GSE51052   Details

GSE Accession GSE51052
Title Translational control through ribosome traffic jams and aborted protein synthesis
Submission Date 9/20/13
Last Update Date 5/15/14
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Experiment Type Expression profiling by high throughput sequencing
Contributor Arvind,R,Subramaniam; Erin O'Shea
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Organism Escherichia coli BW25113; Escherichia coli str. K-12 substr. MG1655
Organism ID 679895; 511145
Organism Synonym Escherichia coli strain BW25113; Escherichia coli str. BW25113; Escherichia coli MG1655; Escherichia coli str. MG1655; Escherichia coli str. K12 substr. MG1655; Escherichia coli strain MG1655
Summary 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.
Overall Design 6 samples for ribosome profiling and 6 samples for total mRNA profiling
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Timepoint Count 0
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