Evidence map›Paper›PMID 36927548›Full record

ArticleBMC genomics2023

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

Yaowen Chang, Wenxia Sun, Alastair I H Murchie, Dongrong Chen

Open access · goldFull text read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
1.1field-weighted citation impact, top 23% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed, 7 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

4 authors at 3 institutions in 1 country.

Yaowen Chang *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.
Wenxia Sun *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.
Alastair I H MurchieFudan University Pudong Medical Center, and Institute of Biomedical Sciences, Shanghai Medical College, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, 200032, Shanghai, China. AIHM@fudan.edu.cn.
Dongrong ChenFudan University Pudong Medical Center, and Institute of Biomedical Sciences, Shanghai Medical College, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, 200032, Shanghai, China. drchen@fudan.edu.cn.
Pudong Medical Center · CNFudan University · CNShanghai Medical College of Fudan University · CN

Funding

National Natural Science Foundation of China 32271345 and 32250710140
6 · The paper itself

Abstract

backgroundThe 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).

resultsOver 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.

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

Indexed as

Escherichia coliRNAAminoglycosidesAnti-Bacterial AgentsKanamycinRNA, MessengerRNA, RibosomalAminoglycosidesAnti-Bacterial AgentsbekanamycinKanamycinRNARNA, MessengerRNA, RibosomalGenome-wide aminoglycoside RNA interactionsKanamycin BPull-down assayRNA-seq

Identifiers

PMID36927548
PMCPMC10018874
OpenAlexW4327676937

What OpenQuestion holds

Textfull text, public
LicenceCC BY
measurements read26
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.