Structural Bases for the Fitness Cost of the Antibiotic-Resistance and Lethal Mutations at Position 1408 of 16S rRNA.

Jiro Kondo,Mai Koganei

doi:10.3390/molecules25010159

Abstract

To understand a structural basis for the fitness cost of the A1408G antibiotic-resistance mutation in the ribosomal A-site RNA, we have determined crystal structures of its A1408C and A1408U lethal mutants, and made comparison with previously solved structures of the wild type and the antibiotic-resistant mutant. The A-site RNA containing an asymmetric internal loop functions as a molecular switch to discriminate a single cognate tRNA from several near-cognate tRNAs by its conformational ON/OFF switching. Overall structures of the “off” states of the A1408C/U lethal mutants are very similar to those of the wild type and the A1408G antibiotic-resistant mutant. However, significant differences are found in local base stacking interactions including the functionally important A1492 and A1493 residues. In the wild type and the A1408G antibiotic-resistant mutant “off” states, both adenines are exposed to the solvent region. On the other hand, one of the corresponding adenines of the lethal A1408C/U mutants stay deeply inside their A-site helices by forming a purine-pyrimidine AoC or A-U base pair and is sandwiched between the upper and lower bases. Therefore, the ON/OFF switching might unfavorably occur in the lethal mutants compared to the wild type and the A1408G antibiotic-resistant mutant. It is probable that bacteria manage to acquire antibiotic resistance without losing the function of the A-site molecular switch by mutating the position 1408 only from A to G, but not to pyrimidine base C or U.

Highlights

The aminoacyl-tRNA decoding site (A site) is one of the active sites of the ribosome where a single cognate tRNA is accurately discriminated from several near-cognate tRNAs [1,2,3,4]
It would appear that the bulged-in A1492 residue of the wild type
Aminoacyl-tRNA is delivered to the A site

Summary

Introduction

The aminoacyl-tRNA decoding site (A site) is one of the active sites of the ribosome where a single cognate tRNA is accurately discriminated from several near-cognate tRNAs [1,2,3,4]. An RNA internal loop (Figure 1) composed of fifteen nucleotide residues functions as a molecular switch by changing its conformation between “off” and “on” states. Two consecutive adenines A1492 and A1493 in the asymmetric internal loop are the most important residues for the function of the molecular switch. In the absence of aminoacyl-tRNA, these two adenines can take various conformations, which are called as “off”. Once an aminoacyl-tRNA is delivered to and occupies the A site, the RNA molecular switch changes its conformation to a unique “on” state, in which two adenines

Methods

Discussion

Conclusion