rRNA Binding Sites and the Molecular Mechanism of Action of the Tetracyclines

Abstract

The tetracycline antibiotics are known to be effective in the treatment of both infectious and noninfectious disease conditions. The 16S rRNA binding mechanism currently held for the antibacterial action of the tetracyclines does not explain their activity against viruses, protozoa that lack mitochondria, and noninfectious conditions. Also, the mechanism by which the tetracyclines selectively inhibit microbial protein synthesis against host eukaryotic protein synthesis despite conservation of ribosome structure and functions is still questionable. Many studies have investigated the binding of the tetracyclines to the 16S rRNA using the small ribosomal subunit of different bacterial species, but there seems to be no agreement between various reports on the exact binding site on the 16S rRNA. The wide range of activity of the tetracyclines against a broad spectrum of bacterial pathogens, viruses, protozoa, and helminths, as well as noninfectious conditions, indicates a more generalized effect on RNA. In the light of recent evidence that the tetracyclines bind to various synthetic double-stranded RNAs (dsRNAs) of random base sequences, suggesting that the double-stranded structures may play a more important role in the binding of the tetracyclines to RNA than the specific base pairs, as earlier speculated, it is imperative to consider possible alternative binding modes or sites that could help explain the mechanisms of action of the tetracyclines against various pathogens and disease conditions.

FIG 1

(A) Structures of the 50S and 30S bacterial ribosomal subunits, showing the secondary structures of rRNA (orange) in association with ribosomal proteins (gray). (B) Structures of dsDNA and dsRNA, showing hydrogen bonds between bases (blue) and other intramolecular bonds (green). Structure templates were obtained from the Protein Data Bank (PDB) and drawn using Jmol (an open-source Java viewer for chemical structures in three dimensions).

FIG 2

Chemical structures of tetracycline antibiotics in three dimensions. Gray balls represent carbons in the rings, red balls represent oxygens, and blue balls represent nitrogens. Structure templates were obtained from the Protein Data Bank (PDB) and drawn using Jmol.

FIG 3

Graphic representation of the binding of tetracyclines to double-stranded segments of cellular RNA.