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

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

PROVIDER: PRJNA770675 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16301570.fastq.gz	Fastqsanger.gz
	SRR16301571.fastq.gz	Fastqsanger.gz
	SRR16301572.fastq.gz	Fastqsanger.gz
	SRR16301573.fastq.gz	Fastqsanger.gz
	SRR16301574.fastq.gz	Fastqsanger.gz

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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

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 exhibits considerable medical potential. Previous studies suggested that KSG interferes with translation by blocking binding of canonical messenger RNA (mRNA) and initiator transfer tRNA (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. Even at saturating concentrations, KSG does not completely abolish translation, allowing for continuing expression of some Escherichia coli proteins. 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 an example of a small ribosomal subunit-targeting antibiotic with a well-pronounced context specificity of action.

| S-EPMC8794815 | biostudies-literature

Context specificity of the EMT transcriptional response

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Context-specific action of macrolide antibiotics on the eukaryotic ribosome

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Dynamic DNA methylation landscape defines brown and white cell specificity during adipogenesis

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Asymmetry of STAT action in driving IL-27 and IL-6 transcriptional outputs and cytokine specificity

Project description:IL-6 and IL-27 have antagonistic and overlapping functions, signal through a shared receptor subunit and employ the same downstream STAT proteins. To evaluate the degree of specificity and redundancy for these cytokines, we quantified global transcriptomic changes induced by the two cytokines and determined the relative contributions of STAT1 and STAT3 using genetic models and ChIP-seq. We found a high degree of overlap of the transcriptomes induced by IL-6 and IL-27 and extremely few examples in which the cytokines acted in opposition. Using STAT deficient cells and T cells from patients with gain-of-function STAT1 mutations, we show that STAT3 was responsible for the overall transcriptional output driven by both cytokines, whereas STAT1 was the driver of cytokine specificity. STAT1 did not compensate for the lack STAT3; on the contrary, much of STAT1 binding to chromatin was STAT3 dependent. Thus, STAT1 shapes the specific cytokine signature superimposed upon STAT3’s action. Integrated analysis of transcriptome and transcription factor binding data from cytokine treated CD4+T cells

2015-05-27 | E-GEOD-65621 | biostudies-arrayexpress

Asymmetry of STAT action in driving IL-27 and IL-6 transcriptional outputs and cytokine specificity

2015-05-27 | GSE65621 | GEO

Asymmetry of STAT action in driving IL-27 and IL-6 transcriptional outputs and cytokine specificity

Project description:Asymmetry of STAT action in driving IL-27 and IL-6 transcriptional outputs and cytokine specificity

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Subcellular location defines GPCR signal transduction

Project description:G protein-coupled receptors in intracellular organelles can be activated in response to membrane permeant ligands, which contributes to the diversity and specificity of agonist action. The opioid receptors (ORs) provide a striking example, where small molecule opioid drugs activate ORs in the Golgi apparatus within seconds of drug addition. To date, our knowledge on the signaling of intracellular GPCRs remains incomplete and it is unknown if the downstream events triggered by ORs in plasma membrane and Golgi apparatus differ. To address this gap, we analyzed OR-mediated phosphorylation changes in cells treated with SNC80 (signaling control) or ICI-SNC80 (Golgi-restricted signaling) for 5 min or 25 min. We show that OR activation in the plasma membrane or Golgi apparatus have strikingly different downstream effects on protein phosphorylation. The study delineates OR signal transduction with unprecedented resolution and reveals that the subcellular location defines the signaling effect promoted by opioid drugs.

2023-04-25 | PXD038921 | Pride

Context-specific translation arrest by evernimicin, an inhibitor of tRNA accommodation

Project description:Antibiotics of the orthosomycin class bind at a distinct site on the large subunit of the bacterial ribosome not used by any other known protein synthesis inhibitor. Structural and biochemical in vitro studies suggested that orthosomycins should block accommodation of aminoacyl-tRNAs in the ribosomal A-site arresting the ribosome at the start codons of the genes. However, the mode of action of orthosomycins in the living cell remains unknown. Here, to get a general and unbiased view of the mode of action of orthosomycin antibiotics, we carried out genome-wide ribosome profiling analysis in Escherichia coli cells exposed to evernimicin, one of the most active antibiotics of this class. Our in vivo data, supported by the analysis of evernimicin action upon in vitro translation of a variety of mRNAs, argue that orthosomycins preferentially inhibit translation elongation and act in a context specific manner. We show that evernimicin predominantly arrests translation when the ribosome needs to accommodate Pro-tRNA or Leu-tRNA in the A site while polymerizing specific amino acid sequences. We further show that the discovered context specificity of orthosomycins is exploited for the programmed translation arrest that apparently regulates resistance to these antibiotics.

2022-04-15 | GSE193270 | GEO

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