Extended Data Fig. 5: Supplement for Fig. 4.

(a) Heatmap of relative protein concentration changes across different cell sizes. Each size is represented by two replicate columns. Size mutants correspond to asynchronous whi5Δ, WT, and cln3Δ cultures. G1 arrest time corresponds to four time points after G1 arrest taken at 1-hour intervals (using the genetic systems described in Fig. 2). (b and c) Coulter counter measurements of (b) MSN2 MSN4 and (c) msn2Δmsn4Δ G1-arrested cells. Biological replicate experiments are differentially shaded. (d) Proteins whose expression is dependent on msn2Δmsn4Δ are denoted in blue. Proteins highlighted in blue are the same set depicted in Fig. 4d. Msn2/4-dependency was defined as decrease in concentration of > 1.6-fold. (e) Fig. 4d is re-plotted here for reference. The same genes identified in (d) as Msn2/4-dependent are shown in blue. (f) Relative surface area (that is, surface area-to-volume ratio) for individual yeast cells was calculated from wide-field images of asynchronously proliferating cells. Yeast mothers and buds are assumed to be prolate ellipsoids. By measuring the polar (major axis) and equatorial (minor axis) radii, the surface area S and volume V of each ellipsoid was calculated (see methods). (g) Relative surface area (μm² / μm³) measurements for individual cells of the indicated strain background. Average surface area-to-volume ratio for each strain is marked by the dashed horizontal line. (h) Coulter counter measurements of the indicated strains. Biological replicate experiments are differentially shaded. SILAC channels were swapped for replicate experiments to maximize measurement accuracy. (i) Correlation of protein slope values (G1 arrest time) with the concentration ratios calculated from the binary comparison of the indicated strains. Protein slope values are the average from three replicate experiments (see Fig. 2). Each concentration ratio is the average of two SILAC label-swapped replicate experiments. Core histone proteins are shown in red. Blue dots are x-binned data and error bars represent the 99% confidence interval. r value denotes Pearson correlation coefficient.