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Eukaryotic Cell, October 2004, p. 1088-1100, Vol. 3, No. 5
1535-9778/04/$08.00+0     DOI: 10.1128/EC.3.5.1088-1100.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

Introns and Splicing Elements of Five Diverse Fungi{dagger}

Doris M. Kupfer,1,{ddagger} Scott D. Drabenstot,2 Kent L. Buchanan,3 Hongshing Lai,1 Hua Zhu,1 David W. Dyer,2 Bruce A. Roe,1 and Juneann W. Murphy2*

Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City,2 Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma,1 Department of Microbiology and Immunology, Tulane University Health Sciences Center, New Orleans, Louisiana3

Received 30 October 2003/ Accepted 12 July 2004

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.

* Corresponding author. Mailing address: Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, P.O. Box 26901, BMSB 1053, Oklahoma City, OK 73190. Phone: (405) 271-6622. Fax: (405) 271-3117. E-mail: juneann-murphy{at}ouhsc.edu.

{dagger} Supplemental material for this article may be found at http://ec.asm.org/.

{ddagger} Present address: Mutational Profiling, Genome Sequencing Center, Washington University School of Medicine, St. Louis, MO 63108.

Eukaryotic Cell, October 2004, p. 1088-1100, Vol. 3, No. 5
1535-9778/04/$08.00+0     DOI: 10.1128/EC.3.5.1088-1100.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.



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