Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Bacterial ribosome pause sites surveyed by an integration of ribosome profiling and nascent chain profiling II

ABSTRACT: Bacterial ribosome pause sites surveyed by an integration of ribosome profiling and nascent chain profiling II

PROVIDER: PRJNA748395 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR15201722.fastq.gz	Fastqsanger.gz
	SRR15201723.fastq.gz	Fastqsanger.gz

Items per page:

1 - 2 of 2

Similar Datasets

Bacterial ribosome pause sites surveyed by an integration of ribosome profiling and nascent chain profiling

Project description:Bacterial ribosome pause sites surveyed by an integration of ribosome profiling and nascent chain profiling

| PRJNA673802 | ENA

Bacterial ribosome pause sites surveyed by an integration of ribosome profiling and nascent chain profiling

Project description:Ribosome pauses are associated with diverse co-translational events and determine the fate of mRNAs and proteins. Thus the identification of the precise pause sites across transcriptome is a key, however, the landscape in bacterial has remained ambiguous. Here, we harnessed the multiple ribosome profiling strategies (standard, high-salt-wash, and disome) to survey the robust ribosome pause sites in E. coli. The found pause sites showed the correspondence with biochemical validation by integrated nascent chain profiling (iNP), which detects polypeptidyl-tRNA, an elongation intermediate. Among the list, ribosome pause at Asn586 of ycbZ was ensured by biochemical reporter assay, tRNA-seq, and cryo-electron microscopy. Our results provide a useful resource of ribosome stalling sites in bacteria.

2021-11-23 | GSE160623 | GEO

Bacterial ribosome pause sites surveyed by an integration of ribosome profiling and nascent chain profiling II

2021-11-23 | GSE180482 | GEO

Nascent chain folding status modulates ribosome dynamics and mRNA stability through the ribosome-associated chaperone Zuo1

Project description:Ribosome dynamics during mRNA translation elongation regulate mRNA stability. Yet, known regulators of ribosome transit, such as codon usage, cannot fully explain transcriptome-wide decay rates. Here, we demonstrate that nascent polypeptide folding modulates elongation rates, with Zuotin (Zuo1) serving as an essential mediator. Using reporter constructs encoding co-translationally unstructured proteins and RNA sequencing under proteotoxic stress, we show that Zuo1 is required for selective destabilization of transcripts whose nascent peptides fail to fold properly. This process relies on the co-translational mRNA decay factor Not5, which detects slowed ribosomes. 35S labeling indicates that nascent peptide folding defects correlate with reduced elongation rates in a Zuo1-dependent manner, and ribosome profiling reveals that global protein misfolding induces Zuo1-dependent ribosome pausing. These findings position Zuo1 as a key mediator linking nascent peptide folding status to ribosome dynamics and mRNA stability. Furthermore, this work suggests an expanded role for Not5 beyond codon optimality sensing.

2023-06-01 | GSE151370 | GEO

Nascent chain folding status modulates ribosome dynamics and mRNA stability through the ribosome-associated chaperone Zuo1

Project description:Ribosome dynamics during mRNA translation elongation regulate mRNA stability. Yet, known regulators of ribosome transit, such as codon usage, cannot fully explain transcriptome-wide decay rates. Here, we demonstrate that nascent polypeptide folding status modulates elongation rates, with Zuotin (Zuo1) serving as an essential mediator, and this also influences mRNA stability. Using reporter constructs encoding co-translationally unstructured proteins and RNA sequencing under proteotoxic stress, we show that Zuo1 is required for the selective destabilization of transcripts whose nascent peptides fail to fold properly. This process is independent of codon optimality but relies on the co-translational mRNA decay factor Not5, which detects slowed ribosomes. 35S labeling indicates that nascent peptide folding defects correlate with reduced elongation rates in a Zuo1-dependent manner, and ribosome profiling reveals that global protein misfolding induces Zuo1-dependent ribosome pausing. These findings position Zuo1 as a key mediator linking nascent peptide folding status to ribosome dynamics and mRNA stability. Furthermore, this work suggests an expanded role for Not5 beyond codon optimality sensing.

2026-07-24 | GSE319659 | GEO

Selective stalling of human translation through small molecule engagement of the ribosome nascent chain

Project description:We use ribosome profiling to demonstrate the selectivity of a small molecule, PF-06446846 that inhibits translation of its target by selectively inducing ribosome-stalling in a nascent chain sequence dependent manner.

2017-06-05 | GSE94454 | GEO

Analysis of stalled ribosome-nascent chain complexes by quantitative proteomics

Project description:The cellular environment is critical for efficient protein maturation, but how proteins fold during biogenesis remains poorly understood. To understand how the cellular environment modulates folding, we studied the cotranslational chaperone-assisted folding of Escherichia coli dihydrofolate reductase (DHFR). To sample folding intermediates along the pathway of vectorial synthesis, we prepared a series of stalled ribosome:nascent chain complexes (RNCs) representing snapshots of DHFR folding in vivo. Proteomic analysis of RNCs revealed their composition and allowed us to define chaperone interactions as a function of NC length. These data set the stage for further studies aimed at resolving the conformation of the nascent polypeptide on the ribosome.

2025-05-06 | PXD036784 | Pride

Nascent elongating transcript sequencing (NET-seq) for Escherichia coli and Bacillus subtilis reveals a consensus pause sequence enriched at translation start sites.

Project description:Transcription by RNA polymerase (RNAP) is interrupted by pauses that play diverse regulatory roles. Although individual pauses have been studied in vitro, the determinants of pauses in vivo and their distribution throughout the bacterial genome remain unknown. Using nascent transcript sequencing we identify a 16 nt consensus pause sequence in E. coli that accounts for known regulatory pause sites as well as ~20,000 new in vivo pause sites. In vitro single-molecule and ensemble analyses demonstrate that these pauses result from RNAP/nucleic-acid interactions that inhibit next-nucleotide addition. The consensus sequence also leads to pausing by RNAPs from diverse lineages and is enriched at translation start sites in both E. coli and B. subtilis. Our results thus implicate a conserved mechanism unifying known and newly identified pause events. Examination of nascent transcripts in E. coli and B. subtilis. 6 samples of E. coli NET-seq, 1 sample of E. coli mRNA-seq, and 1 sample of B. subtilis NET-seq.

2014-05-05 | E-GEOD-56720 | biostudies-arrayexpress

Translational control through ribosome traffic jams and aborted protein synthesis

Project description:Translational control is a widespread mode of gene regulation in organisms ranging from bacteria to mammals. Computational models posit that translational control of protein expression during elongation is exerted through a traffic jam of multiple ribosomes at ribosome pause sites on mRNAs. Yet neither the in vivo frequency of ribosome traffic jams nor the contribution of such traffic jams to protein expression has been measured in any organism. Here we show that upon starvation for single amino acids in the bacterium Escherichia coli, ribosome traffic jams are pervasive across the transcriptome, but they occur at only a subset of codons cognate to the limiting amino acid, and their severity is determined by the translation efficiency of mRNAs. Surprisingly, a computational model based on the observed traffic jams at ribosome pause sites is quantitatively inconsistent with measured protein synthesis rates. By comparison, a model incorporating abortion of protein synthesis at ribosome pause sites in addition to ribosome traffic jams predicts protein synthesis rate with higher accuracy. Consistent with the latter model, a significant fraction of the nascent polypeptides at ribosome pause sites is degraded through the activity of the transfer-messenger RNA during amino acid starvation in E. coli. Our work provides a minimal, experimentally-constrained model for predicting protein expression from ribosome dynamics, and it suggests the existence of a trade-off between the cellular translational capacity and the processivity of protein synthesis in vivo. 6 samples for ribosome profiling and 5 samples for total mRNA profiling

2014-05-15 | E-GEOD-51052 | biostudies-arrayexpress

Nascent chain folding status modulates ribosome dynamics and mRNA stability through the ribosome-associated chaperone Zuo1

Project description:Nascent chain folding status modulates ribosome dynamics and mRNA stability through the ribosome-associated chaperone Zuo1

| PRJNA635625 | ENA