Interactions of Escherichia coli transcription termination factor rho with RNA. II. Electron microscopy and nuclease protection experiments

Structural aspects of the interaction between Escherichia coli transcription termination factor rho and RNA have been investigated, using nuclease protection assays and electron microscopy. A synthetic RNA, poly(rC), has been used as a substrate for these studies, since it binds tightly to rho and acts as a strong activator of the ATPase activity of rho. Digestion of oligo(rC)-rho complexes with ribonuclease A yields oligo(rC) fragments with a maximum length of 70 to 80 nucleotide residues. Electron micrographs demonstrate that rho binds to poly(rC) as a toroid-shaped oligomer with an outside diameter of approximately 120 Å. Taken together with data from the accompanying paper, which shows that the RNA binding site size per rho monomer is 13(±1) nucleotide residues, we infer that rho binds RNA as a hexamer with an oligomeric site size of 72 to 84 residues. Further analysis of the electron micrographs has revealed that the polynucleotide chain is wrapped around, or condensed within, the protein oligomer, rho hexamers bind to poly(rC) with moderate co-operativity (ω = 380 ± 60), displaying no significant preference for binding to chain ends versus internal sites on the polynucleotide chain. These findings and those of the companion paper are discussed in terms of various models for the structure of the rho-RNA complex in transcription termination.