Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Mar 16;24(1):120.
doi: 10.1186/s12864-023-09234-3.

Genome-wide identification of Kanamycin B binding RNA in Escherichia coli

Affiliations

Genome-wide identification of Kanamycin B binding RNA in Escherichia coli

Yaowen Chang et al. BMC Genomics. .

Abstract

Background: The aminoglycosides are established antibiotics that inhibit bacterial protein synthesis by binding to ribosomal RNA. Additional non-antibiotic aminoglycoside cellular functions have also been identified through aminoglycoside interactions with cellular RNAs. The full extent, however, of genome-wide aminoglycoside RNA interactions in Escherichia coli has not been determined. Here, we report genome-wide identification and verification of the aminoglycoside Kanamycin B binding to Escherichia coli RNAs. Immobilized Kanamycin B beads in pull-down assays were used for transcriptome-profiling analysis (RNA-seq).

Results: Over two hundred Kanamycin B binding RNAs were identified. Functional classification analysis of the RNA sequence related genes revealed a wide range of cellular functions. Small RNA fragments (ncRNA, tRNA and rRNA) or small mRNA was used to verify the binding with Kanamycin B in vitro. Kanamycin B and ibsC mRNA was analysed by chemical probing.

Conclusions: The results will provide biochemical evidence and understanding of potential extra-antibiotic cellular functions of aminoglycosides in Escherichia coli.

Keywords: Genome-wide aminoglycoside RNA interactions; Kanamycin B; Pull-down assay; RNA-seq.

References

    1. Davies J, Davis B. Misreading of ribonucleic acid code words induced by aminoglycoside antibiotics. The effect of drug concentration. J Biol Chem. 1968;243(12):3312–6. - PubMed - DOI
    1. Fourmy D, Recht M, Blanchard S, Puglisi J. Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic. Science (New York, NY). 1996;274(5291):1367–71. - DOI
    1. Carter AP, Clemons WM, Brodersen DE, Morgan-Warren RJ, Ramakrishnan V. Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature. 2000;407(6802):340–8. - PubMed - DOI
    1. Saswati S, Chattopadhyay MK, Hans-Peter G. The multifaceted roles of antibiotics and antibiotic resistance in nature. Front Microbiol. 2013;4:47.
    1. Davies J, Davies D. Origins and Evolution of Antibiotic Resistance. Microbiol Mol Biol Rev. 2010;3:74.