|
| Status |
Public on Jan 30, 2017 |
| Title |
Operon mRNAs are organized into ORF-centric structures that predict translation efficiency |
| Organism |
Escherichia coli |
| Experiment type |
Expression profiling by high throughput sequencing
Other
|
| Summary |
Bacterial mRNAs are organized into operons consisting of discrete open reading frames (ORFs) in a single polycistronic mRNA. Individual ORFs on the mRNA are differentially translated, with rates varying as much as 100-fold. The signals controlling differential translation are poorly understood. Our genome-wide mRNA secondary structure analysis indicated that operonic mRNAs are comprised of ORF-wide units of secondary structure that vary across ORF boundaries such that adjacent ORFs on the same mRNA molecule are structurally distinct. ORF translation rate is strongly correlated with its mRNA structure in vivo, and correlation persists, albeit in a reduced form, with its structure when translation is inhibited and with that of in vitro refolded mRNA. These data suggests that intrinsic ORF mRNA structure encodes a rough blueprint for translation efficiency. This structure is then amplified by translation, in a self-reinforcing loop, to provide the structure that ultimately specifies the translation of each ORF.
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| |
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| Overall design |
mRNA-seq and ribosome profiling of E. coli MG1655 (wild-type) cells at 37°C and DMS-seq of in vivo modified mRNA from wild-type cells, kasugamycin-treated or untreated ΔgcvB cells, as well as in vitro modified mRNA refolded at 37°C or denatured at 95°C. Reads from replicates of the same experiment were pooled in wiggle files.
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| |
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| Contributor(s) |
Burkhardt DH, Rouskin S, Zhang Y, Li G, Weissman JS, Gross CA |
| Citation(s) |
28139975 |
| Submission date |
Feb 05, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Yan Zhang |
| E-mail(s) |
yan.jenny.zhang@gmail.com
|
| Organization name |
UC San Francisco
|
| Department |
Microbiology and Immunology
|
| Lab |
Carol Gross
|
| Street address |
600 16th Street
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL14548 |
Illumina HiSeq 2000 (Escherichia coli) |
| GPL21433 |
Illumina HiSeq 4000 (Escherichia coli) |
|
| Samples (17)
|
| GSM2055261 |
DMS-seq 37°C in vitro WT |
| GSM2055262 |
DMS-seq 95°C in vitro WT |
| GSM2055270 |
DMS-seq 37°C in vivo WT_2 |
| GSM2055271 |
DMS-seq 37°C in vivo dusB-M3 mutant |
| GSM2055272 |
DMS-seq 37°C in vivo dusB-M3:2 mutant |
| GSM2055273 |
DMS-seq 37°C in vivo ∆gcvB |
| GSM2055274 |
DMS-seq 37°C in vivo ∆gcvB+ksg |
| GSM2055285 |
DMS-seq 37°C 16S rRNA |
| GSM2462933 |
ribosome profiling 37°C in WT with control plasmid |
| GSM2462934 |
ribosome profiling 37°C in WT with plasmid expressing mini-ORF CUA |
| GSM2462935 |
ribosome profiling 37°C in WT with plasmid expressing mini-ORF CUG |
| GSM2462936 |
mRNA-seq 37°C in WT with control plasmid |
| GSM2462937 |
mRNA-seq 37°C in WT with plasmid expressing mini-ORF CUA |
| GSM2462938 |
mRNA-seq 37°C in WT with plasmid expressing mini-ORF CUG |
|
| Relations |
| BioProject |
PRJNA311041 |
| SRA |
SRP069339 |
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