Effect of viomycin on dihydrostreptomycin binding to bacterial ribosomes

The structural basis for inhibition of ribosomal translocation by viomycin

Viomycin, an antibiotic that has been used to fight tuberculosis infections, is believed to block the translocation step of protein synthesis by inhibiting ribosomal subunit dissociation and trapping the ribosome in an intermediate state of intersubunit rotation. The mechanism by which viomycin stabilizes this state remains unexplained. To address this, we have determined cryo-EM and X-ray crystal structures of Escherichia coli 70S ribosome complexes trapped in a rotated state by viomycin. The 3.8-Å resolution cryo-EM structure reveals a ribosome trapped in the hybrid state with 8.6° intersubunit rotation and 5.3° rotation of the 30S subunit head domain, bearing a single P/E state transfer RNA (tRNA). We identify five different binding sites for viomycin, four of which have not been previously described. To resolve the details of their binding interactions, we solved the 3.1-Å crystal structure of a viomycin-bound ribosome complex, revealing that all five viomycins bind to ribosomal RNA. One of these (Vio1) corresponds to the single viomycin that was previously identified in a complex with a nonrotated classical-state ribosome. Three of the newly observed binding sites (Vio3, Vio4, and Vio5) are clustered at intersubunit bridges, consistent with the ability of viomycin to inhibit subunit dissociation. We propose that one or more of these same three viomycins induce intersubunit rotation by selectively binding the rotated state of the ribosome at dynamic elements of 16S and 23S rRNA, thus, blocking conformational changes associated with molecular movements that are required for translocation.

Effect of neomycin and protein S1 on the binding of streptomycin to the ribosome

The binding of [3H]dihydrostreptomycin to the 70-S ribosome or to the 30-S subunit has been investigated in the presence of neomycin by the Millipore filtration or the equilibrium dialysis procedure. It was observed that dihydrostreptomycin binds equally well to the 30-S subunit and the 70-S ribosome, and that neomycin stimulates the binding of dihydrostreptomycin to the ribosome by increasing the association constant and not by creating new binding sites. Specific removal of protein S1 from the 30-S subunit neither affected the binding of dihydrostreptomycin to the ribosome nor the stimulation of dihydrostreptomycin binding by neomycin.

Comparison of the action of streptomycin and neomycin on the structure of the bacterial ribosome

The influence of streptomycin and neomycin upon the conformation of the ribosome has been investigated using spin-labeled and fluorescent analogs of the sulfhydryl reagent, N-ethylmaleimide. Changes in the electron paramagnetic resonance spectra or in the polarization of fluorescence of labeled ribosomes reveal that streptomycin alters the mobility of labels bound to the sulfhydryl group of protein S18 while neomycin affects the mobility of labels bound to the sulfhydryl groups of proteins S1, S21 and/or L10. It is also observed that both streptomycin and neomycin interfere with changes in the mobility of labels induced by storage under inactivating conditions. From these results, it is concluded that: 1. streptomycin and neomycin distort the conformation of the ribosome at different sites, streptomycin disturbing preferentially the area around the sulfhydryl group of protein S18 while neomycin affects the environment of the sulfhydryl groups of proteins S1, S21 and/or L10; 2. streptomycin and neomycin interefere with the ability of the ribosome to undergo conformational changes.

Ribosomal function and its inhibition by antibiotics in prokaryotes

Most of the known antibiotics act at the level of protein biosynthesis probably due to the extraordinary complexity of the translation machinery which can be interfered with at many points. At first a survey is given of our present knowledge covering the structure and function of the prokaryotic ribosome. The most important antibiotics acting at the translational level are integrated into this network of data. The binding sites and the inhibition mechanisms of the drugs, together with the ribosomal components altered in resistant mutants are described. Finally, the points of interference with the translational machinery are indicated in an extended scheme of ribosomal functions.

Viomycin favours the formation of 70S ribosome couples

The peptide antibiotic viomycin at a concentration of 10 muM inhibits E. coli ribosomes to the extent of about 70% as measured in the poly (U) system, and to about 85% in a natural mRNA (R17) system. Ribosomes from M. smegmatis show no activity at all at this concentration of the antibiotic. Experiments on the Mg+2 dependent dissociation and association of the ribosomal subunits revealed that viomycin stabilizes the 70S couples and promotes association of ribosomal subunits. This response is related to the drug action as indicated by the observation that viomycin resistant strains are not affected by viomycin with respect to dissociation and 70S couple information. A model for the inhibitory action of the drug is proposed.