Basis of Prokaryotic Selectivity in the Antibiotic Paromomycin

Abstract

Ribosomes are responsible for protein synthesis and are a major target of antibiotics. While translation is a universally conserved cellular process, the ability of drugs to target prokaryotic ribosomes depends on subtle variations from eukaryotic ribosomes. The ribosome is composed of ribosomal RNA (rRNA) and protein. The small ribosomal subunit, called 30s in prokaryotes, contains 21 proteins and one rRNA (16S) and the large subunit, called 50S, contains 31 proteins and two rRNAs (23S and 5S). Recent crystal structures reveal that the rRNAs adopt a 3D fold generating (I) decoding center for codon‐anticodon recognition, (II) a peptidyl‐transfer center (PTC) for a peptide bond formation and (III) an exit tunnel through which the nascent protein emerges. Paromomycin, used in the treatment of intestinal infections, inhibits prokaryotic ribosomes at the decoding site. Paromomycin physically restructures helix H44 of the 16S rRNA, preventing proper rotation of A1492 and A1493 during anticodon:codon recognition, decreasing tRNA selection accuracy in prokaryotic ribosomes. However, paromomycin fails to affect eukaryotes due to an A to G transition at position 1408. The Brookfield Academy SMART Team (Students Modeling A Research Topic) modeled a prokaryotic ribosome, highlighting nucleotides responsible for the prokaryotic specificity of paromomycin. (Supported by a grant from the NIH‐CTSA UL1RR031973)