Zhang et al. 2022 (PRJNA754447)
General Details
| Title | Global and gene-specific translational regulation in Escherichia coli across different conditions |
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| Organism | |
| Number of Samples | 36 |
| Release Date | 2021/08/13 00:00 |
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| Protocol Details |
Study Links
| GWIPS-viz | Trips-Viz |
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Repository Details
| SRA | SRP332494 |
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| ENA | SRP332494 |
| GEO | GSE182100 |
| BioProject | PRJNA754447 |
Publication
| Title | |
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| Authors | Zhang D,Li SH,King CG,Wingreen NS,Gitai Z,Li Z |
| Journal | PLoS computational biology |
| Publication Date | 2022 Oct |
| Abstract | How well mRNA transcript levels represent protein abundances has been a controversial issue. Particularly across different environments, correlations between mRNA and protein exhibit remarkable variability from gene to gene. Translational regulation is likely to be one of the key factors contributing to mismatches between mRNA level and protein abundance in bacteria. Here, we quantified genome-wide transcriptome and relative translation efficiency (RTE) under 12 different conditions in Escherichia coli. By quantifying the mRNA-RTE correlation both across genes and across conditions, we uncovered a diversity of gene-specific translational regulations, cooperating with transcriptional regulations, in response to carbon (C), nitrogen (N), and phosphate (P) limitations. Intriguingly, we found that many genes regulating translation are themselves subject to translational regulation, suggesting possible feedbacks. Furthermore, a random forest model suggests that codon usage partially predicts a gene's cross-condition variability in translation efficiency; such cross-condition variability tends to be an inherent quality of a gene, independent of the specific nutrient limitations. These findings broaden the understanding of translational regulation under different environments and provide novel strategies for the control of translation in synthetic biology. In addition, our data offers a resource for future multi-omics studies. |
| PMC | PMC9624429 |
| PMID | 36264977 |
| DOI |
| Run Accession | Study Accession | Scientific Name | Cell Line | Library Type | Treatment | GWIPS-viz | Trips-Viz | Reads | BAM | BigWig (F) | BigWig (R) | ||
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| SRR15446776 | PRJNA754447 | Escherichia coli | Ribo-Seq |  |
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| SRR15446777 | PRJNA754447 | Escherichia coli | Ribo-Seq | |
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| SRR15446778 | PRJNA754447 | Escherichia coli | Ribo-Seq | |
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| SRR15446779 | PRJNA754447 | Escherichia coli | Ribo-Seq | |
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| SRR15446780 | PRJNA754447 | Escherichia coli | Ribo-Seq | |
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| SRR15446781 | PRJNA754447 | Escherichia coli | Ribo-Seq | |
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| SRR15446782 | PRJNA754447 | Escherichia coli | Ribo-Seq | |
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| SRR15446783 | PRJNA754447 | Escherichia coli | Ribo-Seq | |
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| SRR15446784 | PRJNA754447 | Escherichia coli | Ribo-Seq | |
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| SRR15446785 | PRJNA754447 | Escherichia coli | Ribo-Seq | |
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| SRR15446786 | PRJNA754447 | Escherichia coli | Ribo-Seq | |
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| SRR15446787 | PRJNA754447 | Escherichia coli | Ribo-Seq | |
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| SRR15446788 | PRJNA754447 | Escherichia coli | Ribo-Seq | |
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| SRR15446789 | PRJNA754447 | Escherichia coli | Ribo-Seq | |
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| SRR15446790 | PRJNA754447 | Escherichia coli | Ribo-Seq | |
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| SRR15446791 | PRJNA754447 | Escherichia coli | Ribo-Seq | |
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| SRR15446792 | PRJNA754447 | Escherichia coli | Ribo-Seq | |
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| SRR15446793 | PRJNA754447 | Escherichia coli | Ribo-Seq | |
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| SRR15446794 | PRJNA754447 | Escherichia coli | Ribo-Seq | |
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| SRR15446795 | PRJNA754447 | Escherichia coli | Ribo-Seq | |
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| SRR15446796 | PRJNA754447 | Escherichia coli | Ribo-Seq | |
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| SRR15446797 | PRJNA754447 | Escherichia coli | Ribo-Seq | |
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| SRR15446798 | PRJNA754447 | Escherichia coli | Ribo-Seq | |
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| SRR15446799 | PRJNA754447 | Escherichia coli | Ribo-Seq | |
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| SRR15446800 | PRJNA754447 | Escherichia coli | Ribo-Seq | |
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| SRR15446801 | PRJNA754447 | Escherichia coli | Ribo-Seq | |
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| SRR15446802 | PRJNA754447 | Escherichia coli | Ribo-Seq | |
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| SRR15446803 | PRJNA754447 | Escherichia coli | Ribo-Seq | |
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| SRR15446804 | PRJNA754447 | Escherichia coli | Ribo-Seq | |
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| SRR15446805 | PRJNA754447 | Escherichia coli | Ribo-Seq | |
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| SRR15446806 | PRJNA754447 | Escherichia coli | Ribo-Seq | |
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| SRR15446807 | PRJNA754447 | Escherichia coli | Ribo-Seq | |
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| SRR15446808 | PRJNA754447 | Escherichia coli | Ribo-Seq | |
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| SRR15446809 | PRJNA754447 | Escherichia coli | Ribo-Seq | |
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| SRR15446810 | PRJNA754447 | Escherichia coli | Ribo-Seq | |
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| SRR15446811 | PRJNA754447 | Escherichia coli | Ribo-Seq | |
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| Run Accession | Study Accession | Scientific Name | Cell Line | Library Type | Treatment | GWIPS-viz | Trips-Viz | Reads | BAM | BigWig (F) | BigWig (R) |
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