, M.K. Efflux pump proteins in antifungal resistance. Front. Pharmacol. 2014, 5, 202. [Google Scholar] [CrossRef] [Green Version]
- Víglaš, J.; Olejníková, P. An update on ABC transporters of filamentous fungi—From physiological substrates to xenobiotics. Microbiol. Res. 2021, 246, 126684. [Google Scholar] [CrossRef]
- Bahn, Y.S.; Xue, C.; Idnurm, A.; Rutherford, J.C.; Heitman, J.; Cardenas, M.E. Sensing the environment: Lessons from fungi. Nat. Rev. Microbiol. 2007, 5, 57–69. [Google Scholar] [CrossRef]
- Brown, N.A.; Schrevens, S.; van Dijck, P.; Goldman, G.H. Fungal G-protein-coupled receptors: Mediators of pathogenesis and targets for disease control. Nat. Microbiol. 2018, 3, 402–414. [Google Scholar] [CrossRef]
- Versele, M.; Lemaire, K.; Thevelein, J.M. Sex and sugar in yeast: Two distinct GPCR systems. EMBO Rep. 2001, 2, 574–579. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Sridhar, P.S.; Trofimova, D.; Subramaniam, R.; González-Peña Fundora, D.; Foroud, N.A.; Allingham, J.S.; Loewen, M.C. Ste2 receptor-mediated chemotropism of Fusarium graminearum contributes to its pathogenicity against wheat. Sci. Rep. 2020, 10, 10770. [Google Scholar] [CrossRef] [PubMed]
- Turrà, D.; El Ghalid, M.; Rossi, F.; Di Pietro, A. Fungal pathogen uses sex pheromone receptor for chemotropic sensing of host plant signals. Nature 2015, 527, 521–524. [Google Scholar] [CrossRef] [PubMed]
- Rocha, C.H.L.; Rocha, F.M.G.; Bitencourt, T.A.; Martins, M.P.; Sanches, P.R.; Rossi, A.; Rossi, N.M.M. Synergism between the Antidepressant Sertraline and Caspofungin as an Approach to Minimise the Virulence and Resistance in the Dermatophyte Trichophyton rubrum. J. Fungi 2022, 8, 815. [Google Scholar] [CrossRef]
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Lopes, M.E.R.; Bitencourt, T.A.; Sanches, P.R.; Martins, M.P.; Oliveira, V.M.; Rossi, A.; Martinez-Rossi, N.M. Alternative Splicing in Trichophyton rubrum Occurs in Efflux Pump Transcripts in Response to Antifungal Drugs. J. Fungi 2022, 8, 878. https://doi.org/10.3390/jof8080878
Lopes MER, Bitencourt TA, Sanches PR, Martins MP, Oliveira VM, Rossi A, Martinez-Rossi NM. Alternative Splicing in Trichophyton rubrum Occurs in Efflux Pump Transcripts in Response to Antifungal Drugs. Journal of Fungi. 2022; 8(8):878. https://doi.org/10.3390/jof8080878
Chicago/Turabian StyleLopes, Marcos E. R., Tamires A. Bitencourt, Pablo R. Sanches, Maíra P. Martins, Vanderci M. Oliveira, Antonio Rossi, and Nilce M. Martinez-Rossi. 2022. "Alternative Splicing in Trichophyton rubrum Occurs in Efflux Pump Transcripts in Response to Antifungal Drugs" Journal of Fungi 8, no. 8: 878. https://doi.org/10.3390/jof8080878