Prediction of Gene and Genomic Regulation in Candida Species, Using the PathoYeastract Database: A Comparative
Pedro Pais1,2, Jorge Oliveira3,4, Romeu Viana1,2
1iBB-Institute for Bioengineering and Biosciences, Biological Sciences Research Group, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.
Methods in Molecular Biology (Clifton, N.J.)
|May 6, 2022
Summary
This study introduces PathoYeastract, a tool for predicting gene regulation in pathogenic yeasts like Candida. It helps understand how transcription factors control gene expression and adapt to environmental changes.
Area of Science:
- Microbiology
- Systems Biology
- Bioinformatics
Background:
- Organism survival depends on gene expression programs for adaptation.
- Transcriptional networks are complex, with transcription factors (TFs) acting as activators or repressors.
- Understanding these networks is crucial for studying gene regulation.
Purpose of the Study:
- To provide a guide for using PathoYeastract to predict gene and genomic regulation in Candida species.
- To demonstrate the prediction of transcription factors regulating individual genes, genes regulated by a specific TF, and genome-wide responses.
- To explore new functionalities like cross-species network comparison.
Main Methods:
- Utilized PathoYeastract, a database within the YEASTRACT+ portal.
- Performed step-by-step analyses of regulatory associations in human pathogenic yeasts.
- Illustrated capabilities with case studies involving Candida glabrata gene regulation, TF regulons, and responses to fluconazole.
Main Results:
- Successfully predicted TF networks for specific genes (e.g., C. glabrata QDR2).
- Identified regulons controlled by TFs (e.g., C. glabrata Rpn4).
- Mapped regulatory networks underlying transcriptional changes in response to antifungal drugs.
Conclusions:
- PathoYeastract is a valuable tool for predicting gene regulation in Candida species.
- The database facilitates understanding of transcriptional networks and adaptation mechanisms.
- Cross-species comparisons offer new insights into conserved regulatory principles.
