在大肠杆菌中全基因组鉴定卡那霉素 B 结合 RNA。

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

机构信息

Fudan University Pudong Medical Center, and Institute of Biomedical Sciences, Shanghai Medical College, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, 200032, Shanghai, China.

Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.

出版信息

BMC Genomics. 2023 Mar 16;24(1):120. doi: 10.1186/s12864-023-09234-3.

DOI:10.1186/s12864-023-09234-3

PMID:36927548

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10018874/

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.

摘要

背景

氨基糖苷类抗生素通过与核糖体 RNA 结合来抑制细菌蛋白质的合成。通过氨基糖苷类抗生素与细胞 RNA 的相互作用，也确定了其他非抗生素氨基糖苷类抗生素的细胞功能。然而，大肠杆菌中全基因组范围内氨基糖苷类抗生素 RNA 相互作用的程度尚未确定。在这里，我们报告了氨基糖苷类抗生素卡那霉素 B 与大肠杆菌 RNA 结合的全基因组鉴定和验证。固定在下拉测定中的卡那霉素 B 珠用于转录组分析（RNA-seq）。