|
| Status |
Public on May 15, 2014 |
| Title |
An Integrated Approach Reveals Regulatory Controls on Bacterial Translation Elongation |
| Organisms |
Escherichia coli str. K-12 substr. MG1655; Escherichia coli BW25113 |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Ribosomes elongate at a nonuniform rate during translation. Theoretical models and experiments disagree on the in vivo determinants of elongation rate and the mechanism by which elongation rate affects protein levels. To resolve this conflict, we measured transcriptome-wide ribosome occupancy under multiple conditions and used it to formulate a whole-cell model of translation in E. coli. Our model predicts that elongation rates at most codons during nutrient-rich growth are not limited by the intracellular concentrations of aminoacyl-tRNAs. However, elongation pausing during starvation for single amino acids is highly sensitive to the kinetics of tRNA aminoacylation. We further show that translation abortion upon pausing accounts for the observed ribosome occupancy along mRNAs during starvation. Abortion reduces global protein synthesis, but it enhances the translation of a subset of mRNAs. These results suggest a regulatory role for aminoacylation and abortion during stress, and our study provides an experimentally constrained framework for modeling translation.
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| |
|
| Overall design |
7 samples for ribosome profiling and 4 samples for total mRNA profiling
|
| |
|
| Contributor(s) |
Subramaniam AR, Zid BM, O'Shea EK |
| Citation(s) |
25416955 |
| Submission date |
Sep 20, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Arvind R Subramaniam |
| E-mail(s) |
rasi@fredhutch.org
|
| Phone |
6174968433
|
| Organization name |
Harvard University
|
| Department |
Molecular and Cellular Biology
|
| Street address |
52 Oxford St
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02138 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL15010 |
Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655) |
| GPL15206 |
Illumina HiSeq 2000 (Escherichia coli BW25113) |
|
| Samples (11)
|
|
| Relations |
| BioProject |
PRJNA219750 |
| SRA |
SRP030123 |
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