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| Status |
Public on Apr 24, 2014 |
| Title |
Absolute quantification of protein production reveals principles underlying protein synthesis rates |
| Organism |
Escherichia coli |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
A quantitative view of cellular functions requires precise measures of the rates of biomolecule production, especially proteins-the direct effectors of biological processes. Here we present a genome-wide approach, based on ribosome profiling, for measuring absolute protein synthesis rates. The resultant E. coli dataset transforms our understanding of the extent to which protein synthesis is precisely controlled to optimize function and efficiency. For example, members of multi-protein complexes are made in precise proportion to their stoichiometry, whereas components of functional modules are produced differentially according to their hierarchical role. Estimates of absolute protein abundance also reveal principles used to optimize design. These include how the level of different types of transcription factors is optimized for rapid response, and how a metabolic pathway (methionine biosynthesis) balances production cost with activity requirements. More broadly, our studies reveal how general principles, important both for understanding natural systems and for synthesizing new ones, emerge from global quantitative analyses of protein synthesis.
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| Overall design |
4 samples of E. coli ribosome profiling and mRNA-seq, including biological replicates
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| Contributor(s) |
Li G, Burkhardt D, Gross CA, Weissman JS |
| Citation(s) |
24766808 |
| Submission date |
Jan 02, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Gene-Wei Li |
| E-mail(s) |
gene-wei.li@ucsf.edu
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| Organization name |
UCSF
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| Street address |
1700 4th Street, BH404
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
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| Platforms (2) |
| GPL14548 |
Illumina HiSeq 2000 (Escherichia coli) |
| GPL18133 |
Illumina HiSeq 2500 (Escherichia coli) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA232843 |
| SRA |
SRP034871 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE53767_fp_min_pooled_f.wig.gz |
10.8 Mb |
(ftp)(http) |
WIG |
| GSE53767_fp_min_pooled_r.wig.gz |
11.6 Mb |
(ftp)(http) |
WIG |
| GSE53767_fp_rdm_pooled_f.wig.gz |
9.8 Mb |
(ftp)(http) |
WIG |
| GSE53767_fp_rdm_pooled_r.wig.gz |
10.4 Mb |
(ftp)(http) |
WIG |
| GSE53767_mrna-rdm-pooled_f.wig.gz |
8.4 Mb |
(ftp)(http) |
WIG |
| GSE53767_mrna-rdm-pooled_r.wig.gz |
9.0 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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