Proteostasis collapse, a hallmark of aging, hinders the chaperone-Start network and arrests cells in G1
- CSIC, Spain
- King’s College London, United Kingdom
- King's College London, United Kingdom
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, France
- Université de Strasbourg, France
- Pázmány Péter Catholic University, Hungary
- Universitat Internacional de Catalunya, Spain
Figures
Figure 1 with 1 supplement
Yeast mother cells die mostly in G1 with low nuclear levels of cyclin Cln3.
(A) A yeast mother cell (arrow) expressing Whi5-GFP during aging at the G1 phase of indicated cycles before death. (B) Interdivision times (mean ±CL, n = 50) aligned to the last budding event. (C) …
-
Figure 1—source data 1
Yeast mother cells die mostly in G1 with low nuclear levels of cyclin Cln3.
- https://doi.org/10.7554/eLife.48240.004
Figure 1—figure supplement 1
Yeast mother cells delay G1 progression with no major effects in growth during aging.
(A) Cell labeling and MEP activation steps used for FACS analysis. (B) FACS distributions of cells labeled as in A after 20 hr and 35 hr of MEP induction to identify aging mother cells (circled) and …
Figure 2 with 2 supplements
Mobility and spatio-temporal coincidence of Ssa1 and Ydj1 are reduced in aging cells.
(A) Levels of Ssa1-mCh, Ydj1-GFP and Hsp104-mCh (mean ±CL, n = 50) in aging cells aligned at the last budding event. (B) FLIP analysis of Ssa1-GFP in representative young and old (MEP-aged) cells. (C…
-
Figure 2—source data 1
Mobility and spatio-temporal coincidence of Ssa1 and Ydj1 are reduced in aging cells.
- https://doi.org/10.7554/eLife.48240.010
Figure 2—figure supplement 1
Chaperone availability is compromised in aging cells.
(A) Distribution by Hsp104 levels of young and old (MEP-aged) cells. (B) Nuclear and cellular mCtr-Cln311A levels (mean ±CL) in young cells after AZC addition. A representative cell expressing …
Figure 2—figure supplement 2
Correction of the mobility index obtained by FLIP as a function of cell size.
BF305 (cln1,2 GALp-CLN3) cells expressing GFP from endogenous sequences were grown in glucose for different periods of time to obtain a large range of cell volumes. The plot shows the obtained raw …
Figure 3 with 1 supplement
Firefly luciferase aggregates become visible during the last cycle before cell death.
(A) Representative images of FFL-GFP expressed from a regulatable promoter in young and old (MEP-aged) cells. (B) Percentage (±CL, n = 230) of young and old (MEP-aged) cells with FFL-GFP foci. (C) …
-
Figure 3—source data 1
Firefly luciferase aggregates become visible during the last cycle before cell death.
- https://doi.org/10.7554/eLife.48240.013
Figure 3—figure supplement 1
FFL-GFP and Hsp104 co-localization in heat-shocked and aging cells.
(A) Representative images of heat-shocked young or aging cells expressing FFL-GFP and Hsp104-mCh. (B) Distribution of FFL-GFP/Hsp104-mCh co-localization percentages in heat-shocked and aging cells. …
Figure 4 with 3 supplements
Asymmetric aggregate inheritance predicts a decrease in chaperone availability and a G1 arrest in aging cells.
(A) Scheme of the integrative mathematical model with chaperones playing concurrent roles in proteostasis and Start. (B–E) Predicted aggregate protein (B), available chaperone (C), and free folded …
-
Figure 4—source data 1
Asymmetric aggregate inheritance predicts a decrease in chaperone availability and a G1 arrest in aging cells.
- https://doi.org/10.7554/eLife.48240.018
Figure 4—figure supplement 1
Wiring diagram of the integrative mathematical model.
Wiring diagram of the model to describe the interaction between a minimal Start network and the protein folding/aggregation pathway. Chaperones can bind to all forms of unfolded and misfolded …
Figure 4—figure supplement 2
The integrative model predicts a decrease in chaperone availability and free Cln3 at the first generation after the SEP.
(A) Interdivision times obtained by simulations. Independent runs were aligned at the generation in which the interdivision time was maintained over a fixed threshold afterwards so as to simulate …
Figure 4—figure supplement 3
Lifespan of mutants and growth conditions as predicted by the integrative mathematical model.
(A) Survival curves predicted for the indicated genotypes of cells (n = 75). (B) Survival curves predicted for wild-type fast-, medium- and slow-growing cells (n = 75). (C) Survival curves predicted …
Figure 5 with 1 supplement
Enforced expression of Cln3 increases lifespan in a chaperone-dependent manner.
(A) Survival curves of control and CLN3 overexpressing cells (n > 300). Curves predicted by the integrative model in Figure 4A are also shown (inset). (B) Budding volume distributions (n > 250) of …
-
Figure 5—source data 1
Enforced expression of Cln3 increases lifespan in a chaperone-dependent manner.
- https://doi.org/10.7554/eLife.48240.021
Figure 5—figure supplement 1
Lifespan analysis by MEP-induced microcolony size.
(A) Schematic of a microcolony formed by the accumulation of G2-arrested daughter cells (orange) produced after MEP induction by a single mother cell (M, green) during successive division cycles. (B)…
Figure 6 with 1 supplement
Protein aggregation hinders chaperone mobility and nuclear accumulation of Cln3 in young cells.
(A) Representative young cells expressing the prion-forming domain (PFD)-mCh and either Ssa1-GFP or Ydj1-GFP. (B) Mobility of Ssa1-GFP, Ydj1-GFP and GFP in young cells expressing control CD or …
-
Figure 6—source data 1
Protein aggregation hinders chaperone mobility and nuclear accumulation of Cln3 in young cells.
- https://doi.org/10.7554/eLife.48240.024
Figure 6—figure supplement 1
Enforced protein aggregation and CLN3 overexpression effects in young cells.
(A) PAPA-score and fold-index plots as a function of amino acid position in the indicated peptides. (B) Western blot analysis of the indicated protein fusions after gel electrophoresis under full …
Figure 7 with 1 supplement
Lifespan shortening by protein aggregation can be overcome by enforced expression of chaperones or Cln3.
(A) Lifespan effects of CD or PFD expression in young cells in the CLiC microfluidics chamber (n = 50). Cells with PFD aggregates at the initial time point are indicated (*). Median ±Q values are …
-
Figure 7—source data 1
Lifespan shortening by protein aggregation can be overcome by enforced expression of chaperones or Cln3.
- https://doi.org/10.7554/eLife.48240.027
Figure 7—figure supplement 1
Enforced protein aggregation increases levels of Hsp104 and budding size during aging.
(A) Distribution by Hsp104 levels of young cells displaying PFD aggregates or expressing CD as control. (B) Mean budding volume (n0 = 50) during the lifespan of cells expressing PFD or CD.
Videos
Video 1
Movie of a representative Whi5-GFP (green) Hsp104-mCh (red) cell in the CLiC microfluidic chamber.
Images were taken every 10 min. The frame where the last budding event takes place is indicated.
Video 2
Movie of a representative mCitrine-Cln311A (yellow) cell in the CLiC microfluidic chamber.
Images were taken every 10 min. The frame where the last budding event takes place is indicated.
Tables
Key resources table
| Reagent type or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background (Saccharomyces cerevisiae) | BY4741 | Lab stock | MATa his3-Δ1 leu2Δ0 met15Δ0 ura3Δ0, from S288C | |
| Strain, strain background (S. cerevisiae) | MAG248 | This work | MATa his3-Δ1 leu2Δ0 met15Δ0 ura3Δ0 NAT::TEFp-GFP, from S288C | |
| Strain, strain background (S. cerevisiae) | MAG261 | (Moreno et al., 2019) | MATa his3-Δ1 leu2Δ0 met15Δ0 ura3Δ0 YDJ1-GFP-FS::HIS3, from S288C | |
| Strain, strain background (S. cerevisiae) | MAG1078 | This work | MATa his3-Δ1 leu2Δ0 met15Δ0 ura3Δ0 YDJ1-GFP-FS::HIS3 SSA1-mCherry::HYG, from S288C | |
| Strain, strain background (S. cerevisiae) | MAG1689 | This work | MATa his3-Δ1 leu2Δ0 met15Δ0 ura3Δ0 SSA1-GFP::HIS3 OLE1-mCherry::GEN, from S288C | |
| Strain, strain background (S. cerevisiae) | YOR083W-GFP | Lab stock | MATa his3-Δ1 leu2Δ0 met15Δ0 ura3Δ0 WHI5-yGFP::HIS3, from S288C | |
| Strain, strain background (S. cerevisiae) | CML128 | (Gallego et al., 1997) | MATa leu2-3,112 ura3-52 trp1-1 his4-1 canr, from 1788 | |
| Strain, strain background (S. cerevisiae) | MAG1077 | This work | MATa leu2-3,112 ura3-52 trp1-1 his4-1 canr WHI5-sGFP::GEN HSP104-mCherry::HYG, from 1788 | |
| Strain, strain background (S. cerevisiae) | MAG1512 | (Moreno et al., 2019) | MATa leu2-3,112 ura3-52 trp1-1 his4-1 canr NAT::TEF1p-mCherry, from 1788 | |
| Strain, strain background (S. cerevisiae) | MAG1767 | This work | MATa leu2-3,112 ura3-52 trp1-1 his4-1 canr mCitrine-CLN3(11A)::NAT, from 1788 | |
| Strain, strain background (S. cerevisiae) | MAG1767 | This work | MATa leu2-3,112 ura3-52 trp1-1 his4-1 canr HSP104-mCherry::HYG, from 1788 | |
| Strain, strain background (S. cerevisiae) | UCC5179 | (Lindstrom and Gottschling, 2009) | MATa ade2::hisG his3 leu2 lys2 ura3Δ0 trp1Δ63 hoΔ::SCW11pr-Cre-EBD78-NatMX loxP-UBC9-loxP-LEU2 loxP-CDC20-intron-loxP-HPHMX, from S288C | |
| Strain, strain background (S. cerevisiae) | MAG1013 | This work | MATa ade2::hisG his3 leu2 lys2 ura3Δ0 trp1Δ63 hoΔ::SCW11pr-Cre-EBD78-NatMX loxP-UBC9-loxP-LEU2 loxP-CDC20-intron-loxP-HPHMX (ARS-CEN URA3 HSP104 SSA1 YDJ1 HSC82 CDC37 CDC48 UFD1 NPL1), from S288C | |
| Strain, strain background (S. cerevisiae) | MAG1095 | This work | MATa ade2::hisG his3 leu2 lys2 ura3Δ0 trp1Δ63 hoΔ::SCW11pr-Cre-EBD78-NatMX loxP-UBC9-loxP-LEU2 loxP-CDC20-intron-loxP-HPHMX YDJ1-GFP-FS::HIS3, from S288C | |
| Strain, strain background (S. cerevisiae) | MAG1096 | This work | MATa ade2::hisG his3 leu2 lys2 ura3Δ0 trp1Δ63 hoΔ::SCW11pr-Cre-EBD78-NatMX loxP-UBC9-loxP-LEU2 loxP-CDC20-intron-loxP-HPHMX SSA1-GFP::HIS3, from S288C | |
| Strain, strain background (S. cerevisiae) | MAG1578 | This work | MATa ade2::hisG his3 leu2 lys2 ura3Δ0 trp1Δ63 hoΔ::SCW11pr-Cre-EBD78-NatMX loxP-UBC9 -loxP-LEU2 loxP-CDC20-intron-loxP-HPHMX ydj1Δ::GEN, from S288C | |
| Strain, strain background (S. cerevisiae) | MAG1745 | This work | MATa ade2::hisG his3 leu2 lys2 ura3Δ0 trp1Δ63 hoΔ::SCW11pr-Cre-EBD78-NatMX loxP-UBC9-loxP-LEU2 loxP-CDC20-intron-loxP-HPHMX YDJ1-GFP-FS::HIS3 SSA1-mCherry::KAN, from S288C | |
| Strain, strain background (S. cerevisiae) | MAG1952 | This work | MATa ade2::hisG his3 leu2 lys2 ura3Δ0 trp1Δ63 hoΔ:: SCW11pr-Cre-EBD78-NatMX loxP-UBC9-loxP-LEU2 loxP-CDC20-intron-loxP-HPHMX Hsp104-mCherry::GEN, from S288C | |
| Strain, strain background (S. cerevisiae) | MAG2060 | This work | MATa ade2::hisG his3 leu2 lys2 ura3Δ0 trp1Δ63 hoΔ::SCW11pr-Cre-EBD78-NatMX loxP-UBC9-loxP-LEU2 loxP-CDC20-intron-loxP-HPHMX GAL1p-CLN3 URA3::TRP1, from S288C | |
| Strain, strain background (S. cerevisiae) | MAG1253 | This work | MATa ade2::hisG his3 leu2 lys2 ura3Δ0 trp1Δ63 hoΔ::SCW11pr-Cre-EBD78-NatMX loxP-UBC9-loxP-LEU2 loxP-CDC20-intron-loxP-HPHMX trp1Δ63::SCW11pr-Cre-EBD78 -KanMX4, from S288C | |
| Strain, strain background (S. cerevisiae) | MAG1569 | This work | MATa ade2::hisG his3 leu2 lys2 ura3Δ0 trp1Δ63 hoΔ:: SCW11pr-Cre-EBD78-NatMX loxP-UBC9-loxP-LEU2 loxP-CDC20-intron-loxP-HPHMX trp1Δ63::SCW11pr-Cre-EBD78- KanMX4 CLB2-GFP::HIS3MX, from S288C | |
| Strain, strain background (S. cerevisiae) | MAG1576 | This work | MATa ade2::hisG his3 leu2 lys2 ura3Δ0 trp1Δ63 hoΔ::SCW11pr-Cre-EBD78-NatMX loxP-UBC9-loxP-LEU2 loxP-CDC20-intron-loxP-HPHMX trp1Δ63::SCW11pr-Cre-EBD78-KanMX4 CLB2-GFP::HIS3 GALp-CLN3-URA3::TRP1, from S288C | |
| Strain, strain background (S. cerevisiae) | MAG1795 | This work | MATa ade2::hisG his3 leu2 lys2 ura3Δ0 trp1Δ63 hoΔ::SCW11pr-Cre-EBD78-NatMX loxP-UBC9-loxP-LEU2 loxP-CDC20-intron-loxP-HPHMX trp1Δ63::SCW11pr-Cre-EBD78-KanMX4 CLB2-GFP::HIS3MX Δcln3::URA3MX, from S288C | |
| Strain, strain background (S. cerevisiae) | W303-1A | Lab stock | MATa ade2-1 trp1-1 leu2-3,111 his3-11,75 ura3 can1-100, from W303 | |
| Strain, strain background (S. cerevisiae) | KSY083-5 | (Schmoller et al., 2015) | MATa ADE2 trp1-1 leu2-3,111 his3-11,75 ura3 can1-100 mCitrine-CLN3-11A::NAT | |
| Strain, strain background (S. cerevisiae) | MAG876 | This work | MATa ade2-1 trp1-1 leu2-3,111 his3-11,75 ura3 can1-100 SSA1-GFP::HIS3, from W303 | |
| Recombinant DNA reagent | YCplac22 | Lab stock | Centromeric TRP1 vector | |
| Recombinant DNA reagent | YCplac33 | Lab stock | Centromeric URA3 vector | |
| Recombinant DNA reagent | YCpGAL | Lab stock | GAL1/10 p in YCplac22 | |
| Recombinant DNA reagent | p425MET25-FFL-GFP | (Abrams and Morano, 2013) | MET25p-FFL-GFP in pRS425 | |
| Recombinant DNA reagent | pCYC87 | Lab stock | GAL1/10p-CLN3-3HA in YCplac33 | |
| Recombinant DNA reagent | pMAG438 | (Moreno et al., 2019) | SSA1 YDJ1 HSC82 CDC37 CDC48 UFD1 NPL4 in YAC URA3 | |
| Recombinant DNA reagent | pMAG600 | This work | GAL1/10p-Sup35Nm3-GFP in YCplac22 | |
| Recombinant DNA reagent | pMAG602 | This work | GAL1/10p-PFD-GFP in YCplac22 | |
| Recombinant DNA reagent | pMAG604 | This work | GAL1/10p-CD-GFP in YCplac22 | |
| Recombinant DNA reagent | pMAG605 | This work | GAL1/10p-Sup35N-GFP in YCplac22 | |
| Recombinant DNA reagent | pMAG610 | This work | GAL1/10p-GFP in YCplac22 | |
| Recombinant DNA reagent | pMAG633 | This work | GAL1/10p-PFD-mCh in YCplac33 | |
| Recombinant DNA reagent | pMAG634 | This work | GAL1/10p-CD-mCh in YCplac33 | |
| Recombinant DNA reagent | pMAG1182 | This work | GAL1p-SSA1 GAL10p-YDJ1 in YCplac33 | |
| Recombinant DNA reagent | pMAG1228 | Lab stock | TE1Fp-GFP in YCplac33 | |
| Antibody | αGFP (Mouse monoclonal) | Merck | G1546 | |
| Chemical compound, drug | Azetidine-2-carboxilic acid | Sigma-Aldrich | A0760 | |
| Chemical compound, drug | β-estradiol | Sigma-Aldrich | E2758 | |
| Software, algorithm | MODEL1901210001 | This work | BioModels database | |
| Software, algorithm | ImageJ | Wayne Rasband, NIH | imagej.nih.gov/ij/download.html | |
| Software, algorithm | BudJ | (Ferrezuelo et al., 2012) | ibmb.csic.es/groups/spatial-control-of-cell-cycle-entry | |
| Software, algorithm | CoinRICSJ | (Moreno and Aldea, 2019) | ibmb.csic.es/groups/spatial-control-of-cell-cycle-entry | |
| Software, algorithm | RICS analysis plugins | Jay Unruh, Stowers Institute | research.stowers.org/imagejplugins | |
| Software, algorithm | Microcolony_size.ijm | This work | ibmb.csic.es/groups/spatial-control-of-cell-cycle-entry | |
| Software, algorithm | PAPA | (Toombs et al., 2012) | combi.cs.colostate.edu/supplements/papa |
Additional files
-
Supplementary file 1
Chemical reactions of the integrative mathematical model.
- https://doi.org/10.7554/eLife.48240.028
-
Supplementary file 2
Parameter set of the integrative mathematical model.
- https://doi.org/10.7554/eLife.48240.029
-
Supplementary file 3
Parameter modifications to simulate different genotypes or relevant physiological conditions.
- https://doi.org/10.7554/eLife.48240.030
-
Transparent reporting form
- https://doi.org/10.7554/eLife.48240.031
