Footprinting studies with the purine-modifying agent dimethyl sulphate were
performed in Paracentrotus lividus eggs and embryos to analyze in vivo the
interactions between protein and mitochondrial DNA. Footprinting in the sm
all non-coding region and at the boundary between the ND5 and ND6 genes rev
ealed two strong contact sites corresponding with the in vitro binding sequ
ences of mitochondrial D-loop-Binding Protein (mtDBP). The analysis of the
pause region of mtDNA replication showed a strong footprint corresponding w
ith the binding site of the mitochondrial Pause region-Binding Protein-2 (m
tPBP-2), but only a very weak signal at the binding site of the mitochondri
al Pause region-Binding Protein-1 (mtPBP-1), which in vitro binds DNA with
high efficiency. In vitro and in vivo analysis of the 3' end-region of the
two rRNA genes showed no significant protein-DNA interactions, suggesting t
hat, in contrast to mammals, the 3' ends of sea urchin mitochondrial rRNAs
are not generated by a protein-dependent transcription termination event. T
hese and other data support a model in which expression of mitochondrial ge
nes in sea urchins is regulated post-transcriptionally. Footprinting at the
five AT-rich consensus regions allowed the detection of a binding site in
the non-coding region for an as-yet unidentified protein, mtAT-1BP. The occ
upancy of this site appears to be developmentally regulated, being detectab
le in the pluteus larval stage, but not in unfertilized eggs.