The early transcriptional and post-transcriptional responses to fluconazole in sensitive and resistant Candida albicans

Irene Stevens¹, Gerald Silao Fitz², Susanne Huch¹, Kicki Ryman², Honglian Liu¹, Adriana Carvajal Jimenez¹, Per O. Ljungdahl², Vicent Pelechano¹

¹ Scilifelab, Department of Microbiology, Tumor and Cell Biology, Karolinska Universitet, Solna, Sweden.
² Science for Life Laboratory (SciLifeLab), Department of Molecular Biosciences, Stockholm University, Stockholm, Sweden.

Abstract

Candida albicans is a leading cause of fungal infections in immunocompromised patients. Management of candidemia relies on a few antifungal agents, with fluconazole being first line therapy. The emergence of fluconazole-resistant strains highlights the pressing need to improve our molecular understanding of the drug response mechanisms. By sequencing the 5’P mRNA degradation intermediates, we show that co-translational mRNA decay is common in C. albicans and characterize how in vivo 5´-3´ exonuclease degradation trails the last translating ribosome. Thus, the study of the 5'P mRNA degradome (5PSeq) offers a simple and affordable way to measure ribosome dynamics and identify codon specific ribosome stalls in response to drugs and amino acid deprivation. Building upon this, we combine RNA-Seq and 5PSeq to study the early response of sensitive and resistant C. albicans isolates to fluconazole. Our results highlight that transcriptional responses, rather than changes in ribosome dynamics, are the main driver of Candida resistance to fluconazole.

Data

Count tables from the fivepseq package are available in the Data folder.

Scripts for reproduction of manuscript figures

All manuscript figures may be reproduced from the R scripts within this repository, with the exception of those not prepared in R.

Main Figures

Figure 1: Rscript Markdown.
Figure 2: Rscript Markdown.
Figure 3: Rscript Markdown.
Figure 4: Rscript Markdown.

Additional analyses pertaining to the study

Differential Expression Analysis.
Functional Annotation Analysis

Supplementary Tables

Table S1: Candida albicans strains used in study

Table S2: Sequencing and alignment quality metrics

Table S3: Differentially expressed genes

Table S4: Enriched DAVID Terms, related to Figures 2 and 4

Contact

For questions regarding the 5'P sequencing, please contact:
Vicente Pelechano

For questions regarding the strains used in this study, please contact:
Per O. Ljungdahl

Links to relevant websites

Fivepseq package for Candida
Fivepseq package User Guide
Pelechano Lab website
Per Ljundahl lab website