Principles of cellular resource allocation revealed by condition-dependent proteome profiling
- Weizmann Institute of Science, Israel
Figures
Figure 1 with 1 supplement
Proteomic analysis of budding yeast grown in different conditions.
(A) Proteome profiles in our dataset clusters into two main groups on their fermentative or respiratory growth mode: Shown is the Pearson correlation matrix between proteome compositions in the …
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Figure 1—source data 1
DAmP and WT LC-MS/MS proteomic data as described in Materials and methods.
- https://doi.org/10.7554/eLife.28034.004
Figure 1—figure supplement 1
Proteome composition.
(A) The proteome composition under different conditions: Left column - proteome composition of all protein groups analyzed as indicated in Figure 1C. Right column – same protein groups as in the …
Figure 2 with 1 supplement
Ribosome content scales linearly with cell growth rate.
(A) Shown is the fraction of the proteome coding for the ribosomal proteins in each condition as a function of cell growth rate. Note that here and henceforth, growth rate is shown in units of …
Figure 2—figure supplement 1
The proteome profiles of budding yeast cells growing in different conditions.
(A) Same as Figure 2B top, specifying the condition. (B) Ribosomal proteome fraction from cells forced to transcribe unstable DAmP transcripts are shown (Kafri et al., 2016b). Error bars represent …
Figure 3
A substantial fraction of ribosomes is not actively translating at a given time.
(A) Estimating the fraction of inactive ribosomes using polysomal profiling: Cells were grown in the indicated conditions and their ribosomal content was analyzed on sucrose gradients as an …
Figure 4 with 1 supplement
The scaling between ribosome content and growth rate changes when balanced growth is perturbed.
(A) The scaling between ribosome content and growth rate changes when cells prepare to enter stationary phase: Cells grown in batch culture were followed as they increase in density (top panel), and …
Figure 4—figure supplement 1
The scaling between ribosome content and growth rate changes when balanced growth is perturbed.
(A) The fraction of the transcriptome encoding ribosomal proteins in cells growing in low phosphate: Exponentially growing cells in SC media were diluted into low phosphate media (0.06 mM). Samples …
Figure 5 with 1 supplement
Forcing unneeded protein production reduces the pool of free ribosomes.
(A) Scaling of ribosomal proteins with growth rate in protein-burdened strains: Five strains expressing increasing amounts of mCherry proteins were generated and their proteome profiles and growth …
Figure 5—figure supplement 1
Cells forced to produce unneeded proteins have a smaller pool of excess ribosomes.
(A) Relative growth rates of burdened cells: The growth effect of mCherry copy number in different conditions is plotted; black low pi, green SC; red low N. Relative growth rate was calculated using …
Figure 6
The ratio of active to inactive ribosomes remains invariant to protein burden.
(A) The ratio of active to inactive ribosome predicted by proteomic data: Shown is the ratio of active to inactive ribosomes ra/r0, as predicted from our analysis of proteomic data as a function of …
Figure 7
Model for ribosome allocation.
Cells tune their ribosome content and ribosome efficiency based on signaling from the environment. Evolutionary tuning of this signaling results in a precise scaling of ribosome content with growth …
Additional files
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Supplementary file 1
Proteome functional groups: We divided the proteome into 12 groups, 11 of which were based on SGD GO annotations or KEGG annotations, which together account for 80% of the proteome (by protein abundance).
The rest were grouped together as an additional 12th group.
- https://doi.org/10.7554/eLife.28034.014
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Supplementary file 2
Proteins group used for Figure 1B.
- https://doi.org/10.7554/eLife.28034.015
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Supplementary file 3
One copy mCherry calculation: LC-MS/MS proteomic data for one genomic copy of mCherry and for fused mCherry (see Materials and methods).
- https://doi.org/10.7554/eLife.28034.016
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Transparent reporting form
- https://doi.org/10.7554/eLife.28034.017
