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| Status |
Public on Sep 19, 2019 |
| Title |
Global Analysis of the dermatophyte Trichophyton rubrum when shifted from glucose to keratin |
| Organism |
Trichophyton rubrum |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: We evaluated T. rubrum transcriptome using high-throughput RNA-sequencing (RNA-seq) technology aiming to identify metabolic pathways modulated the development in keratin.
Methods: T. rubrum strain CBS118892 was 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 (treatment) as the 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 Hiseq 2000 sequencer. Paired-end reads 150 bp in size were generated. Raw read data obtained were filtered 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, with a log2 fold change ± 1.5 and postulated as a significantly modulated transcript abundance level. Genes surpassing these thresholds are hereinafter referred to as differentially expressed genes (DEG). They were functionally categorized with the Gene Ontology (GO) terms assigned by the Blast2GO algorithm. Highly represented categories were determined by enrichment analysis with the BayGO algorithm.
Results: Our results present adaptive strategies in response to culture media. The global modulation in response to keratin supports fungal virulence and proper adaptation to the environment, in comparison to the availability of glucose as a carbon source.
Conclusions: Our results revealed a profile of the adaptive events to the host environment, crucial to the establishment and maintenance of the infection. The observed metabolic modulation is necessary for fungus survival and perpetuation in the initial steps of the infective process in their host.
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| Overall design |
We examined at the transcriptomic level the effects of carbon source switching from glucose to keratin in Trichophyton rubrum metabolism. We aimed to evaluate the transcriptional pattern during the early stages of the infection in the host.
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| Contributor(s) |
Martins MP, Silva LG, Rossi A, Sanches PR, Souza LD, Martinez-Rossi NM |
| Citation(s) |
31608026, 34169004, 35783403, 38203573 |
| |
| Submission date |
Jul 17, 2019 |
| Last update date |
Jan 18, 2024 |
| Contact name |
Pablo Rodrigo Sanches |
| E-mail(s) |
[email protected]
|
| Organization name |
University of São Paulo
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| Department |
Genetics
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| Lab |
Molecular Biology and Genetics of fungi
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| Street address |
Av. Bandeirantes, 3900
|
| City |
Ribeirão Preto |
| State/province |
SP |
| ZIP/Postal code |
14049-900 |
| Country |
Brazil |
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| Platforms (1) |
| GPL23937 |
Illumina HiSeq 2000 (Trichophyton rubrum) |
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| Samples (18)
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| Relations |
| BioProject |
PRJNA555056 |
| SRA |
SRP215019 |
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