Introns and Splicing Elements of Five Diverse Fungi

Abstract

Genomic sequences and expressed sequence tag data for a diverse group of fungi (Saccharomyces cerevisiae, Schizosaccharomyces pombe, Aspergillus nidulans, Neurospora crassa, and Cryptococcus neoformans) provided the opportunity to accurately characterize conserved intronic elements. An examination of large intron data sets revealed that fungal introns in general are short, that 98% or more of them belong to the canonical splice site (ss) class (5GU. . .AG3), and that they have polypyrimidine tracts predominantly in the region between the 5 ss and the branch point. Information content is high in the 5 ss, branch site, and 3 ss regions of the introns but low in the exon regions adjacent to the introns in the fungi examined. The two yeasts have broader intron length ranges and correspondingly higher intron information content than the other fungi. Generally, as intron length increases in the fungi, so does intron information content. Homologs of U2AF spliceosomal proteins were found in all species except for S. cerevisiae, suggesting a nonconventional role for U2AF in the absence of canonical polypyrimidine tracts in the majority of introns. Our observations imply that splicing in fungi may be different from that in vertebrates and may require additional proteins that interact with polypyrimidine tracts upstream of the branch point. Theoretical protein homologs for Nam8p and TIA-1, two proteins that require U-rich regions upstream of the branch point to function, were found. There appear to be sufficient differences between S. cerevisiae and S. pombe introns and the introns of two filamentous members of the Ascomycota and one member of the Basidiomycota to warrant the development of new model organisms for studying the splicing mechanisms of fungi.Based on studies with a limited number of organisms, fungal genes appear to differ from those of higher eukaryotes in that fungal genes have relatively long exons and short introns (14,37,53). From these data, we hypothesized that fungi as a group would have exon and intron features that are similar as well as different from those of higher eukaryotes. Our approach to testing this hypothesis was to compare the exon and intron characteristics of two well-studied members of the Ascomycota group of fungal organisms, the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe (7,12,20,30,34,68), with the intron and exon characteristics of three additional fungi for which genomic sequences and expressed sequence tag (EST) data are available: two filamentous members of the Ascomycota, Aspergillus nidulans and Neurospora crassa (http://www.broad.mit.edu/annotation/fungi /aspergillus/, http://www.broad.mit.edu/annotation/fungi /neurospora/, and http://www.genome.ou.edu/fungal.html) (19,36,72), and a member of the Basidiomycota, Cryptococcus neoformans (http://www-sequence.stanford.edu/group /C.neoformans/ and http://www.genome.ou.edu/cneo.html). The availability of genomic sequences and EST data for the latter three fungi permitted the establishment...

Lariat sequencing in a unicellular yeast identifies regulated alternative splicing of exons that are evolutionarily conserved with humans

“…Nearly 50% of S. pombe genes contain an intron, and almost half of those contain multiple introns (18,19). Moreover, the splice site sequences found within S. pombe introns do not conform to the tight consensus sequences seen in some other unicellular fungi, but rather are marked by a degeneracy more similar to that seen in human introns (20,21). Importantly, a single bona fide member of the serine/arginine-rich (SR) family of splicing regulators and several SR-like proteins implicated in the regulation of alternative splicing are encoded within the S. pombe genome (22,23).…”

Differentiation of entomopathogenic fungus Beauveria bassiana (Ascomycetes: Hypocreales) isolates by PCR-RFLP

“…Polymorphisms in the rDNA gene region have been attributed to small insertions/deletions, multiple duplications or, most often, to the presence of group-I introns. These introns are found in a diverse range of higher organisms, including fungi, protists and green algae, where they occur in the nuclear, mitochondrial and chloroplast genomes (Belshaw and Bensasson 2006;Bhattacharya et al 2005;Haugen et al 2005;Kupfer et al 2004;Mattick 1994).…”

Fungal Genomic Annotation

“…For example, in C. neoformans, preliminary analysis has shown that introns have a very tight distribution around 68bp and therefore, when annotating this genome, authors explicitly coded this 'spiked' intron length distribution in the TWINSCAN program instead of the default geometric distribution used in the original program (Tenney et al 2004). Kupfer et al (Kupfer et al 2004) provided the first comprehensive analysis of introns and splicing sites in five diverse fungi, which included the yeasts S. cerevisae and S. pombe; two well-studied Ascomycetes, A. nidulans and N crassa; and one Basidmycete, C. neoformans. Based on EST data they found that for all studied fungi more than 98% of all splice sites have the canonical 5'GT ... AG3' donor-acceptor pairs in agreement with vertebrate splice sites.…”