Reliable cell cycle commitment in budding yeast is ensured by signal integration
- Peking University, China
- China Three Gorges University, China
Figures
Figure 1 with 9 supplements
G1 length is inversely proportional to the average Cln3.
(A) Schematic of the Start regulatory network in wild-type (upper panel) and in strains used in this study (lower panel). (B) G1 length is defined as the time interval during which Whi5 resides in …
Figure 1—figure supplement 1
Definition of G1 length.
(A) Nuclear Whi5-tdTomato intensity in a representative single cell; open circle shows the raw data; solid red line shows the spline smoothing. (B) The first derivative of the smoothed data; pink …
Figure 1—figure supplement 2
The promoter GlacSpr is repressed by LacI and induced by IPTG.
(A) The sequence of GlacSpr. (B) The dose–response curve of GlacSpr. The transcriptional activity of GlacSpr in the OFF state is a little higher than GAL1pr in glucose, as the result, GlacSpr is not …
Figure 1—figure supplement 3
The homologous structure of Cln3-Cdk1 complex.
Cln3 is shown in dim grey and Cdk1 in light grey. The Cln3 in this model only contains amino acid 70-312. The hydrophobic patch is indicated in red, while the interface to Cdk1 is indicated in …
Figure 1—figure supplement 4
Cell size and GFP brightness of selected Cln3 mutants under full induction.
https://doi.org/10.7554/eLife.03977.007
Figure 1—figure supplement 5
Size control is maintained with the mutant Cln3, Cln3*.
(A) The correlation between birth size and GFP-GFP-Cln3* intensity under full induction, Pearson Coefficient is 0.75. (B) The correlation between birth size and G1 length under full induction, …
Figure 1—figure supplement 6
The correlation between G1 length and average Cln3 fluorescence intensity in mother and daughter cells (YCT2003).
https://doi.org/10.7554/eLife.03977.009
Figure 1—figure supplement 7
The correlation between G1 length and average Cln3 fluorescence intensity with different Cln3 signals: CLNR108A (YCT2003) and CLN3D166A (YCT2004).
https://doi.org/10.7554/eLife.03977.010
Figure 1—figure supplement 8
The correlation between G1 length and average Cln3 fluorescence intensity with different G1 length markers: WHI5-tdTomato (YCT2003) and MCM-mCherry (YCT2010).
https://doi.org/10.7554/eLife.03977.011
Figure 1—figure supplement 9
G1 length is inversely proportional to averaged Cln3 intensity without deducting asymptotes.
Open circle denotes raw data in log–log scale; closed square denotes the binned data; solid line is the best linear fit of the middle part; error bars are standard deviation.
Figure 2 with 3 supplements
The integration of Cln3 reduces the variability of G1 length.
(A) Representative Cln3 profiles in single cells. Each color represents simulation of a single cell. In the Instantaneous Model, Start is triggered at the time TG1 (vertical blue dash line) when …
-
Figure 2—source data 1
Meaning, value and reference of the parameters to generate Figure 2.
- https://doi.org/10.7554/eLife.03977.014
Figure 2—figure supplement 1
Stochastic simulation of Cln3 profile and Start triggering process with nucleus volume increase.
(A) Representative Cln3 concentration profiles in single cells. Each color represents simulation of a single cell. (B–C) The distributions of TG1 in the Instantaneous (blue) and Integration (red) …
Figure 2—figure supplement 2
The Instantaneous Model fails with the Cln3 profiles measured in experiment.
(A) Schematic plot of the test. The test is considered a pass if the timing of Start is near the timing of Cln3 peak by the specified tolerance value. The Cln3 profiles are from the real data. Open …
Figure 2—figure supplement 3
Measuring the memory length through Whi5 nuclear entry when Cdk1 is inactivated.
(A) Dynamics of nuclear Whi5 intensity in a representative single cell (YCT2016). 50 μM 1-NM-PP-1 was added to the medium to inhibit Cdk1 activity at 30 min. Open circles are the raw data; solid …
Figure 3 with 2 supplements
Whi5 acts as the integrator of Cln3-Cdk1 activity.
Correlations between G1 length and the average Cln3 fluorescence in log–log scale in (A) cln3Δ bck2Δ whi5Δ strain (Strain YCT2008) (blue), (B) cln3Δ bck2Δ 2XWHI5 strain (Strain YCT2007) (red), (D) cl…
Figure 3—figure supplement 1
Correlations between G1 length and the average Cln3 fluorescence in (A) cln3Δ bck2Δ whi5Δ strain (Strain YCT2008) (blue), (B) cln3Δ bck2Δ 2XWHI5 strain (Strain YCT2007) (red), (C) cln3Δ bck2Δ CDC14 overexpressing strain (Strain YCT2009) (purple), (D) cln3Δ bck2Δ cln1Δ strain (Strain YCT2013) (green), (E) cln3Δ bck2Δ cln2Δ (Strain YCT2014) (pink) and (F) cln3Δ BCK2+ strain (YCT2015) (wine), in comparison with in cln3Δ bck2Δ strain (Strain YCT2003) (black).
Each dot represents a measurement from one cell cycle event; error bars indicate standard deviation; solid lines are simulation results from the ODE model (Supplementary file 1B). Note we didn't fit …
Figure 3—figure supplement 2
Variation of G1 length in low Cln3 region is due to the variance in Whi5tot.
(A) The Cln3-TG1 correlation indicating Whi5tot intensity of each cell by colors. (B) Whi5tot distribution of cells with Cln3 intensity less than 300. Red line is the Gaussian envelop. (C) Average …
Figure 4 with 6 supplements
Cells modulate Whi5tot concentration to coordinate cell division with nutrient conditions.
(A) Whi5tot intensity is negatively correlated with growth rate in various nutrient conditions (Strain YCT2001). (B–C) G1 length is positively correlated with Whi5tot intensity for mothers (B) and …
-
Figure 4—source data 1
(A)The growth rates and Whi5tot intensities in different nutrient conditions.
(B) The Whi5tot intensities and G1 lengths in different nutrient conditions.
- https://doi.org/10.7554/eLife.03977.022
Figure 4—figure supplement 1
The correlations between Cln3 concentration, Whi5tot intensity and G1 length in suboptimal nutrient conditions.
(A, D and G) The correlations between G1 length and the average Cln3 fluorescence in 2% raffinose (A), limited nitrogen (D) and 0.05% glucose (G), comparing with in 2% glucose (Strain YCT2003). Each …
Figure 4—figure supplement 2
The correlations between the integral A and Whi5tot fluorescence intensity in 2% glucose (A), 2% raffinose (B), limited nitrogen (C) and 0.05% glucose (D) (Strain YCT2003).
https://doi.org/10.7554/eLife.03977.024
Figure 4—figure supplement 3
The inverse correlations in raffinose comparing with in glucose with the MCM marker as a measure of G1 length (YCT2010).
(A and B) The Cln3-TG1 correlations with the MCM marker as a measure of G1 length in glucose and raffinose in linear (A) and log–log scale (B). The solid lines in B are linear fits of the binned …
Figure 4—figure supplement 4
The correlation between growth rate and Whi5tot fluorescence intensity in single cells in different nutrient conditions (YCT2001).
https://doi.org/10.7554/eLife.03977.026
Figure 4—figure supplement 5
The correlation between Whi5tot intensity and G1 length in single cells in different nutrient conditions in mother (A) and daughter (B) cells (YCT2001).
Legend is the same as in Figure 4—figure supplement 4.
Figure 4—figure supplement 6
The adaptation of Whi5 and G1 length after nutrient transitions (YCT2001).
(A–E) The raw data of Whi5 dynamics and G1 length from representative single cells in constant 2% (A), constant 0.01% (B), 0.01–2% (C) and 2–0.01% (D–E) glucose media; 0.01% glucose period is marked …
Author response image 1
The Instantaneous Model fails with the Cln3 profiles measured in experiment. (A) Schematic plot of the test. The test is considered a pass if the timing of Start is near the timing of Cln3 peak by …
Additional files
-
Supplementary file 1
(A) Mathematic model of Whi5 kinetics. (B) ODE model of the Start network.
- https://doi.org/10.7554/eLife.03977.029
-
Supplementary file 2
(A) Yeast Strain list. (B) Plasmid list.
- https://doi.org/10.7554/eLife.03977.030
