DNA sequence and secondary structures of the large subunit rRNA coding regions and its two class I introns of...

DNA sequence analysis has shown that the gene coding for the mitochondrial (mt) large subunit ribosomal RNA (rRNA) from Podospora anserina is interrupted by two class I introns. The coding region for the large subunit rRNA itself is 3715 bp and the two introns are 1544 (r1) and 2404 (r2) bp in length. Secondary structure models for the large subunit rRNA were constructed and compared with the equivalent structure from Escherichia coli 23S rRNA. The two structures were remarkably similar despite an 800-base difference in length. The additional bases in the P. anserina rRNA appear to be mostly in unstructured regions in the 3' part of the RNA. Secondary structure models for the two introns show striking similarities with each other as well as with the intron models from the equivalent introns in Saccharomyces cerevisiae, Neurospora crassa, and Aspergillus nidulans. The long open reading frames in each intron are different from each other, however, and the nucleotide sequence similarity diverges as it proceeds away from the core structure. Each intron is located within regions of the large subunit rRNA gene that are highly conserved in both sequence and structure. Computer analysis showed that the open reading frame for intron r1 contained a common maturase-like polypeptide. The open reading frames of intron r2 appeared to be chimeric, displaying high sequence similarity with the open reading frames in the r1 and ATPase 6 introns of N. crassa.