Identification of an Exceptionally Long Intron in the <i>HAC1</i> Gene of <i>Candida parapsilosis</i>

Abstract

The unfolded protein response (UPR) in the endoplasmic reticulum (ER) is well conserved in eukaryotes from metazoa to yeast. The transcription factor <i>HAC1</i> is a major regulator of the UPR in many eukaryotes. Deleting <i>HAC1</i> in the yeast <i>Candida parapsilosis</i> rendered cells more sensitive to DTT, a known inducer of the UPR. The deletion strain was also sensitive to Congo red, calcofluor white, and the antifungal drug ketoconazole, indicating that <i>HAC1</i> has a role in cell wall maintenance. Transcriptomic analysis revealed that treatment of the wild type with DTT resulted in the increased expression of 368 genes. Comparison with mutant cells treated with DTT reveals that expression of 137 of these genes requires <i>HAC1</i> Enriched GO term analysis includes response to ER stress, cell wall biogenesis and glycosylation. Orthologs of many of these are associated with UPR in <i>Saccharomyces cerevisiae</i> and <i>Candida albicans</i> Unconventional splicing of an intron from <i>HAC1</i> mRNA is required to produce a functional transcription factor. The spliced intron varies in length from 19 bases in <i>C. albicans</i> to 379 bases in <i>Candida glabrata</i>, but has not been previously identified in <i>Candida parapsilosis</i> and related species. We used RNA-seq data and <i>in silico</i> analysis to identify the <i>HAC1</i> intron in 12 species in the CTG-Ser1 clade. We show that the intron has undergone major contractions and expansions in this clade, reaching up to 848 bases. Exposure to DTT induced splicing of the long intron in <i>C. parapsilosis</i><i>HAC1</i>, inducing the UPR.<b>IMPORTANCE</b> The unfolded protein response (UPR) responds to the build-up of misfolded proteins in the endoplasmic reticulum. The UPR has wide-ranging functions from fungal pathogenesis to applications in biotechnology. The UPR is regulated through the splicing of an unconventional intron in the <i>HAC1</i> gene. This intron has been described in many fungal species and is of variable length. Until now it was believed that some members of the CTG-Ser1 clade such as <i>C. parapsilosis</i> did not contain an intron in <i>HAC1</i>, suggesting that the UPR was regulated in a different manner. Here we demonstrate that <i>HAC1</i> plays an important role in regulating the UPR in <i>C. parapsilosis</i> We also identified an unusually long intron (626 bp) in <i>C. parapsilosis</i><i>HAC1</i> Further analysis showed that <i>HAC1</i> orthologs in several species in the CTG-Ser1 clade contain long introns.