Binding Sites of E. coli DNA-dependent RNA polymerase on spinach chloroplast DNA

Under stringent conditions E. coli DNA-dependent RNA polymerase holoenzyme binds selectively to some spinach chloroplast DNA fragments generated by restriction endonucleases. The strongest of these binding sites, as judged by the initial rate of complex formation, are located in the large single-copy DNA region (Crouse et al. 1978) of this molecule and correspond in map location with known protein coding sequences. Some of these binding sites have characteristics of complex formation comparable with those of the PR and PL promoters of phage lambda DNA.Binding sites located close to the rRNA operons on the chloroplast DNA bind polymerase less strongly than those described above. Since the rRNAs are the most abundant transcription products in vivo and in isolated chloroplasts (Hartley and Head 1979; Bohnert et al. 1977) this suggests that the E. coli and chloroplast enzymes do not recognize all of the major promoters in chloroplast DNA with the same efficiency of binding.We have investigated in detail one region of the chloroplast DNA from spinach which contains three strong binding sites. This region has been shown to contain at least the gene for a 32,000 dalton protein (Driesel et al. 1980) which is most probably the so-called photogene (Bedbrook et al. 1978).One of these three E. coli RNA polymerase binding sites is not more than approximately 150 by apart from what, by hybridization studies using isolated mRNA, we know to be the coding sequence for this protein.The results suggest that for some genes on the chloroplast DNA the bacterial RNA polymerase may be used to search for transcription initiation sites.