Capacity of ribosomal RNA promoters of E. coli to bind RNA polymerase.

The rate of in vitro transcription of the rRNA genes of E. coli is more than 20 fold higher than the averaged transcription rate of other genome segments of the same size. This "preferential transcription" of rRNA genes reflects a high efficiency of their promoters in chain initiation. We show that the high initiation rate at rRNA promoters results from a high rate of RNA polymerase binding to these promoters as measured by the formation of heparin-resistant RNA polymerase-DNA complexes. The results indicate that the preferential binding of RNA polymerase to rRNA promoters is mainly due to their large binding capacity rather than to a high rate constant of polymerase binding to a single binding site. The polymerase binding capcity of rRNA promoters was estimated from the number of rRNA chains initiated by heparin-resistant complexes under conditions of template saturation and from the number of rRNA transcription units participating in the binding reaction. At least 30 RNA polymerase molecules were found to be protected from heparin per rRNA transcription unit. The rest of the genome (99.4%; possibly sufficient to encode 4000 nonribosomal RNA species) protects under these conditions 2000 enzyme molecules. These results suggest that a high multiplicity of RNA polymerase binding may be responsible for the high efficiency of rRNA promoters. The validity of this hypothesis is discussed.