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ABSTRACT: Context-dependent translation inhibition by the polyketide antibiotic Tetracenomycin X

PROVIDER: PRJNA854319 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19905808_1.fastq.gz	Fastqsanger.gz
	SRR19905808_2.fastq.gz	Fastqsanger.gz
	SRR19905809_1.fastq.gz	Fastqsanger.gz
	SRR19905809_2.fastq.gz	Fastqsanger.gz
	SRR19905810_1.fastq.gz	Fastqsanger.gz

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Project description:Context-dependent translation inhibition by the polyketide antibiotic Tetracenomycin X

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Context-dependent translation inhibition as a novel oncology therapeutic modality

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Context specificity of oxazolidinones-mediated translation inhibition is modulated by antibiotic structure

Project description:Context specificity of oxazolidinones-mediated translation inhibition is modulated by antibiotic structure

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Context-dependent translation inhibition as a novel oncology therapeutic modality [RNA-seq]

Project description:Context-dependent translation inhibition as a novel oncology therapeutic modality [RNA-seq]

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Context specificity of oxazolidinones-mediated translation inhibition is modulated by antibiotic structure [RNA-Seq]

Project description:Context specificity of oxazolidinones-mediated translation inhibition is modulated by antibiotic structure [RNA-Seq]

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Context specificity of oxazolidinones-mediated translation inhibition is modulated by antibiotic structure [Ribo-Seq]

Project description:Context specificity of oxazolidinones-mediated translation inhibition is modulated by antibiotic structure [Ribo-Seq]

| PRJNA1425039 | ENA

The context of the ribosome binding site in mRNAs defines specificity of action of kasugamycin, an inhibitor of translation initiation

Project description:Kasugamycin (KSG) is an aminoglycoside antibiotic widely used in agriculture and exhibiting considerable medical potential. Previous studies suggested that KSG interferes with translation by blocking binding of canonical mRNA and initiator tRNA to the small ribosomal subunit thereby preventing initiation of protein synthesis. Here, by using genome-wide approaches, we show that KSG can interfere with translation even after the formation of the 70S initiation complex on mRNA, as the extent of KSG-mediated translation inhibition correlates with increased occupancy of start codons by 70S ribosomes. We also show that KSG inhibits protein synthesis in a gene- and context-specific manner as even saturating concentrations of KSG do not completely abolish translation of all Escherichia coli genes. Differential action of KSG significantly depends on the nature of the mRNA residue immediately preceding the start codon, with guanine in this position being the most conducive to inhibition by the drug. In addition, the activity of KSG is attenuated by translational coupling as genes whose start codons overlap with the coding regions or the stop codons of the upstream cistrons tend to be less susceptible to drug-mediated inhibition. Altogether, our findings reveal KSG as the first example of a small ribosomal subunit-targeting antibiotic with a well-pronounced context specificity of action.

2022-02-02 | GSE185757 | GEO

Context specificity of oxazolidinones-mediated translation inhibition is modulated by antibiotic structure [Ribo-Seq]

Project description:The oxazolidinone antibiotic linezolid binds to the peptidyl transferase center of the ribosome, where it inhibits a subset of peptide bond formation events. This context-specificity of translation inhibition is dictated by the nature of the amino acid at the penultimate position of the nascent peptide. It remains unknown whether this is a general feature of oxazolidinones and whether it can be modulated by their structural alterations. Here, we show that the oxazolidinone tedizolid also inhibits translation in a context-specific manner, but with dramatically altered selectivity, favoring Ile, His, and Gln as the penultimate residues. Delpazolid, which shares the C5 hydroxymethyl moiety with tedizolid, shows a similar preference. Structural analysis of the ribosome with tedizolid and a stalled nascent peptide showed a compacted, helical conformation of the nascent chain induced by the drug. Our findings reveal that stalling preferences of oxazolidinones can be modulated by structural modifications within this antibiotic class.

2026-02-20 | GSE319739 | GEO

Context specificity of oxazolidinones-mediated translation inhibition is modulated by antibiotic structure [RNA-Seq]

2026-02-20 | GSE319738 | GEO

RNAP stalling-derived genome instability underlies ribosomal antibiotics efficacy and resistance evolution (ChIP-seq data)

Project description:Bacteria often evolve antibiotic resistance through mutagenesis. However, the processes causing the mutagenesis have not been fully resolved. Here we found that a broad range of ribosome-targeting antibiotics caused mutations through an underexplored pathway. Focusing on the clinically important aminoglycoside gentamicin, we found that the translation inhibitor caused genome-wide premature stalling of RNA polymerase (RNAP) in a loci-dependent manner. Further analysis showed that the stalling was caused by disruption of transcription-translation coupling. Anti-intuitively, the stalled RNAPs subsequently induced lesions to the DNA via transcription-coupled repair. While most of the bacteria were killed by genotoxicity, a small subpopulation acquired mutations via SOS-induced mutagenesis. Given that these processes were triggered shortly after antibiotic addition, resistance rapidly emerged in the population. Our work revealed a new mechanism of action of ribosomal antibiotics, illustrates the importance of dissecting the complex interplay between multiple molecular processes in understanding antibiotic efficacy, and suggests new strategies for countering the development of resistance.

2024-05-15 | GSE267245 | GEO

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