We have studied gene conversion initiated by the ai3 intron of the Sac
charomyces cerevisiae mitochondrial (mt) COXI gene and its homologous
intron (S.cap.ail) from Saccharomyces capensis. The approach used invo
lved the measurement of intron transmission amongst the progeny of cro
sses between constructed recipient and donor strains. We found that th
e S. cerevisiae ai3 intron is extremely active as a donor in gene conv
ersion, whereas its homologous S. capensis intron is not. We have esta
blished the sequence of S.cap.ail and compared its open reading frame
(ORF) with that of I-SceIII encoded by the homologous S. cerevisiae in
tron. The two protein-coding intron sequences are almost identical, ex
cept that the S. capensis ORF contains an in-frame stop codon. This fi
nding provides a strong indication that the 3' part of the S. cerevisi
ae intron ORF encoding I-SceIII (which should not be translated in the
S. capensis intron) must be critical for function of mtDNA endonuclea
ses to mediate intron mobility.