Limits...
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

Coarse-grained metabolic flow of protein production and the three modes of growth limitationThrough the (carbon) catabolic section, the cells take up external carbon sources and break them down into the set of standard carbon skeletons (pyruvate, oxaloacetate, etc.). The carbon skeletons are interconvertible through the central metabolism section. The anabolic section synthesizes amino acids from the carbon skeletons and other necessary elements such as ammonia and sulfur. The amino acids are then assembled into proteins by the polymerization section. The three modes of growth limitation were imposed on the metabolic sections as shown. The C-limitation (C-lim) and A-limitation (A-lim) were carried out with strains constructed for titrating the catabolic and anabolic flux, respectively; see Supplementary Figs S1 and S2, and Supplementary Table S1. The R-limitation (R-lim) was realized for the WT strain by supplying the growth medium with various levels of an antibiotic, chloramphenicol.
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fig01: Coarse-grained metabolic flow of protein production and the three modes of growth limitationThrough the (carbon) catabolic section, the cells take up external carbon sources and break them down into the set of standard carbon skeletons (pyruvate, oxaloacetate, etc.). The carbon skeletons are interconvertible through the central metabolism section. The anabolic section synthesizes amino acids from the carbon skeletons and other necessary elements such as ammonia and sulfur. The amino acids are then assembled into proteins by the polymerization section. The three modes of growth limitation were imposed on the metabolic sections as shown. The C-limitation (C-lim) and A-limitation (A-lim) were carried out with strains constructed for titrating the catabolic and anabolic flux, respectively; see Supplementary Figs S1 and S2, and Supplementary Table S1. The R-limitation (R-lim) was realized for the WT strain by supplying the growth medium with various levels of an antibiotic, chloramphenicol.

Mentions: To probe gene expression, cell growth was perturbed by imposing three different modes of growth limitation at crucial bottlenecks in the metabolic network. A coarse-grained metabolic flow diagram for protein production by E. coli growing in minimal medium is shown in Fig1. Four metabolic sections act in concert to convert external carbon sources to proteins, incorporating nitrogen and sulfur elements during the process. Following the work of You et al (You et al, 2013), growth limitation was imposed on three of the four metabolic sections. The limitation imposed on the catabolic section (C-limitation or C-lim) was implemented by titrating the expression of lactose permease for cells growing on lactose (Supplementary Fig S1). The limitation on the anabolic section (A-limitation or A-lim) was realized by titrating a key enzyme (GOGAT) in the ammonia assimilation pathway (Supplementary Fig S2). Such ‘titratable uptake systems’ have been characterized in detail and found comparable to other modes of growth limitations such as those derived from continuous culture or microfluidic devices (You et al, 2013). To impose growth limitation on the polymerization sections, sublethal amounts of a translation inhibitor antibiotic, chloramphenicol, were supplied to the growth medium to inhibit translation by ribosomes (R-limitation or R-lim). The collective response of the E. coli proteome to these applied growth limitations was monitored using quantitative mass spectroscopy.


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)

Coarse-grained metabolic flow of protein production and the three modes of growth limitationThrough the (carbon) catabolic section, the cells take up external carbon sources and break them down into the set of standard carbon skeletons (pyruvate, oxaloacetate, etc.). The carbon skeletons are interconvertible through the central metabolism section. The anabolic section synthesizes amino acids from the carbon skeletons and other necessary elements such as ammonia and sulfur. The amino acids are then assembled into proteins by the polymerization section. The three modes of growth limitation were imposed on the metabolic sections as shown. The C-limitation (C-lim) and A-limitation (A-lim) were carried out with strains constructed for titrating the catabolic and anabolic flux, respectively; see Supplementary Figs S1 and S2, and Supplementary Table S1. The R-limitation (R-lim) was realized for the WT strain by supplying the growth medium with various levels of an antibiotic, chloramphenicol.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig01: Coarse-grained metabolic flow of protein production and the three modes of growth limitationThrough the (carbon) catabolic section, the cells take up external carbon sources and break them down into the set of standard carbon skeletons (pyruvate, oxaloacetate, etc.). The carbon skeletons are interconvertible through the central metabolism section. The anabolic section synthesizes amino acids from the carbon skeletons and other necessary elements such as ammonia and sulfur. The amino acids are then assembled into proteins by the polymerization section. The three modes of growth limitation were imposed on the metabolic sections as shown. The C-limitation (C-lim) and A-limitation (A-lim) were carried out with strains constructed for titrating the catabolic and anabolic flux, respectively; see Supplementary Figs S1 and S2, and Supplementary Table S1. The R-limitation (R-lim) was realized for the WT strain by supplying the growth medium with various levels of an antibiotic, chloramphenicol.
Mentions: To probe gene expression, cell growth was perturbed by imposing three different modes of growth limitation at crucial bottlenecks in the metabolic network. A coarse-grained metabolic flow diagram for protein production by E. coli growing in minimal medium is shown in Fig1. Four metabolic sections act in concert to convert external carbon sources to proteins, incorporating nitrogen and sulfur elements during the process. Following the work of You et al (You et al, 2013), growth limitation was imposed on three of the four metabolic sections. The limitation imposed on the catabolic section (C-limitation or C-lim) was implemented by titrating the expression of lactose permease for cells growing on lactose (Supplementary Fig S1). The limitation on the anabolic section (A-limitation or A-lim) was realized by titrating a key enzyme (GOGAT) in the ammonia assimilation pathway (Supplementary Fig S2). Such ‘titratable uptake systems’ have been characterized in detail and found comparable to other modes of growth limitations such as those derived from continuous culture or microfluidic devices (You et al, 2013). To impose growth limitation on the polymerization sections, sublethal amounts of a translation inhibitor antibiotic, chloramphenicol, were supplied to the growth medium to inhibit translation by ribosomes (R-limitation or R-lim). The collective response of the E. coli proteome to these applied growth limitations was monitored using quantitative mass spectroscopy.

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