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TranscriptomicsGenome-wide ribosome profiling to identify regulatory targets of small RNA RyhB in E.coli
The effects of RyhB expression were examined by Ribo-seq and RNA-seq after 10 min to avoid indirect effects. Expression of RyhB was induced by arabinose from cells carrying pBAD-ryhB plasmid. The RyhB expression was confirmed by real-time PCR. As a control, cells with vector pNM12 were grown and ind...
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2014-11-01 | E-MTAB-2903 | biostudies-arrayexpress
TranscriptomicsOptimization of codon translation rates via tRNA modifications maintains proteome integrity
Proteins begin to fold as they emerge from translating ribosomes. The kinetics of ribosome transit along a given mRNA can influence nascent chain folding, but the extent to which individual codon translation rates impact proteome integrity remains unknown. Here, we show that slower decoding of discr...
ORGANISM(S): Caenorhabditis elegans 
2015-06-04 | E-GEOD-67387 | biostudies-arrayexpress
ProteomicsRibosome r-protein content during stationary phase
The aim of this study was to determine the fate of ribosomes and r-proteins. In this respect, SILAC (Stable Isotope Labeled Amino acids in cell Culture) based experimental approach was used (Fig. 1). E.coli cells were grown in MOPS medium supplemented with “heavy” labeled arginine (Arg10) and lysine...
ORGANISM(S): Escherichia coli 
2023-09-01 | PXD035923 | Pride
Ribosome Ribosomal proteins Proteome E.coli 
ProteomicsAnalysis of stalled ribosome-nascent chain complexes by quantitative proteomics
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 reductas...
ORGANISM(S): Escherichia coli 
2025-05-06 | PXD036784 | Pride
Protein biosynthesis Ribosome-nascent chain complexes Interactome Protein folding Lc-ms/ms 
ProteomicsE.coli Ribosome protein composition
Ribosomes are essential macromolecular complexes conducting protein biosynthesis in all domains of life. Cells can have heterogeneous ribosomes, i.e. ribosomes with various ribosomal RNA (rRNA) and ribosomal protein (r-protein) composition. However, the functional importance of heterogeneous ribosom...
ORGANISM(S): Escherichia coli 
2020-10-20 | PXD018123 | Pride
Ribosome Escherichia coli Lc-ms/ms 
ProteomicsCross-linking/Mass Spectrometry Combined with Ion Mobility on a timsTOF Pro Instrument for Structural Proteomics
The combination of cross-linking/mass spectrometry (XL-MS) and ion mobility is still underexplored for conducting protein conformational and protein-protein interaction studies. We present a method for analyzing cross-linking mixtures on a timsTOF Pro mass spectrometer that allows separating ions ba...
ORGANISM(S): Bos taurus (Bovine) Homo sapiens (Human) Escherichia coli 
2022-03-17 | PXD027234 | Pride
Ion mobility Mass spectrometry Chemical cross-linking Protein 3d-structure Protein interaction networks 
ProteomicsBarley newly synthesized ribosomal proteome: E.coli control samples
Ribosomal proteome profiling control for project: Plants synthesize new ribosomal proteins and recycle others in cold-acclimated ribosomes and these in turn synthesize a differential proteome in barley root meristems.
ORGANISM(S): Escherichia coli 
2024-05-23 | PXD032938 | Pride
E.coli 70s ribosomes rproteome 
GenomicsGenome-wide ribosome profiling to identify regulatory targets of small RNA RyhB in E.coli
Genome-wide ribosome profiling to identify regulatory targets of small RNA RyhB in E.coli
PRJEB7301 | ENA
ProteomicsIdentification of MS-Cleavable and Non-Cleavable Chemically Crosslinked Peptides with MetaMorpheus
The present work describes a novel search program for the detection of both MS-cleavable and non-cleavable crosslinked peptides and it is the first software program reported with both capacities. The search strategy has been implemented in the computer program MetaMorpheus, which has a user-friendly...
ORGANISM(S): Escherichia coli 
2018-07-16 | PXD009000 | Pride
Proteomics Ms-cleavable chemical crosslink Protein-protein interactions Ion index 
ProteomicsBactericidal effect of tetracycline in E. coli strain ED1a may be associated with ribosome dysfunction
Ribosomes translate the genetic code into proteins. Recent technical advances have facilitated in situ structural analyses of ribosome functional states inside eukaryotic cells and the minimal bacterium Mycoplasma. However, such analyses of Gram-negative bacteria are lacking, despite their ribosomes...
ORGANISM(S): Escherichia coli 
2024-04-29 | PXD044697 | Pride
Cryo-et E.coli Tetracycline Gut bacteria 
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