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Sequence selectivity of macrolide-induced translational regulation

ABSTRACT: We sequenced a total of 12 cDNA libararies derived from fragmented total mRNA and ribosome protected mRNAs from azithromycin-treated and -untreated S. aureus samples. The data represented 2 independent biological replicates.

ORGANISM(S): Staphylococcus aureus subsp. aureus NCTC 8325

PROVIDER: GSE57175 | GEO | 2014/11/03

SECONDARY ACCESSION(S): PRJNA245830

REPOSITORIES: GEO

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Sequence selectivity of macrolide-induced translational regulation

Project description:We sequenced a total of 12 cDNA libararies derived from fragmented total mRNA and ribosome protected mRNAs from azithromycin-treated and -untreated S. aureus samples. The data represented 2 independent biological replicates. Examination of the impact of azithromycin on global translatome, mRNA abundance and the ribosome density along the transcripts.

2014-11-03 | E-GEOD-57175 | biostudies-arrayexpress

Ribosome hibernation factor promotes Staphyloccocal survival and differentially represses translation

Project description:We sequenced a total of 16 cDNA libararies derived from fragmented total mRNA and ribosome protected mRNAs from S. aureus hpf mutant (NE838) and its parental strain JE2 grown in tryptic soy broth (TSB) or minimal medium (MM). The data represented 2 independent biological replicates.

2016-03-29 | GSE74197 | GEO

Sequence selectivity of macrolide-induced translational attenuation.

Project description: Not available

| S-EPMC4217412 | biostudies-literature

Ribosome hibernation factor promotes Staphyloccocal survival and differentially represses translation

2016-03-29 | E-GEOD-74197 | biostudies-arrayexpress

Transcription profiling of human airway epithelium treated with azithromycin and SMM

Project description:Microarrays were used to evaluate the effects of azithromycin and an inflammatory stimulus (SMM) on human airway epithelium. Effects of azithromycin treatment were evaluated at 6, 24 and 48 hours. Effects of SMM were evaluated at 6 and 24 hours. In addition, pretreatment with azithromycin was used to evaluate the modulatory effects on SMM-induced inflammation. SMM=supernatant from microcorpulent material from human cystic fibrosis airways. Experiment Overall Design: 10 treatments total, 3-4 samples (patient codes = replicates) per treatment.

2009-05-27 | E-GEOD-10592 | biostudies-arrayexpress

The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria

Project description:Protein synthesis by ribosomes takes place on a linear substrate but at variable speeds. Transient pausing of ribosomes can impact a variety of co-translational processes, including protein targeting and folding. These pauses are influenced by the sequence of the mRNA. Thus redundancy in the genetic code allows the same protein to be translated at different rates. However, our knowledge of both the position and the mechanism of translational pausing in vivo is highly limited. Here we present a genome-wide analysis of translational pausing in bacteria using ribosome profiling-deep sequencing of ribosome-protected mRNA fragments. This approach enables high-resolution measurement of ribosome density profiles along most transcripts at unperturbed, endogenous expression levels. Unexpectedly, we found that codons decoded by rare tRNAs do not lead to slow translation under nutrient-rich conditions. Instead, Shine-Dalgarno-(SD) like features within coding sequences cause pervasive translational pausing. Using an orthogonal ribosome possessing an altered anti-SD sequence, we demonstrated that pausing is due to hybridization between mRNA and the 16S rRNA of the translating ribosome. In protein coding sequences, internal SD sequences are disfavoured, which leads to biased usage, avoiding codons and codon pairs that resemble canonical SD sites. Our results indicate that internal SD-like sequences are a major determinant of translation rates and a global driving force for the coding of bacterial genomes. Identification of translation pause sites in vivo using ribosome profiling

2012-04-01 | E-GEOD-35641 | biostudies-arrayexpress

Translational landscape of photomorphogenic Arabidopsis

Project description:We report the application of ribosome profiling method to map ribosome locations on transcripts in de-etiolating Arabidopsis seedlings Examine steady-state mRNA and ribosome-protected mRNA abundance in 4-day-old etiolated seedlings with/without 4-h light treatment

2013-11-08 | E-GEOD-43703 | biostudies-arrayexpress

ribosome frofiling with or without 16 mg/L azithromycin treated in pseudomonas aeruginosa UCBPP-PA14

Project description:Azithromycin binds to the nascent peptide exit tunnel (NPET) close to the peptidyltransferase center (PTC) of the ribosome, which obstructs the NPET and subsequently induces ribosome stalling and depletion of intracellular pools of tRNAs. To understand the mechanism through which azithromycin represses the transcription of mutation promoting genes, we utilized ribosome profiling to analyze azithromycin caused redistribution of ribosomes on the cellular mRNAs. Wild type PA14 was treated with 16 mg/L azithromycin for 3 hours.

2024-01-01 | GSE245932 | GEO

Tau drives translational selectivity by interacting with ribosomal proteins

Project description:There is a fundamental gap in understanding the consequences of tau-ribosome interactions. Tau oligomers and filaments hinder protein synthesis in vitro, and they associate strongly with ribosomes in vivo. Here, we investigated the consequences of tau interactions with ribosomes in vivo and in human brain tissues to identify tau as a direct modulator of ribosomal selectivity. We performed microarrays and nascent proteomics to measure changes in protein synthesis using rTg4510 tau transgenic mice. We determined that tau expression differentially shifts the transcriptome and the proteome and that the synthesis of ribosomal proteins is reversibly dependent on tau levels. We further extended these results to human brains and show that tau pathologically interacts with ribosomal protein S6 (rpS6 or S6). Consequently, synthesis of ribosomal proteins coded by 5’TOP-mRNAs was reduced under tauopathic conditions in Alzheimer’s disease brains. Our data establish tau as a driver of RNA translation selectivity. Moreover, considering that regulation of protein synthesis is critical to learning and memory, aberrant tau-ribosome interactions in disease could explain the linkage between virtually every tauopathy and cognitive impairment and memory decline.

2019-03-30 | GSE121264 | GEO

Disome-seq reveals sequence-mediated coupling of translational pauses and protein structures

Project description:The regulation of translation elongation plays a vital role in protein folding; an adequate translational pause provides time and cellular environments for the co-translational folding of nascent peptides. However, the genomic landscape, sequence determinants, and molecular consequences of translational pausing remain mostly unknown. In this study, we performed disome-seq that sequenced mRNA fragments protected by two consecutive ribosomes – a product of severe translational pauses during which the upstream ribosome collides into the paused one. We detected severe translational pauses on ~75% of yeast genes. These pauses were often explained by one of the three mechanisms: 1) slow ribosome releasing at stop codons, 2) slow peptide formation from proline, glycine, asparagine, and cysteine, and 3) slow leaving of polylysine from the exit tunnel of ribosomes. Notably, these amino acids also terminate the α-helical conformation. Such dual roles of amino acids establish an inborn coupling between the synthetic completion of a structural motif and a translational pause. Furthermore, paused ribosomes often recruit chaperones to assist protein folding. As a consequence, emergent protein structures during evolution should be ready to be correctly folded. Collectively, our study shows widespread translational pauses and sheds lights on a better understanding of the regulation of co-translational protein folding.

2020-12-10 | PXD015271 | Pride

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