PXD001467 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Proteome resource allocation in bacteria |
Description | A central aim of cell biology is to understand the strategy of gene expression in response to the environment. Here we study gene expression response to metabolic challenges in exponentially growing Escherichia coli using mass spectrometry. Despite enormous complexity in the details of the underlying regulatory network, we find that the proteome partitions into several coarse-grained sectors, with each sector’s total mass abundance exhibiting positive or negative linear relations with the growth rate. The growth-rate dependent components of the proteome fractions comprise about half of the proteome by mass, and their mutual dependencies can be characterized by a simple flux model involving only two effective parameters. The success and apparent generality of this model arises from tight coordination between proteome partition and metabolism, suggesting a principle for resource-allocation in proteome economy of the cell. This strategy of global gene regulation should serve as a basis for future studies on gene expression and constructing synthetic biological circuits. Coarse-graining may be an effective approach to derive predictive phenomenological models for other ‘omics’ studies. |
HostingRepository | PRIDE |
AnnounceDate | 2015-02-12 |
AnnouncementXML | Submission_2015-04-01_05:47:09.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Sheng Hui |
SpeciesList | scientific name: Escherichia coli; NCBI TaxID: 562; |
ModificationList | monohydroxylated residue; carbamoylated residue |
Instrument | TripleTOF 5600 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2014-11-06 02:02:45 | ID requested | |
1 | 2015-02-12 09:37:11 | announced | |
⏵ 2 | 2015-04-01 05:47:11 | announced | Updated publication reference for PubMed record(s): 25678603. |
Publication List
Hui S, Silverman JM, Chen SS, Erickson DW, Basan M, Wang J, Hwa T, Williamson JR, Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria. Mol Syst Biol, 11(1):784(2015) [pubmed] |
Keyword List
curator keyword: Biomedical, Biological |
submitter keyword: Escherichia coli, growth physiology, proteome partition |
Contact List
Terence Hwa |
contact affiliation | Department of Physics and Section of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0374 USA |
contact email | hwa@ucsd.edu |
lab head | |
Sheng Hui |
contact affiliation | University of California, San Diego |
contact email | tonyshenghui@gmail.com |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD001467
- Label: PRIDE project
- Name: Proteome resource allocation in bacteria