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Context-specific inhibition of mitochondrial ribosomes by phenicol and oxazolidinone antibiotics

ABSTRACT: Context-specific inhibition of mitochondrial ribosomes by phenicol and oxazolidinone antibiotics

PROVIDER: PRJNA1140603 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR30008766.fastq.gz	Fastqsanger.gz
	SRR30008767.fastq.gz	Fastqsanger.gz
	SRR30008768.fastq.gz	Fastqsanger.gz
	SRR30008769.fastq.gz	Fastqsanger.gz
	SRR30008770.fastq.gz	Fastqsanger.gz

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Context-specific inhibition of mitochondrial ribosomes by phenicol and oxazolidinone antibiotics

Project description:The antibiotics chloramphenicol (CHL) and oxazolidinones including linezolid (LZD) are known to inhibit mitochondrial translation. This can result in serious, potentially deadly, side effects when used therapeutically. Although the mechanism by which CHL and LZD inhibit bacterial ribosomes has been elucidated in detail, their mechanism of action against mitochondrial ribosomes has yet to be explored. CHL and oxazolidinones bind to the ribosomal peptidyl transfer center (PTC) of the bacterial ribosome and prevent incorporation of incoming amino acids under specific sequence contexts, causing ribosomes to stall only at certain sequences. Through mitoribosome profiling, we show that inhibition of mitochondrial ribosomes is similarly context-specific – CHL and LZD lead to mitoribosome stalling primarily when there is an alanine, serine, or threonine in the penultimate position of the nascent peptide chain. Our findings could help inform the rational development of future, less mitotoxic, antibiotics, which are critically needed in the current era of increasing antimicrobial resistance.

2024-10-01 | GSE273206 | GEO

Context-specific inhibition of translation by ribosomal antibiotics targeting the peptidyl transferase center

Project description:We report the context-specific activity of two peptidyl transferase targeting antibiotics, chloramphenicol and linezolid. By generating ribosome profiling data in the presence or absence of either chloramphenicol or linezolid we mapped the relative change of ribosome density induced by these antibiotics. We find that both inhibitors preferentially arrest ribosomes that carry either an alanine, serine, or threonine in the penultimate (-1) position of the nascent peptide chain. Additionally ribosomes that carry a glycine in either the P site (0) or A-site (+1) counteract the inhibitory activity of both inhibitors. The context-specific action of chloramphenicol illuminates the operation of the mechanism of inducible resistance that relies on programmed drug-induced translation arrest. In addition, our findings expose the functional interplay between the nascent chain and the peptidyl transferase center.

2016-09-08 | GSE86536 | GEO

Context-specific inhibition of mitochondrial ribosomes by phenicol and oxazolidinone antibiotics.

Project description: Not available

| S-EPMC11795202 | biostudies-literature

Context-specific inhibition of mitochondrial ribosomes by phenicol and oxazolidinone antibiotics.

Project description: Not available

| S-EPMC11370408 | biostudies-literature

Context-specific action of macrolide antibiotics on the eukaryotic ribosome

Project description:80S ribosomes of S.cerevisiae carry G2400A mutation in the 25S rRNA which makes them sensitive to macrolide antibiotics

2021-05-25 | GSE164275 | 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.

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

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The general mode of translation inhibition by macrolide antibiotics

Project description:Macrolides are clinically important antibiotics thought to inhibit bacterial growth by impeding the passage of newly synthesized polypeptides through the nascent peptide exit tunnel of the bacterial ribosome. Recent data challenged this view by showing that macrolide antibiotics can differentially affect synthesis of individual proteins. In order to understand the general mechanism of macrolide action, we used genome-wide ribosome profiling and analyzed the redistribution of ribosomes translating highly expressed genes in bacterial cells treated with high concentrations of macrolide antibiotics. The metagene analysis indicated that inhibition of early rounds of translation, which would be characteristic of the conventional view of macrolide action, occurs only at a limited number of genes. Translation of most genes proceeds past the 5' proximal codons and can be arrested at more distal codons when the ribosome encounters specific short sequence motifs. The sequence motifs enriched in the sites of arrest are confined to the nascent peptide residues in the peptidyl transferase center but not to the peptide segments that contact the antibiotic molecule in the exit tunnel. This led to the conclusion that the general mode of macrolide action involves selective inhibition of peptide bond formation between specific combinations of donor and acceptor substrates. Additional factors operating in the living cell but not during in vitro protein synthesis may modulate site-specific action of macrolide antibiotics. Comparing ribosome distribution in bacterial cells treated with macrolide antibiotics against the control cells.

2014-11-03 | E-GEOD-61619 | biostudies-arrayexpress

YBEY is an essential biogenesis factor for mitochondrial ribosomes

Project description:YBEY is an essential biogenesis factor for mitochondrial ribosomes

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The general mode of translation inhibition by macrolide antibiotics

2014-11-03 | GSE61619 | GEO