UV-induced modifications in the peptidyl transferase loop of 23S rRNA dependent on binding of the streptogramin B antibiotic, pristinamycin IA

The naturally occurring streptogramin B antibiotic, pristinamycin IA, which inhibits peptide elongation, can produce two modifications in 23S rRNA whe n bound to the Escherichia coli 70S ribosome and irradiated at 365 nm. Both drug-induced effects map to highly conserved nucleotides within the functi onally important peptidyl transferase loop of 23S rRNA at positions m(2)A25 03/Psi 2504 and G2061/A2062. The modification yields are influenced strongl y, and differentially, by P-site-bound tRNA and strongly by some of the pep tidyl transferase antibiotics tested, with chloramphenicol producing a shif t in the latter modification to A2062/C2063. Pristinamycin IA can also prod uce a modification on binding to deproteinized, mature 23S rRNA, at positio n U2500/C2501. The same modification occurs on an similar to 37-nt fragment , encompassing positions similar to 2496-2532 of the peptidyl transferase l oop that was excised from the mature rRNA using RNAse H. In contrast, no an tibiotic-induced effects were observed on in vitro T7 transcripts of full-l ength 23S rRNA, domain V, or on a fragment extending from positions similar to 2496-2566, which indicates that one or more posttranscriptional modific ations within the sequence Cm-C-U-C-G-m(2)A-Psi-G(2505) are important for p ristinamycin IA binding and/or the antibiotic-dependent modification of 23S rRNA.