DNA sequence of the excision sites of a mitochondrial plasmid from senescent Podospora anserina

During senescence in Podospora anserina, specific gene regions of the mitochondrial genome are excised and amplified. The most prevalent, termed alpha-event senDNA, is a 2600 bp circular molecule which is excised from the contiguous Hae III fragments 23,14 region of the mitochondrial DNA restriction map. We have cloned alpha-DNA plasmid from races s+ and A+ as well as the genomic fragments Hae III 23,14 and have sequenced those regions which constitute the alpha-junction sites. We have found that one excision site (J1) is located 24 bp from the proximal Hae III 23 restriction site and the other (J2) 172 bp from the distal Hae III 14 site. Flanking the alpha-DNA sequences on the mitochondrial genome, there are 10 bp palindromic sequences: CAATATATTG, ending 3 bases from the J1 site, and ATTATATAAT which starts 8 bases from the J2 site. Neither of these 10 bp palindromes are present on the alpha-DNA plasmid. Abutting the J1 site on the alpha-DNA there is a 5 bp sequence (GTGCT) which is repeated 8 bp downstream. In joining the two distal J1 and J2 sites, a 7 bp repeat (ACGTGCG) is produced. These results are discussed within the context of site-specific recombination.