The exon context and distribution of Euascomycetes rRNA spliceosomal introns.
BACKGROUND
We have studied spliceosomal introns in the ribosomal (r)RNA of fungi to discover the forces that guide their insertion and fixation.


RESULTS
Comparative analyses of flanking sequences at 49 different spliceosomal intron sites showed that the G - intron - G motif is the conserved flanking sequence at sites of intron insertion. Information analysis showed that these rRNA introns contain significant information in the flanking exons. Analysis of all rDNA introns in the three phylogenetic domains and two organelles showed that group I introns are usually located after the most conserved sites in rRNA, whereas spliceosomal introns occur at less conserved positions. The distribution of spliceosomal and group I introns in the primary structure of small and large subunit rRNAs was tested with simulations using the broken-stick model as the null hypothesis. This analysis suggested that the spliceosomal and group I intron distributions were not produced by a random process. Sequence upstream of rRNA spliceosomal introns was significantly enriched in G nucleotides. We speculate that these G-rich regions may function as exonic splicing enhancers that guide the spliceosome and facilitate splicing.


CONCLUSIONS
Our results begin to define some of the rules that guide the distribution of rRNA spliceosomal introns and suggest that the exon context is of fundamental importance in intron fixation.
Bhattacharya
Debashish
D
Department of Biological Sciences and Center for Comparative Genomics, University of Iowa, Iowa City, USA. dbhattac@blue.weeg.uiowa.edu
Simon
Dawn
D
Huang
Jian
J
Cannone
Jamie J
JJ
Gutell
Robin R
RR
D001203:Ascomycota / Q000235:genetics*; D001482:Base Composition; D001483:Base Sequence; D017124:Conserved Sequence; D005091:Exons / Q000235:genetics*; D006147:Guanine / Q000378:metabolism; D007438:Introns / Q000235:genetics*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012322:RNA Precursors / Q000235:genetics / Q000378:metabolism; D012326:RNA Splicing / Q000235:genetics; D012331:RNA, Fungal / Q000235:genetics; D012335:RNA, Ribosomal / Q000235:genetics* / Q000378:metabolism; D017381:Spliceosomes / Q000235:genetics* / Q000378:metabolism
D012322:RNA Precursors; D012331:RNA, Fungal; D012335:RNA, Ribosomal; D006147:Guanine