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Dilution of the cell cycle inhibitor Whi5 controls budding-yeast cell size

Abstract

Cell size fundamentally affects all biosynthetic processes by determining the scale of organelles and influencing surface transport1,2. Although extensive studies have identified many mutations affecting cell size, the molecular mechanisms underlying size control have remained elusive3. In the budding yeast Saccharomyces cerevisiae, size control occurs in G1 phase before Start, the point of irreversible commitment to cell division4,5. It was previously thought that activity of the G1 cyclin Cln3 increased with cell size to trigger Start by initiating the inhibition of the transcriptional inhibitor Whi5 (refs 6, 7, 8). Here we show that although Cln3 concentration does modulate the rate at which cells pass Start, its synthesis increases in proportion to cell size so that its total concentration is nearly constant during pre-Start G1. Rather than increasing Cln3 activity, we identify decreasing Whi5 activity—due to the dilution of Whi5 by cell growth—as a molecular mechanism through which cell size controls proliferation. Whi5 is synthesized in S/G2/M phases of the cell cycle in a largely size-independent manner. This results in smaller daughter cells being born with higher Whi5 concentrations that extend their pre-Start G1 phase. Thus, at its most fundamental level, size control in budding yeast results from the differential scaling of Cln3 and Whi5 synthesis rates with cell size. More generally, our work shows that differential size-dependency of protein synthesis can provide an elegant mechanism to coordinate cellular functions with growth.

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Figure 1: The cell cycle inhibitor Whi5 is diluted by growth in G1.
Figure 2: Differential size-dependence of Cln3 and Whi5.
Figure 3: Whi5 concentration determines the rate at which cells progress through Start.
Figure 4: Cln3 and Whi5 concentrations determine the rate at which cells pass Start irrespective of ploidy and cell size.

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Acknowledgements

We thank O. Atay and J. Feldman for reagents, R. de Bruin, A. Gladfelter, M. Cyert, and M. Loog for comments on the manuscript, the Burroughs Wellcome Fund (CASI), the National Science Foundation (CAREER), National Institutes of Health training grant GM007276 (to J.J.T.), and Human Frontier Science Program (postdoctoral fellowships to K.M.S. and M.K.) for funding.

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Authors and Affiliations

Authors

Contributions

All authors designed experiments and wrote the manuscript; K.M.S., J.T. and M.K. performed experiments.

Corresponding author

Correspondence to Jan M. Skotheim.

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The authors declare no competing financial interests.

Extended data figures and tables

Extended Data Figure 1 Size distributions of strains expressing mCitrine fusion proteins or CLN3 mutant alleles.

a, Cell size distributions were measured in a Coulter counter for five strains expressing the indicated mCitrine fusion proteins from the endogenous locus and a WT control. These five strains were used in Fig. 1. All strains were grown on synthetic complete 2% glycerol, 1% ethanol. b, Size distributions measured using a Coulter counter for cln3Δ cells expressing CLN3 alleles from a CLN3 promoter integrated at the URA3 locus. See Methods for description of CLN3 mutant alleles. Cells were grown on synthetic complete 2% glucose.

Extended Data Figure 2 mCitrine–Cln3-11A is consistently nuclear during G1.

We see no evidence of a rapid re-localization of Cln3-11A into the nucleus at mid-G1 (n = 471). Nuclear signal measured and nucleus segmented as described in ref. 31. Thick line denotes mean; shaded area denotes s.e.m.

Extended Data Figure 3 Single-cell analysis of Whi5 dilution and synthesis.

a, We randomly selected 40 out of 339 single-cell traces that correspond to the data shown in Fig. 1f for display here. The relative change of Whi5 concentration during G1 is shown in grey (thin lines). Blue thick line shows the mean of all 339 cells. b, We randomly selected 40 out of 147 single-cell traces of Whi5 amount for display. Traces are aligned by bud emergence (t = 0). G1 (cell birth to bud emergence) is shown in red (mean of all 147 cells is shown in blue). S/G2/M (bud emergence to cytokinesis) is shown in green (mean is shown in black). Black crosses denote time points of full nuclear Whi5 exit, blue crosses denote time points of full nuclear Whi5 re-entry. The rate of synthesis of Whi5 in S/G2/M phase is 6.6-fold higher than in G1 phase. Eighty-nine per cent of total Whi5 in this experiment is synthesized in S/G2/M. c, d, Control for the effect of Whi5 localization on concentration measurements. Rapid relocalization of Whi5 at Start (c), and just before cytokinesis (d), does not affect concentration measurements. c, Mean relative change of cellular Whi5 concentration during G1 aligned by Start (50% nuclear Whi5 exit as determined from a logistic fit to the nuclear signal) and s.e.m. are shown in blue. The corresponding nuclear Whi5 signal is shown in black (mean and s.e.m.; nuclear signal measured and nucleus segmented as described in ref. 31); n = 320. d, Mean relative change of cellular Whi5 amount during S/G2/M in mother-bud pairs aligned by the time point of 50% Whi5 entry into the nucleus (as determined from a logistic fit to the nuclear signal) and s.e.m. are shown in blue. The corresponding nuclear Whi5 signal is shown in black (mean and s.e.m.; nuclear signal measured and nucleus segmented as described in ref. 31); n = 133. Cells express Whi5–mCitrine from the endogenous locus. Cells were grown on synthetic complete 2% glycerol, 1% ethanol.

Extended Data Figure 4 Whi5 concentration and synthesis rate.

Single-cell data corresponding to Fig. 2d, f. a, Whi5 concentration at cell birth is shown as a function of cell size for individual haploid (n = 339) and diploid (n = 385) cells. b, The rate of Whi5 synthesis as a function of cell size for each genotype as indicated. c, The rate of Whi5 synthesis as a function of cell size for bck2Δ strains expressing one, two, or four copies of WHI5–mCitrine (n = 353, 129 and 66, respectively). Bars denote means and s.e.m. d, Cell size distributions measured using a Coulter counter for the indicated strains. Cells were grown on synthetic complete 2% glycerol 1% ethanol.

Extended Data Figure 5 Whi5 and Cln3-11A stability.

a, Whi5–mCherry was expressed from a hormone-inducible promoter34 (LexApr-WHI5–mCherry), which was inactivated before the experiment (see Fig. 4d, e). The mean amount of Whi5–mCherry in G1-phase daughter cells was measured for each cell relative to its amount at t = 0. The distance between the black arrows indicates the s.e.m. We estimated a half-life >6 h for cells grown in synthetic complete 2% glucose. b, c, mCitrine–Cln3-11A was expressed from a MET25 promoter for (b) 1 h on SC-Met 2% glucose or (c) >4.5 h on SC-Met 2% glycerol 1% ethanol. Next, transcription was inactivated by switching cells to media composed of either (b) synthetic complete + 10× methionine 2% glucose or (c) synthetic complete + 10× methionine 2% glycerol 1% ethanol. So that the cells had sufficient time to inactivate protein synthesis, we began our protein half-life measurement 21 min (33 min for synthetic complete 2% glycerol 1% ethanol) after methionine addition. Data and exponential fit shown for daughter cells in G1 phase. Black line indicates means; grey area indicates s.e.m. The short half-life of Cln3-11A relative to the doubling time of cell volume, together with the constant concentration of Cln3-11A through G1 (Fig. 12), implies that Cln3-11A synthesis is proportional to cell volume. To see this, consider the time-dependent equation for changes in Cln3 concentration , where r is the rate of Cln3 protein synthesis (units of molecules × time−1), V is the cell volume, d is the degradation rate of Cln3 (units of time−1), and g is the rate of dilution of Cln3 due to cell growth (units of time−1). Since [Cln3] is constant, the left hand side = 0. Also, the half-life of Cln3-11A is larger than that of Cln3, but much smaller than the time it takes to double the cell volume (90 min on SCD, 180 min on synthetic complete 2% glycerol 1% ethanol), so that d g. Thus, the equation simplifies to so that the rate of Cln3 synthesis is proportional to cell volume, . This is consistent with our estimates of Cln3-11A synthesis rates shown in Fig. 2g.

Extended Data Figure 6 Linking Whi5 partitioning and synthesis to concentration at birth.

a, b, Daughter cells begin G1 with 1.49 ± 0.03-fold higher concentration of Whi5 than their mother cells. Shown is the ratio of Whi5–mCitrine concentrations (a) and amount (b) for daughter–mother pairs at the beginning of G1 phase. c, The duration of S/G2/M exhibits small, but significant size-dependence (P < 0.01). d, The total Whi5 concentration in first-generation mother cells just before cytokinesis decreases as a function of cell size. e, The size of daughter cells is correlated with the size of their mothers at the time of bud emergence. Cells were grown on synthetic complete 2% glycerol 1% ethanol; n = 151. Points denote single-cell data. Bars denote mean values and s.e.m.

Extended Data Figure 7 Size control and Whi5 synthesis in hcm1Δ cells.

a, Cell size distributions of WT (blue solid line) and hcm1Δ (red dashed line) cells, both carrying a WHI5–mCitrine allele, were measured in a Coulter counter. b, Size at Start as a function of birth size is shown for WT (n = 339) and hcm1Δ (n = 262) daughter cells. Bars denote mean and s.e.m. Note that small hcm1Δ cells exhibit poor size control (leftmost bin). c, Change in cellular Whi5 concentration during G1 for daughter cells. Cells are born at t = 0 and the change in concentration is shown with s.e.m. Blue denotes WT (see also Fig. 1f), red denotes hcm1Δ cells. d, Whi5 concentration at cell birth is shown as a function of cell size for WT (n = 339) and hcm1Δ (n = 284) daughter cells. e, The rate of Whi5 synthesis as a function of cell size is shown for WT (n = 151) and hcm1Δ (n = 106) cells. Bars denote mean values and s.e.m. Squares and circles denote single-cell data. f, The rate at which daughter cells progress through Start is shown as a function of Whi5–mCitrine concentration for WT (blue, n = 334) and hcm1Δ (red, n = 262) cells. Smooth lines are logistic regressions and the corresponding shaded areas denote 95% confidence intervals. Jagged lines connect means for binned data. Cells were grown on synthetic complete 2% glycerol 1% ethanol.

Extended Data Figure 8 Data supporting Cln3-11A-pulse experiments shown in Fig. 4.

a, Composite phase and fluorescence images of bck2Δ MET25pr–mCitrine–CLN3-11A haploid cells used in the pulse experiment shown in Fig. 4a–c. Cells were grown in the absence of methionine (MET25pr–mCitrine–CLN3-11A on). After 150 min (see image), cells were arrested in G1 by addition of 10× methionine to the SCD-Met medium. After variable lengths of arrest (3 h for the images shown here: see second image), a pulse of Cln3-11A was expressed by removal of methionine from the medium (1 h pulse for the experiment shown here: see third image). b, For daughter cells born during the experiment, we determined the maximum Cln3-11A concentration during the pulse, the corresponding cell volume, and whether the cell budded. Data from 22 different experiments were pooled. c, Cells were binned according to their size. For each 50 fl size bin, we used a logistic regression to calculate budding probability as a function of Cln3-11A peak concentration. d, For each size bin, the critical Cln3-11A concentration was determined as the amplitude of the pulse where 50% of the cells budded. A similar set of experiments was done for diploid cells; n = 1195 for haploids, and n = 405 for diploids. e, The bck2Δ MET25pr-CLN3-11A WHI5–mCitrine cells were arrested in G1 by addition of 10× methionine to the SCD-Met medium. Cells were tracked during the G1 arrest and the median Whi5–mCitrine concentration was measured as a function of size; n = 162 for haploids, and n = 148 for diploids. f, Single-cell data corresponding to Fig. 4e. MET25pr–mCitrine–CLN3-11A LexApr-WHI5–mCherry bck2Δ haploid cells were used for Cln3-11A pulse experiments to decouple cell size and Whi5 concentration. Maximum Cln3-11A concentration, corresponding cell size and Whi5 concentration, and whether or not the cell budded were determined in 18 independent experiments for a total of 471 daughter cells (see Methods). This generated a four-dimensional data set that we used build a logistic regression model. In this model, we predicted cell cycle entry (budding) using a linear combination of cell size, Whi5, and Cln3-11A. This resulted in a model based solely on Cln3-11A and Whi5. Thus, once Cln3-11A and Whi5 concentrations are measured, cell size yields no additional information. To visualize this result in Fig. 4e, we binned our data into six bins based on cell size (greater or less than 295 fl) and Whi5 concentration (<10, 10–25, and 25–40 arbitrary units). For each of these six bins, we performed a logistic regression to estimate the probability of entering the cell cycle as a function of the peak mCitrine–Cln3-11A concentration produced by the pulse.

Extended Data Figure 9 Ploidy increases S/G2/M duration and cell size at birth.

a, Histogram showing the duration of S/G2/M for haploid cells containing an extra copy of WHI5 (blue, n = 220) and WT diploid cells (red, n = 176). b, The size of daughter cells is shown as a function of the size of their mothers at the time of bud emergence. At a given mother size, diploid cells produce larger daughter cells. Cells were grown on synthetic complete 2% glycerol 1% ethanol. Bars denote means and s.e.m.

Extended Data Figure 10 Photobleaching control and size-dependent background subtraction.

a, The concentration of Whi5–mCitrine decreases during G1, as shown in Fig. 1f. Increasing the time between frames from 3 min (n = 339) to 10 min (n = 75) did not significantly affect our concentration measurements, indicating that photobleaching of the mCitrine fluorescent protein was not significant in our experiments. b, Auto-fluorescent signal in the mCitrine channel during G1 arrest for an unlabelled strain (bck2Δ MET25pr-CLN3) in two independent experiments (blue: n = 79; green: n = 89). Cells were grown on SCD + 10× methionine. Bars denote mean and s.e.m. for each size bin. The average of these two experiments was used for background subtraction in Fig. 4. A similar size-dependent background subtraction was performed for each experimental condition and for the mCherry red fluorescent channel. c, Cell-to-cell variation in background-subtracted auto-fluorescence concentration measured in an unlabelled cell. One of the experiments with the unlabelled WT strain used to determine the auto-fluorescence signal for the experiments shown in Fig. 1, 2, 3 is analysed the same way as experiments shown in Fig. 2a, b (n = 164). This illustrates cell-to-cell variation in auto-fluorescence. Owing to experiment-to-experiment variation, a single control experiment with an unlabelled strain will typically result in a mean ‘concentration’ of ±5 arbitrary units (compared with the average autofluorescence used for analysis), while cell-to-cell variability in autofluorescence within one experiment exhibits a standard deviation of 10 arbitrary units. Note that the arbritary units in a and b are not comparable, because different settings were used to export the microscopy data for the pulse experiments shown in Fig. 4.

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Schmoller, K., Turner, J., Kõivomägi, M. et al. Dilution of the cell cycle inhibitor Whi5 controls budding-yeast cell size. Nature 526, 268–272 (2015). https://doi.org/10.1038/nature14908

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