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Genome-wide identification of Kanamycin B binding RNA in Escherichia coli
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Genome-wide identification of Kanamycin B binding RNA in Escherichia coli
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Genome-wide identification of Kanamycin B binding RNA in Escherichia coli
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Journal Article
Genome-wide identification of Kanamycin B binding RNA in Escherichia coli
2023
Overview
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.
Publisher
BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
Subject
/ Aminoglycosides - metabolism
/ Aminoglycosides - pharmacology
/ Analysis
/ Animal Genetics and Genomics
/ Anti-Bacterial Agents - metabolism
/ Anti-Bacterial Agents - pharmacology
/ Binding
/ Biofilms
/ Biomedical and Life Sciences
/ E coli
/ Escherichia coli - metabolism
/ Genes
/ Genome-wide aminoglycoside RNA interactions
/ Genomes
/ Genomics
/ Ligands
/ Microbial Genetics and Genomics
/ RNA
/ RNA-seq
/ rRNA
/ tRNA
