Antibiotic stress-induced modulation of the endoribonucleolytic activity of RNase III and RNase G confers resistance to aminoglycoside antibiotics in Escherichia coli

Wooseok Song,Jung-Hyun Lee,Soonhye Hwang,Yong-Hak Kim,Younghoon Lee,Jihwan Hwang,Jeehyeon Bae,Kangseok Lee,Se-Hoon Sim

doi:10.1093/nar/gku093

Abstract

Here, we report a resistance mechanism that is induced through the modulation of 16S ribosomal RNA (rRNA) processing on the exposure of Escherichia coli cells to aminoglycoside antibiotics. We observed decreased expression levels of RNase G associated with increased RNase III activity on rng mRNA in a subgroup of E. coli isolates that transiently acquired resistance to low levels of kanamycin or streptomycin. Analyses of 16S rRNA from the aminoglycoside-resistant E. coli cells, in addition to mutagenesis studies, demonstrated that the accumulation of 16S rRNA precursors containing 3–8 extra nucleotides at the 5’ terminus, which results from incomplete processing by RNase G, is responsible for the observed aminoglycoside resistance. Chemical protection, mass spectrometry analysis and cell-free translation assays revealed that the ribosomes from rng-deleted E. coli have decreased binding capacity for, and diminished sensitivity to, streptomycin and neomycin, compared with wild-type cells. It was observed that the deletion of rng had similar effects in Salmonella enterica serovar Typhimurium strain SL1344. Our findings suggest that modulation of the endoribonucleolytic activity of RNase III and RNase G constitutes a previously uncharacterized regulatory pathway for adaptive resistance in E. coli and related gram-negative bacteria to aminoglycoside antibiotics.

Highlights

50% of naturally produced antibiotics target the bacterial ribosome by binding to one of three principal ribosomal sites: the decoding site, the peptidyl transferase center and the peptide exit tunnel
These results suggest that certain regulatory pathways that cause noninherited resistance to aminoglycosides in E. coli cells are related to RNase G expression
Consistent with this hypothesis, we found that ribosomes in rng-deleted cells containing incompletely processed 16S ribosomal RNA (rRNA) (16S+3$7) synthesize target proteins in a cell-free translation system as efficiently as ribosomes from wildtype cells (Figure 3A–C; Supplementary Figure S4)

Summary

Introduction

50% of naturally produced antibiotics target the bacterial ribosome by binding to one of three principal ribosomal sites: the decoding site, the peptidyl transferase center and the peptide exit tunnel. Among these antibiotics, macrolides, aminoglycosides, tetracyclines, glycyclines and their derivatives are well known to inhibit protein synthesis by binding to distinct sites on bacterial ribosomes [1,2,3]. Some gram-negative bacteria with noninherited resistance to a broad range of antibiotics are able to cause persistent infections [4,5]. The precise mechanism for the causal relationship between bacterial persistence and antibiotic resistance has not been clearly identified

Methods

Results

Conclusion