We studied transcription initiation in the mitochondria of higher plan
ts, with particular respect to promoter structures. Conserved elements
of these promoters have been successfully identified by in vitro tran
scription systems in different species, whereas the involved protein c
omponents are still unknown. Proteins binding to double-stranded oligo
nucleotides representing different parts of the pea (Pisum sativum) mi
tochondrial atp9 were analyzed by denaturation-renaturation chromatogr
aphy and mobility-shift experiments. Two DNA-protein complexes were de
tected, which appeared to be sequence specific in competition experime
nts. Purification by hydroxyapatite, phosphocellulose, and reversed-ph
ase high-pressure liquid chromatography separated two polypeptides wit
h apparent molecular masses of 32 and 44 kD. Both proteins bound to co
nserved structures of the pea atp9 and the heterologous Oenothera bert
eriana atp1 promoters and to sequences just upstream. Possible functio
ns of these proteins in mitochondrial promoter recognition are discuss
ed.