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| Status |
Public on Feb 21, 2020 |
| Title |
Translational initiation in E. coli occurs at the correct sites genome-wide in the absence of mRNA-rRNA base-pairing |
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
Shine-Dalgarno (SD) motifs are thought to play an important role in translational initiation in bacteria. Paradoxically, ribosome profiling studies in E. coli show no correlation between the strength of the SD in an mRNA and how efficiently it is translated. Performing profiling on ribosomes with altered anti-Shine-Dalgarno sequences, we reveal a genome-wide correlation between SD strength and ribosome occupancy that was previously masked by other contributing factors. Using the antibiotic retapamulin to trap initiation complexes at start codons, we find that the mutant ribosomes select start sites correctly, arguing that start sites are hard-wired for initiation through the action of other mRNA features. We show that A-rich sequences upstream of start codons promote initiation. Taken together, our genome-wide study reveals that SD motifs are not necessary for the ribosome to select where initiation occurs, though they do affect how efficiently initiation occurs at sites whose other features support initiation.
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| Overall design |
Ribosome profiling of purified MS2-tagged ribosomes with anti-Shine Dalgarno mutations from E. coli MG1655
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| Contributor(s) |
Buskirk AR |
| Citation(s) |
32065583 |
| |
| Submission date |
Aug 16, 2019 |
| Last update date |
Mar 02, 2020 |
| Contact name |
Allen R Buskirk |
| E-mail(s) |
buskirk@jhmi.edu
|
| Organization name |
Johns Hopkins University School of Medicine
|
| Department |
Molecular Biology and Genetics
|
| Street address |
725 N. Wolfe St
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
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| Platforms (1) |
| GPL18956 |
Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655) |
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| Samples (41)
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| Relations |
| BioProject |
PRJNA560549 |
| SRA |
SRP218568 |
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