Growth rate is determined by unused protein expression.

<p>(<b>A</b>) To validate that the ME-Model accurately quantifies protein cost, we compare the predicted effect of un-utilized protein (β-Galactosidase) overexpression (red squares) to experimental measurements (blue circles). Experimental data is obtained from Scott et al. [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004998#pcbi.1004998.ref004" target="_blank">4</a>] The x- and y- intercept from a linear regression (dotted line) is consistent with the phenomenological model of Scott et al. [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004998#pcbi.1004998.ref004" target="_blank">4</a>] The effects of the un-utilized and under-utilized protein expression (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004998#pcbi.1004998.g001" target="_blank">Fig 1</a>) on growth rates are quantified in C and D. (<b>B</b>) Predicted growth rates are plotted versus measured growth rates during batch growth on 8 different carbon sources. Predicted growth rates are the computed maximal growth rates by the ME-Model, assuming the un-utilized proteome fraction and <i>in vivo</i> turnover rates are the same across all environments (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004998#sec017" target="_blank">Methods</a>, this assumption is eliminated in panels B and C to assess the effects of un- and under-utilized protein on growth). (<b>C</b>) Predicted maximal growth rates are computed with the ME-Model with the un-utilized proteome fraction set to the values inferred from proteomics data (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004998#sec017" target="_blank">Methods</a> and <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004998#pcbi.1004998.g001" target="_blank">Fig 1C</a>). In addition to the 8 carbon sources (circles), 4 glucose-limited chemostat cultures (triangles) and 4 stress conditions (squares) are also shown. These additional growth conditions are not included in panel A as growth rate predictions would require further information. (<b>D</b>) Predicted maximal growth rates are computed with the ME-Model with both the un-utilized proteome fraction and the <i>in vivo</i> turnover rate (indicative of under-utilized protein, <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004998#pcbi.1004998.g001" target="_blank">Fig 1D</a>) set to the values inferred from proteomics data. Point shape indicates environment type as in B (carbon source batch cultures = circles, glucose-limited chemostat cultures = triangles, stress conditions = squares).