PEPTIDE INHIBITORS OF PEPTIDYLTRANSFERASE ALTER THE CONFORMATION OF DOMAIN-IV AND DOMAIN-V OF LARGE SUBUNIT RIBOSOMAL-RNA - A MODEL FOR NASCENT PEPTIDE CONTROL OF TRANSLATION

Peptides of 5 and 8 residues encoded by the leaders of attenuation reg ulated chloramphenicol-resistance genes inhibit the peptidyltransferas e of microorganisms from the three kingdoms. Therefore, the ribosomal target for the peptides is likely to be a conserved structure and/or s equence, The inhibitor peptides ''footprint'' to nucleotides of domain V in large subunit rRNA when peptide-ribosome complexes are probed wi th dimethyl sulfate, Accordingly, rRNA was examined as a candidate for the site of peptide binding, Inhibitor peptides MVKTD and MSTSKNAD we re mixed with rRNA phenol extracted from Escherichia coil ribosomes, T he conformation of the RNA was then probed by limited digestion with n ucleases that cleave at single-stranded (T1 endonuclease) and double-s tranded (V1 endonuclease) sites, Both peptides selectively altered the susceptibility of domains IV and V of 23S rRNA to digestion by T1 end onuclease, Peptide effects on cleavage by V1 nuclease were observed on ly in domain V. The T1 nuclease susceptibility of domain V of in vitro -transcribed 23S rRNA was also altered by the peptides, demonstrating that peptide binding to the rRNA is independent of ribosomal protein, We propose the peptides MVKTD and MSTSKNAD perturb peptidyltransferase center catalytic activities by altering the conformation of domains I V and V of 23S rRNA. These findings provide a general mechanism throug h which nascent peptides may cis-regulate the catalytic activities of translating ribosomes.