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Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria.

Hui S, Silverman JM, Chen SS, Erickson DW, Basan M, Wang J, Hwa T, Williamson JR - Mol. Syst. Biol. (2015)

Bottom Line: 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.Coarse graining may be an effective approach to derive predictive phenomenological models for other 'omics' studies.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics, University of California at San Diego, La Jolla, CA, USA.

No MeSH data available.


Related in: MedlinePlus

Performance of the proteome-based flux modelThe data points are identical to those in Fig3. The lines here are the result of a global fit to the predictions of the flux-based proteome model (Supplementary Table S6). The growth rate-independent component of each sector (φσ,0) is represented as the height of the filled area in the corresponding plot. See Supplementary Table S7 for parameters of the fitted lines.
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fig05: Performance of the proteome-based flux modelThe data points are identical to those in Fig3. The lines here are the result of a global fit to the predictions of the flux-based proteome model (Supplementary Table S6). The growth rate-independent component of each sector (φσ,0) is represented as the height of the filled area in the corresponding plot. See Supplementary Table S7 for parameters of the fitted lines.

Mentions: In summary, the linear equations in Supplementary Table S6 describe the prediction of the simple flux model (equations 1, 2) on the partitioning of the proteome as a function of growth rate under the three different modes of growth limitation. Although the model contains only 10 adjustable parameters, the quality of the fit of the model to the data (lines in Fig5; Supplementary Table S7) is comparable to the 24-parameter fit for each individual response (Fig3; Supplementary Table S4).


Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria.

Hui S, Silverman JM, Chen SS, Erickson DW, Basan M, Wang J, Hwa T, Williamson JR - Mol. Syst. Biol. (2015)

Performance of the proteome-based flux modelThe data points are identical to those in Fig3. The lines here are the result of a global fit to the predictions of the flux-based proteome model (Supplementary Table S6). The growth rate-independent component of each sector (φσ,0) is represented as the height of the filled area in the corresponding plot. See Supplementary Table S7 for parameters of the fitted lines.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4358657&req=5

fig05: Performance of the proteome-based flux modelThe data points are identical to those in Fig3. The lines here are the result of a global fit to the predictions of the flux-based proteome model (Supplementary Table S6). The growth rate-independent component of each sector (φσ,0) is represented as the height of the filled area in the corresponding plot. See Supplementary Table S7 for parameters of the fitted lines.
Mentions: In summary, the linear equations in Supplementary Table S6 describe the prediction of the simple flux model (equations 1, 2) on the partitioning of the proteome as a function of growth rate under the three different modes of growth limitation. Although the model contains only 10 adjustable parameters, the quality of the fit of the model to the data (lines in Fig5; Supplementary Table S7) is comparable to the 24-parameter fit for each individual response (Fig3; Supplementary Table S4).

Bottom Line: 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.Coarse graining may be an effective approach to derive predictive phenomenological models for other 'omics' studies.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics, University of California at San Diego, La Jolla, CA, USA.

No MeSH data available.


Related in: MedlinePlus