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Elevated Proteasome Capacity Extends Replicative Lifespan in Saccharomyces cerevisiae

Kruegel, Undine, Robison, Brett, Dange, Thomas, Kahlert, Günther, Delaney, Joe R., Kotireddy, Soumya, Tsuchiya, Mitsuhiro, Tsuchiyama, Scott, Murakami, Christopher J., Schleit, Jennifer, Sutphin, George, Carr, Daniel, Tar, Krisztina, Dittmar, Gunnar, Kaeberlein, Matt, Kennedy, Brian K., Schmidt, Marion·2011·PLoS Genetics
DOI 10.1371/journal.pgen.1002253PMC PMC3169524
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Figure 1 Replicative lifespan in cells with proteasome-related gene mutations or deletions. Mean lifespan and cell counts are shown in parenthesis. (A) Proteasome ATPase mutants. Survival curves for cells with individually inactivated proteasomal ATPases (SUB62 strain background). (B) Viable proteasome-related gene deletions. Survival curves for cells deleted for the proteasome maturation factor UMP1, the proteasome associated deubiquitinating enzyme UBP6, the only non-essential CP subunit PRE9, and the proteasome-related transcription factor RPN4 (BY strain background). (C) and (D) RLS lifespan extension in ubr2Δ (C) and mub1Δ (D) cells. Survival curves of cells deleted for RPN4, UBR2, or RPN4 UBR2 (C) or RPN4, MUB1, or RPN4 MUB1 (D). (E) Deletion of TOM1 causes RLS extension independent of RPN4. Survival curves of cells deleted for RPN4, TOM1, or RPN4 TOM1. (F) Lifespan extension induced by loss of UBR2 requires functional proteasomes. Survival curves of cells deleted for PRE9, UBR2, or PRE9 UBR2. A statistical analysis of the data is summarized in Table S2.
Figure 1 Replicative lifespan in cells with proteasome-related gene mutations or deletions. Mean lifespan and cell counts are shown in parenthesis. (A) Proteasome ATPase mutants. Survival curves for cells with individually inactivated proteasomal ATPases (SUB62 strain background). (B) Viable proteasome-related gene deletions. Survival curves for cells deleted for the proteasome maturation factor UMP1, the proteasome associated deubiquitinating enzyme UBP6, the only non-essential CP subunit PRE9, and the proteasome-related transcription factor RPN4 (BY strain background). (C) and (D) RLS lifespan extension in ubr2Δ (C) and mub1Δ (D) cells. Survival curves of cells deleted for RPN4, UBR2, or RPN4 UBR2 (C) or RPN4, MUB1, or RPN4 MUB1 (D). (E) Deletion of TOM1 causes RLS extension independent of RPN4. Survival curves of cells deleted for RPN4, TOM1, or RPN4 TOM1. (F) Lifespan extension induced by loss of UBR2 requires functional proteasomes. Survival curves of cells deleted for PRE9, UBR2, or PRE9 UBR2. A statistical analysis of the data is summarized in Table S2.CC BY · PubMed Central
Figure 2 Extended proteasome biogenesis and subunit abundance upon loss of UBR2 or MUB1. (A) Relative quantification of Rpn4 abundance in WT and ubr2Δ cells via SRM (selected reaction monitoring) (B) Expression of four proteasomal genes in cells deleted for RPN4, UBR2, MUB1 or RPN4 UBR2 and RPN4 MUB1. The mRNA levels of two genes encoding proteasome CP subunits (PRE1 and PRE6) or RP subunits (RPN11 and RPT2) were tested by qRT-PCR and presented relative to the housekeeping gene PRP8 as the mean +/− SEM of three independent experiments. P-values represent the statistical significance relative to WT gene expression. * = P-value of <0.05 ** = P-value of <0.01 *** = P-value of <0.001. A complete table of P-values can be found in Figure S1. (C) Elevated proteasome subunit levels in ubr2Δ and mub1Δ. Normalized lysates of the strains indicated were subjected to SDS-PAGE and immuno-blotting with antibodies directed against CP (anti-CP and anti-α7) or RP subunits (anti-Rpn8 and anti-Rpn5). The position of marker proteins is indicated to the left. (D) Unfractionated lysates of the strains indicated were subjected to native gel electrophoresis followed by an in-gel activity assay with the fluorogenic proteasome-specific substrate Suc-LLVY-AMC. The fluorogenic signals shown represent proteasome holocomplex activity. RP2-CP denotes proteasome core particles (CP) flanked on both sides with regulatory particles (RP), Blm10-CP-RP a proteasome hybrid complex with the CP flanked on one side with the proteasome activator Blm10 and on the other side with RP, RP-CP a singly RP capped CP.
Figure 2 Extended proteasome biogenesis and subunit abundance upon loss of UBR2 or MUB1. (A) Relative quantification of Rpn4 abundance in WT and ubr2Δ cells via SRM (selected reaction monitoring) (B) Expression of four proteasomal genes in cells deleted for RPN4, UBR2, MUB1 or RPN4 UBR2 and RPN4 MUB1. The mRNA levels of two genes encoding proteasome CP subunits (PRE1 and PRE6) or RP subunits (RPN11 and RPT2) were tested by qRT-PCR and presented relative to the housekeeping gene PRP8 as the mean +/− SEM of three independent experiments. P-values represent the statistical significance relative to WT gene expression. * = P-value of <0.05 ** = P-value of <0.01 *** = P-value of <0.001. A complete table of P-values can be found in Figure S1. (C) Elevated proteasome subunit levels in ubr2Δ and mub1Δ. Normalized lysates of the strains indicated were subjected to SDS-PAGE and immuno-blotting with antibodies directed against CP (anti-CP and anti-α7) or RP subunits (anti-Rpn8 and anti-Rpn5). The position of marker proteins is indicated to the left. (D) Unfractionated lysates of the strains indicated were subjected to native gel electrophoresis followed by an in-gel activity assay with the fluorogenic proteasome-specific substrate Suc-LLVY-AMC. The fluorogenic signals shown represent proteasome holocomplex activity. RP2-CP denotes proteasome core particles (CP) flanked on both sides with regulatory particles (RP), Blm10-CP-RP a proteasome hybrid complex with the CP flanked on one side with the proteasome activator Blm10 and on the other side with RP, RP-CP a singly RP capped CP.CC BY · PubMed Central
Figure 3 Elevated peptidase activity of proteasome holocomplexes in ubr2Δ and mub1Δ cells. (A) Elevated cellular proteasomal peptidase activity in ubr2Δ and mub1Δ strains. The three distinct proteasomal peptidase activities of the strains indicated were tested with 50 µg of total protein in the presence of 100 µM of the fluorogenic substrates Suc-LLVY-AMC (chymotrypsin-like activity), Boc-RLR-AMC (trypsin-like activity) and Ac-nLPnLD-AMC (caspase activity). The reactions were recorded in the absence or presence of 50 µg/ml of the proteasome inhibitor MG132 (Figure S2) to demonstrate specificity of the reactions. The mean +/− SEM of three technical replicates is presented. (B) Growth is unaffected in cells with increased proteasome abundance. Growth curves of WT, rpn4Δ, ubr2Δ, mub1Δ, rpn4Δ ubr2Δ and rpn4Δ mub1Δ strains were recorded in a Bioscreen C MB machine in YPD at 30°C. Doubling times are listed in Figure S3.
Figure 3 Elevated peptidase activity of proteasome holocomplexes in ubr2Δ and mub1Δ cells. (A) Elevated cellular proteasomal peptidase activity in ubr2Δ and mub1Δ strains. The three distinct proteasomal peptidase activities of the strains indicated were tested with 50 µg of total protein in the presence of 100 µM of the fluorogenic substrates Suc-LLVY-AMC (chymotrypsin-like activity), Boc-RLR-AMC (trypsin-like activity) and Ac-nLPnLD-AMC (caspase activity). The reactions were recorded in the absence or presence of 50 µg/ml of the proteasome inhibitor MG132 (Figure S2) to demonstrate specificity of the reactions. The mean +/− SEM of three technical replicates is presented. (B) Growth is unaffected in cells with increased proteasome abundance. Growth curves of WT, rpn4Δ, ubr2Δ, mub1Δ, rpn4Δ ubr2Δ and rpn4Δ mub1Δ strains were recorded in a Bioscreen C MB machine in YPD at 30°C. Doubling times are listed in Figure S3.CC BY · PubMed Central
Figure 4 Proteasome-mediated lifespan extension is independent of the oxidative stress response. (A) Survival curves of cells deleted for UBR2, YAP1 or UBR2 YAP1 (left panel) or MUB1, YAP1, or MUB1 YAP1 (right panel). Mean RLS and cell counts are shown in parenthesis. A statistical analysis of the data is summarized in Table S2. (B) Expression of Rpn4 target genes PRE6 and YAP1 as well as four Yap1 target genes SOD2, TRR1, GRX2, and TRX2 in cells deleted for RPN4, UBR2, or RPN4 UBR2. The mRNA levels were tested by qRT-PCR and presented relative to the housekeeping gene PRP8 as the mean +/− SEM of three independent experiments. P-values represent the statistical significance relative to WT gene expression. * = P-value of <0.05, ** = P-value of <0.01, ns = not significant.
Figure 4 Proteasome-mediated lifespan extension is independent of the oxidative stress response. (A) Survival curves of cells deleted for UBR2, YAP1 or UBR2 YAP1 (left panel) or MUB1, YAP1, or MUB1 YAP1 (right panel). Mean RLS and cell counts are shown in parenthesis. A statistical analysis of the data is summarized in Table S2. (B) Expression of Rpn4 target genes PRE6 and YAP1 as well as four Yap1 target genes SOD2, TRR1, GRX2, and TRX2 in cells deleted for RPN4, UBR2, or RPN4 UBR2. The mRNA levels were tested by qRT-PCR and presented relative to the housekeeping gene PRP8 as the mean +/− SEM of three independent experiments. P-values represent the statistical significance relative to WT gene expression. * = P-value of <0.05, ** = P-value of <0.01, ns = not significant.CC BY · PubMed Central
Figure 5 SILAC–based quantitative large-scale proteomics of cells with reduced and increased proteasome capacity. (A) SILAC ratios for rpn4Δ/WT were plotted on the y-axis and SILAC ratios for ubr2Δ/WT were plotted on the x-axis. (A) Proteins transcribed from genes containing the Rpn4 controlled PACE element were colored red. (B) Data points corresponding to proteins with the GO classification: oxidative stress (GO:0006979), were colored orange. (C) SILAC ratios were plotted as described in (A). Data points corresponding to proteins with the GO classification: DNA repair (GO:0006281) were colored orange. For all proteins and subselections Pearson correlation coefficients were calculated and R2 values are presented. Proteins with log2 >0.5 or <−0.5 fold expression changes are listed in Tables S3, S4, S5, S6.
Figure 5 SILAC–based quantitative large-scale proteomics of cells with reduced and increased proteasome capacity. (A) SILAC ratios for rpn4Δ/WT were plotted on the y-axis and SILAC ratios for ubr2Δ/WT were plotted on the x-axis. (A) Proteins transcribed from genes containing the Rpn4 controlled PACE element were colored red. (B) Data points corresponding to proteins with the GO classification: oxidative stress (GO:0006979), were colored orange. (C) SILAC ratios were plotted as described in (A). Data points corresponding to proteins with the GO classification: DNA repair (GO:0006281) were colored orange. For all proteins and subselections Pearson correlation coefficients were calculated and R2 values are presented. Proteins with log2 >0.5 or <−0.5 fold expression changes are listed in Tables S3, S4, S5, S6.CC BY · PubMed Central
Figure 6 Correlation between resistance towards proteotoxic stress and proteasome abundance. Increased resistance to canavanine, ER or oxidative stress upon UBR2 or MUB1 deletion. Serially diluted log phase cultures of WT, rpn4Δ, ubr2Δ, mub1Δ, rpn4Δ ubr2Δ and rpn4Δ mub1Δ strains were spotted on (A) synthetic media in the presence (left panel) or absence (middle panel) of arginine, in the absence (left and middle panel) or presence (right panel) of 3 µg/ml of the arginine analog canavanine, on (B) complete media in the absence (left panel) or presence of 0.5 µg/ml tunicamycin (right panel) or on (C) complete media in the absence (left panel) or presence of 50 µM cadmium chloride (right panel).
Figure 6 Correlation between resistance towards proteotoxic stress and proteasome abundance. Increased resistance to canavanine, ER or oxidative stress upon UBR2 or MUB1 deletion. Serially diluted log phase cultures of WT, rpn4Δ, ubr2Δ, mub1Δ, rpn4Δ ubr2Δ and rpn4Δ mub1Δ strains were spotted on (A) synthetic media in the presence (left panel) or absence (middle panel) of arginine, in the absence (left and middle panel) or presence (right panel) of 3 µg/ml of the arginine analog canavanine, on (B) complete media in the absence (left panel) or presence of 0.5 µg/ml tunicamycin (right panel) or on (C) complete media in the absence (left panel) or presence of 50 µM cadmium chloride (right panel).CC BY · PubMed Central
Figure 7 Cells with higher proteasome capacity exhibit increased turnover of unstable proteasome substrates in vivo. (A) The half-life of the unstable GFP variant Δ2GFP was determined in post diauxic shift WT (upper panel, left), rpn4Δ (upper panel, right), ubr2Δ (lower panel, left) and ubr2Δ rpn4Δ (lower panel, right) cells after blocking new synthesis with lethal doses of CHX, followed by immunodetection of the protein. anti-Pgk1 was used as a loading control (lower panels). (B) Signals in (A) were detected using ECL chemiluminescence in an ImageQuant instrument and quantified with the ImageQuantTL software. Control normalized values are presented.
Figure 7 Cells with higher proteasome capacity exhibit increased turnover of unstable proteasome substrates in vivo. (A) The half-life of the unstable GFP variant Δ2GFP was determined in post diauxic shift WT (upper panel, left), rpn4Δ (upper panel, right), ubr2Δ (lower panel, left) and ubr2Δ rpn4Δ (lower panel, right) cells after blocking new synthesis with lethal doses of CHX, followed by immunodetection of the protein. anti-Pgk1 was used as a loading control (lower panels). (B) Signals in (A) were detected using ECL chemiluminescence in an ImageQuant instrument and quantified with the ImageQuantTL software. Control normalized values are presented.CC BY · PubMed Central
Figure 8 Amelioration of Htt103Q aggregation in cells with higher proteasome capacity. Live cell fluorescence images of WT (A) or ubr2Δ (B) cells expressing inducible Htt103Q-CFP or (C) Htt25Q-CFP were taken after 8 h (left panels) or 14 h of induction. 25Q overexpressing cells exhibit a soluble CFP signal after 8 h and 14 h of induction in WT and UBR2 deleted cells. All fluorescent images were recorded under the same conditions and represent merged Z-stacks. Corresponding transmitted light images (DIC) are shown below each fluorescent image.
Figure 8 Amelioration of Htt103Q aggregation in cells with higher proteasome capacity. Live cell fluorescence images of WT (A) or ubr2Δ (B) cells expressing inducible Htt103Q-CFP or (C) Htt25Q-CFP were taken after 8 h (left panels) or 14 h of induction. 25Q overexpressing cells exhibit a soluble CFP signal after 8 h and 14 h of induction in WT and UBR2 deleted cells. All fluorescent images were recorded under the same conditions and represent merged Z-stacks. Corresponding transmitted light images (DIC) are shown below each fluorescent image.CC BY · PubMed Central
Figure 9 Impact of proteasome capacity on longevity is largely unaffected by known lifespan mediating pathways. Mean lifespan and cell counts are shown in parenthesis. (A) rpn4Δ induced lifespan shortening is partially rescued by tor1Δ or (B) by dietary restriction (DR). Survival curves of rpn4Δ, tor1Δ and rpn4Δ tor1Δ or WT and rpn4Δ in the presence of 2% (A) or 0.05% glucose (B) (DR). (C) ubr2Δ and (D) mub1Δ mediated lifespan extension is independent of GCN4. Survival curves of gcn4Δ, ubr2Δ, and ubr2Δ gcn4Δ or gcn4Δ, mub1Δ, and mub1Δ gcn4Δ cells. (E) ubr2Δ mediated lifespan extension is independent of SIR2 and FOB1. Survival curves of sir2Δ fob1Δ, ubr2Δ, and ubr2Δ sir2Δ fob1Δ cells. A statistical analysis of the data is summarized in Table S2.
Figure 9 Impact of proteasome capacity on longevity is largely unaffected by known lifespan mediating pathways. Mean lifespan and cell counts are shown in parenthesis. (A) rpn4Δ induced lifespan shortening is partially rescued by tor1Δ or (B) by dietary restriction (DR). Survival curves of rpn4Δ, tor1Δ and rpn4Δ tor1Δ or WT and rpn4Δ in the presence of 2% (A) or 0.05% glucose (B) (DR). (C) ubr2Δ and (D) mub1Δ mediated lifespan extension is independent of GCN4. Survival curves of gcn4Δ, ubr2Δ, and ubr2Δ gcn4Δ or gcn4Δ, mub1Δ, and mub1Δ gcn4Δ cells. (E) ubr2Δ mediated lifespan extension is independent of SIR2 and FOB1. Survival curves of sir2Δ fob1Δ, ubr2Δ, and ubr2Δ sir2Δ fob1Δ cells. A statistical analysis of the data is summarized in Table S2.CC BY · PubMed Central

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Authors
Kruegel, U., Robison, B., Dange, T., Kahlert, G., Delaney, J. R., Kotireddy, S., Tsuchiya, M., Tsuchiyama, S., Murakami, C. J., Schleit, J., Sutphin, G., Carr, D., Tar, K., Dittmar, G., Kaeberlein, M., Kennedy, B. K., & Schmidt, M.
Venue
PLoS Genetics
Publisher
Public Library of Science (PLoS)
Published
2011-09-08
Volume
7
Issue
9
Pages
e1002253
ISSN
1553-7404
DOI
10.1371/journal.pgen.1002253
PMC
PMC3169524
Cited by
220
References
9
Language
en
Licence
creativecommons.org/licenses/by/4.0/ (unspecified)

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