Computational and experimental approaches double the number of known introns in the pathogenic yeast Candida albicans

Abstract

Candida albicans is the most common fungal pathogen of humans. Frequently found as a commensal within the digestive tracts of healthy individuals, C. albicans is an opportunistic pathogen that causes a wide variety of clinical syndromes in immuno-compromised individuals. A comprehensive annotation of the C. albicans genome sequence was recently published. Because many C. albicans coding sequences are interrupted by introns, proper intron annotation is essential for the accurate definition of genes in this pathogen. Intron annotation is also important for identifying potential targets of splicing regulation, a common mechanism of gene control in eukaryotes. In this study, we report an improved annotation of C. albicans introns. In addition to correcting the existing intron annotations, 25% of which were incorrect, we have used novel computational and experimental approaches to identify new introns, bringing the total to 415, almost double the number previously known. Our identification methods focus primarily on intron features rather than protein-coding features, overcoming biases of traditional intron annotation methods. Introns are not randomly distributed in C. albicans, and are over-represented in genes involved in specific cellular processes, such as splicing, translation, and mitochondrial respiration. This nonrandom distribution suggests functional roles for these introns, and we demonstrate that splicing of two transcripts whose introns have unusual sequence features is responsive to environmental factors.[Supplemental material is available online at www.genome.org. The microarray data from this study are available at ArrayExpress (http://www.ebi.ac.uk), accession no. E-MEXP-1003.]The yeast Candida albicans commonly inhabits the mucous membranes and digestive tracts of healthy individuals. Perturbation of a host's immune defenses, however, can cause a dramatic shift to invasive, pathogenic growth. Particularly susceptible are those receiving immunosuppressive therapies, such as cancer and transplant patients (Kullberg and Filler 2002), and individuals infected with HIV, more than 90% of whom will at some point suffer candidiasis (Fidel 2002). C. albicans exhibits remarkable adaptability, capable of successfully invading virtually every human organ and tissue (for review, see Odds 1988). During infection, C. albicans is most commonly associated with mucosal surfaces, but in its most devastating form-disseminated candidiasis-it spreads through the host bloodstream and invades multiple tissues, with an associated mortality in excess of 40% (for example, see Alonso-Valle et al. 2003).Eukaryotic genes are often interrupted by introns, which must be spliced out of gene transcripts for coding sequences to be fully expressed. The regulation of intron splicing can also play an important role in controlling gene expression (for reviews, see only 5% of genes in S. cerevisiae contain introns, and most of these genes contain only one (Davis et al. 2000). The loss of introns within the S. cerevisiae lineage has not be...

Evolution of small nuclear RNAs in S. cerevisiae, C. albicans, and other hemiascomycetous yeasts

“…Modulating the transition rates between different spliceosomal conformations, as discussed for the U4/U6-to-U2/U6 transition, could provide novel opportunities for regulating the splicing (and therefore expression) of specific transcripts, perhaps in response to different environmental demands. Indeed, we have observed examples of environmentally regulated splicing in both S. cerevisiae (Pleiss et al 2007) and C. albicans (Mitrovich et al 2007). …”

“…They have experienced a dramatic rate of intron loss, leaving their genomes largely devoid of the introns that litter many eukaryotic genomes (Dujon 2006). Those introns that remain typically number only in the hundreds and are highly stereotyped, with splice sites adhering to unusually strict consensus sequences (Spingola et al 1999;Bon et al 2003;Mitrovich et al 2007). Thus, the diversity of introns with which the spliceosome must contend is greatly reduced in the hemiascomycetes, and this may have reduced certain evolutionary constraints on the snRNA sequences.…”

“…Some of the variation within the snRNAs may also be related to general changes in the intron features of different hemiascomycetes. For example, there are differences between C. albicans and S. cerevisiae in the sequence and spacing of splice sites (Mitrovich et al 2007). An analysis of introns in other hemiascomycetes suggests substantial changes in splice site usage, although sample sizes were too small to draw general conclusions (Bon et al 2003).…”

Nucleotide sequence composition adjacent to intronic splice sites improves splicing efficiency via its effect on pre-mRNA local folding in fungi

“…introns from the UTRs, and function and expression levels of intron-containing genes; e.g., in C. albicans introns are not randomly distributed and are overrepresented in genes involved in specific cellular processes such as splicing, translation, and mitochondrial respiration (Mitrovich et al 2007). In addition, it is easy to see that most of the introns analyzed here do not have homologs in more than one organism.…”

“…Conversely, in Schizosaccharomyces pombe (an organism with ∼5000 genes) there are ∼5000 introns spreading over one-third of its genome, with up to 20 introns mediating a single gene (Wood et al 2002) and with few known genes displaying AS (Habara et al 1998;Okazaki and Niwa 2000;Marshall et al 2013). Other fungi such as Aspergillus nidulans and Candida albicans show variations in intronic characteristics as well (Kupfer et al 2004;Mitrovich et al 2007). Nonetheless, even though eukaryotic evolution has been generally characterized by widespread intron gain and loss events (Jeffares et al 2006;Roy and Gilbert 2006;Carmel et al 2007;Stajich et al 2007;Rogozin et al 2012;Zhu and Niu 2013), the ubiquity of introns and the core of the spliceosome are conserved in all well-characterized eukaryotes (Nilsen 2003;Collins and Penny 2005).…”