Introns and splicing elements of five diverse fungi.
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 (5'GU...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.
Kupfer
Doris M
DM
Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, P.O. Box 26901, BMSB 1053, Oklahoma City, OK 73190, USA.
Drabenstot
Scott D
SD
Buchanan
Kent L
KL
Lai
Hongshing
H
Zhu
Hua
H
Dyer
David W
DW
Roe
Bruce A
BA
Murphy
Juneann W
JW
D001233:Aspergillus nidulans / Q000235:genetics; D001483:Base Sequence; D016384:Consensus Sequence; D003455:Cryptococcus neoformans / Q000235:genetics; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics; D005091:Exons; D020224:Expressed Sequence Tags; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism; D005658:Fungi / Q000235:genetics* / Q000378:metabolism; D016681:Genome, Fungal; D007438:Introns; D009492:Neurospora crassa / Q000235:genetics; D010802:Phylogeny; D012326:RNA Splicing / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics; D012568:Schizosaccharomyces / Q000235:genetics; D013045:Species Specificity; D017381:Spliceosomes / Q000378:metabolism
D004271:DNA, Fungal; D005656:Fungal Proteins