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Nucleic Acids Research, 1992, Vol. 20, No. 20 5383-5387
© 1992

MOLECULAR BIOLOGY

Cytosine nucleoside inhibition of the ATPase of Escherichia coli termination factor rho: evidence for a base specific interaction between rho and RNA

Lislott V. Richardson and John P. Richardson*

Department of Chemistry, Indiana University Bloomington IN 47405, USA

* To whom correspondence should be addressed

Received July 14, 1992. Revised September 17, 1992. Accepted September 17, 1992.

The function of rho factor in transcription termination depends on interactions with nascent RNA molecules that contain unpaired cytldylate residues. We show that cytidine, as a free nucleoside, inhibits the binding of rho to {lambda} cro mRNA and is a competitive inhibitor of rho-ATPase activity with {lambda} cro mRNA as cofactor. The relative ability of various cytidine analogs and other nucteosldes to inhibit the rho-RNA interaction was used to probe features responsible for the base specificity of rho action. The results suggest that rho has a specificity pocket in its polynucleotide-blnding site that apparently can make H-bond interactions with the side of the cytosine ring that normally faces away from the sugar ring and that may involve a relatively close fit along the edge of the ribose ring at the C2' carbon. The nature of the complex of rho with cytidine nucleotides was analyzed further by determining whether incubation with BrCMP caused inactivatlon of rho ATPase. Although BrCMP could form Michaelis inhibition complexes, it did not activate rho. Rho thus lacks a diagnostic property of enzymes that make specific covalent addition complexes with pyrimldines.


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