Correlation of nonanucleotide motifs with transcript initiation of 188 rRNA genes in mitochondria of pea, potato and Arabidopsis

Transcription initiation sites for the mitochondrial 18S rRNA genes in the dicot plants Arabidopsis thaliana, potato and pea were identified by a combination of in vitro capping, primer extension and S-1 analyses. These promoters contain a nonanucleotide motif and an AT-rich sequence similar to many mRNA and tRNA promoters in dicot mitochondria. In Arabidopsis and potato, active promoters are located within 120 nucleotides upstream of the 18S rRNA genes, as in Oenothera. The nucleotide sequence in the corresponding region in pea mitochondria is well conserved, but is not used as promoter in this plant. Instead a novel promoter sequence is used that lies several hundred nucleotides upstream. These results show that rRNAs can be transcribed from the same promoter types as mRNAs and tRNAs in plant mitochondria. However, the sequence features presently attributed to plant mitochondrial promoters - the conserved nonanucleotide and the upstream AT-rich box - do not allow to deduce the presence of an active promoter from genomic sequence data alone.