Nucleotide sequence of a ribosomal RNA gene intron from slime mold Physarum polycephalum (intervening sequences/Physarum 26S rRNA/sequencing/rRNA splicing mechanism/gene evolution)

The Physarum polycephalum 26S ribosomal RNA gene contains two intervening sequences (introns). The DNA se- quence of one of these introns was analyzed together with that of its flanking regions (exons). In addition, the nucleotide sequence of the corresponding region of the reverse transcript of 26S rRNA was determined, and from comparisons of both sequences the precise location and size of the intron were determined. Our find- ings, when compared with those for Tetrahymena and Chlazmdo- monas rRNA gene introns, led to the conclusion that certain char- acteristics exist near the ends of these introns. (i) An exon ends in T at the exon/intron junction and an intron ends in G at the intron/ exon junction in all cases. (ii) For each intron, direct repeats sev- eral nucleotides long are present 5 to -30 nucleotides upstream from both the exon/intron and intron/exon junctions. Many eukaryotic and viral genes are interrupted by intervening sequences (introns) which are not represented in their mature RNAs (1). The primary transcripts from such discontinuous genes contain counterparts of introns as well as structural se- quences (exons) but, on processing, the intron counterparts are removed and those of exons are rejoined to form functional messenger (2-6), ribosomal (7-9), or transfer (10, 11) RNAs by splicing. Analysis of the protein-coding gene introns and their flanking exon regions from various species showed that sequence homol- ogies are present around the splicing sites (12), and some models for the RNA splicing mechanism have been proposed (13-17). However, tRNA gene intron boundaries apparently do not fol- low this rule, and it was suggested that a different splicing mechanism may be necessary for this process (1). For rRNA gene introns, the nucleotide sequence around splicing sites was determined in two species, Tetrahymena (18) and Chlamydo- monas (19), but the information obtained was not sufficient to deduce a general rule or a model for the rRNA splicing mechanism. In attempts to elucidate the rRNA splicing mechanism, we recently cloned the DNA fragment that contains a portion of the 26S rRNA structural sequence and the two introns. We re- port herein the determination of the sequence of one of these introns and its flanking exon regions. Our findings, together with those for Tetrahymena and Chlamydomonas rRNA genes, suggest that a specific mechanism is involved in rRNA splicing.