Failure of amino acid homeostasis causes cell death following proteasome inhibition

Abstract

The ubiquitin-proteasome system targets many cellular proteins for degradation and thereby controls most cellular processes. Although it is well established that proteasome inhibition is lethal, the underlying mechanism is unknown. Here, we show that proteasome inhibition results in a lethal amino acid shortage. In yeast, mammalian cells, and flies, the deleterious consequences of proteasome inhibition are rescued by amino acid supplementation. In all three systems, this rescuing effect occurs without noticeable changes in the levels of proteasome substrates. In mammalian cells, the amino acid scarcity resulting from proteasome inhibition is the signal that causes induction of both the integrated stress response and autophagy, in an unsuccessful attempt to replenish the pool of intracellular amino acids. These results reveal that cells can tolerate protein waste, but not the amino acid scarcity resulting from proteasome inhibition.

Graphical abstract

Figure 1

Amino Acid Insufficiency Mediates the Lethality Resulting from Proteasome Inhibition in Yeast Cells (A) Changes in the content of cellular free amino acids in cim3-1 or wild-type (WT) cells after 5 hr at 37°C in rich medium (YPD). Data are means ± SD (n = 3), normalized to cell number. Significance of all values in wild-type versus mutant cells: p ≤ 0.001. Cells were in exponential growth at 30°C before the temperature switch. Asx: Asn, Asp. Glx: Glu, Gln. (B) Cell death monitored by flow cytometry analysis of propidium iodide labeled yeast cells after 21 hr at 37°C, in the presence of 40 g/l casamino acids (AA) where indicated. (C) Viability of cim3-1 cells exposed to 37°C for 21 hr in liquid cultures (YPD), in the presence of 40 g/l casamino acids (AA) where indicated or kept at 4°C, assessed by spotting serial dilutions on rich media and incubation at 30°C for 2 days. (D and E) Viability of cim3-1 and pre1-1 cells on YPD plates exposed to the indicated temperatures for the indicated times, with or without casamino acids (AA, 40 g/l). A total of 2,000 cells were plated in each condition. (F) Polyubiquitin immunoblots (Ubⁿ) from lysates of wild-type or cim3-1 cells, cultured as indicated. Ponceau staining of the membrane. (G) Immunoblots of GFP-tagged Ura3-3 from lysates of the indicated cells treated with cycloheximide as in Lewis and Pelham (2009) and cultured as indicated. (H) Accumulation of Cyclin B2 (CLB2) in cim3-1 cells at 37°C. CLB2 immunoblots from lysates of wild-type or cim3-1 cells, grown in rich medium with or without casamino acids (AA, 40 g/l) for the indicated times at 30°C or 37°C. Ponceau staining of the membrane prior to probing with antibodies. (I) Autoradiogram of [³⁵S]methionine-labeled proteins in lysates resolved by NuPage after a 8 min pulse labeling of exponentially growing cells cultured as indicated and quantification of labeled proteins. Lower panel is a photomicrograph of the Coomassie-stained gel. Representative results of at least three independent experiments are shown. See also Figure S1.

Figure 2

Failure of Amino Acid Homeostasis Causes Cell Death following Proteasome Inhibition (A) Viability of NIH 3T3 cells, assessed by the reduction of WST-8 into formazan, after 2 days of growth, following treatment with 10 μM MG-132 for 8 hr and a 20 hr washout in regular medium, with or without cysteine (Cys) and/or asparagine (Asn). Data are means ± SD (n = 4). ^∗p ≤ 0.01, ^∗∗p ≤ 0.001, and ^∗∗∗p ≤ 0.0001. n.s., not significant. (B) Polyubiquitin (Ubⁿ) and tubulin immunoblots of lysates from NIH 3T3 cells exposed to 10 μM MG-132 treatment for 6 hr, followed by a washout in regular medium, with or without 1 mM Cys supplementation, for the indicated time. (C) Fluorescence of proteasome reporter-substrates Ub^G76V-GFP (Dantuma et al., 2000), ZsGreen-ODC (Hoyt et al., 2005), and GFP-CL1 (Gilon et al., 1998; Bence et al., 2001) in NIH 3T3 or 293T cells, following treatment with 10 μM MG-132 and a washout for the indicated time, with or without Cys. Data are means ± SD (n = 3). ^∗p ≤ 0.01, ^∗∗p ≤ 0.001, and ^∗∗∗p ≤ 0.0001. n.s., not significant. (D) Fluorescence of proteasome reporter-substrates ZsGreen-ODC (Hoyt et al., 2005) following treatment with 10 μM MG-132 either alone or together with 1 mM Cys where indicated. (E) Polyubiquitin (Ubⁿ), tubulin, and NF-κB (p105 and p50) immunoblots of lysates of 293T cells overexpressing p105 and treated with 10 μM MG-132 for 8 hr, either alone or together with 1 mM Cys, where indicated. Representative results of at least three independent experiments are shown. See also Figure S2.

Figure 3

Amino Acid Supplementation Alleviates the Induction of the Integrated Stress Response upon Proteasome Inhibition (A) Scheme depicting the integrated stress response induction upon proteasome inhibition. The signal responsible for eIF2α phosphorylation (P-eIF2α) upon proteasome inhibition is unknown. (B) Polyubiquitin (Ubⁿ), GADD34, ATF4, phosphorylated eIF2α (P-eIF2α), eIF2α, and CHOP immunoblots of lysates from NIH 3T3 cells treated with 10 μM MG-132 for 6 hr followed by a washout in the presence of 1 mM cysteine (Cys) for the indicated time. (C) Viability of wild-type and CHOP−/− mouse embryonic fibroblasts, assessed by the reduction of WST-8 into formazan, after 2 days of growth, following treatment with 10 μM MG-132 for the indicated time and a washout in regular medium. Data are means ± SD (n = 4), normalized to cell number. ^∗p ≤ 0.01, ^∗∗∗p ≤ 0.0001. (D) GADD34, CHOP, and tubulin immunoblots of lysates from NIH 3T3 cells treated with 10 μM MG-132 for 4 hr followed by a washout in the presence of cycloheximide (CHX, 100 μg/ml), with or without 1 mM Cys for the indicated time. (E) Autoradiogram of [³⁵S]methionine-labeled proteins in lysates resolved by NuPage after a 8 min pulse labeling of exponentially growing cells cultured as indicated. Quantification are presented below each lane. Lower panel is a photomicrograph of the Coomassie-stained gel. (F) eIF2α immunoblots of lysates from GCN2−/− or wild-type mouse embryonic fibroblasts treated with 10 μM MG-132 for the indicated time. (G) Immunoblots of GCN2 immunoprecipitated from lysates of cells either left untreated, leucine-deprived (-Leu), or treated with 10 μM MG-132, with or without 1 mM Cys. The top panel was probed with antisera against the phosphorylated GCN2 and the bottom panel with an antibody recognizing both the phosphorylated and the nonphosphorylated GCN2. (H) Immunoblots of lysates from NIH 3T3 cells following a dose response analysis of UV irradiation, in the presence or in absence of 1 mM cysteine (Cys). Representative results of at least three independent experiments are shown. See also Figure S3.

Figure 4

Amino Acid Supplementation Suppresses Autophagy Resulting from Proteasome Inhibition (A) Confocal micrographs of HeLa cells stably expressing GFP-LC3 (Thurston et al., 2009) either untreated or following 10 μM MG-132 treatment, with or without 1 mM Cys, where indicated. Nuclei were stained with H33258. (B) Quantification of GFP-LC3 dots in at least 100 cells exposed to the indicated treatment. Data are means ± SEM. ^∗∗∗p ≤ 0.0001. (C) LC3 and tubulin immunoblots of lysates from cells treated with 100 nM Bafilomycin A1 (Baf A1) for 15 hr, or 10 μM MG-132 alone or together with 1 mM Cys for the indicated time. (D) Quantification of the LC3-II/tubulin ratio in three independent experiments. Values were normalized to untreated cells. Data are means ± SEM. ^∗p ≤ 0.05. (E) Viability of wild-type and Atg5−/− mouse embryonic fibroblasts, assessed by the reduction of WST-8 into formazan, after 2 days of growth, following treatment with 10 μM MG-132 for the indicated time and a washout in regular medium. Data are means ± SD (n = 4), normalized to cell number. ^∗∗p ≤ 0.001. n.s., not significant. See also Figure S4.

Figure 5

Autophagy and Rag GTPases-Dependent Amino Acid Signaling to mTOR upon Proteasome Inhibition (A) Model for amino acid signaling to mTOR by the Rag GTPases (RagA/B^GTP-RagC/D^GDP). Amino acid sensing by the Rag GTPases is blocked by dominant negative mutants (RagB^GDP-RagC^GTP) (Sancak et al., 2008). (B) Immunoblots of lysates from 293T cells exposed to 10 μM MG-132 treatment revealed with phospho-T398-S6K1 or S6K1 antibodies. Cells were either left untreated or treated with 100 nM Baf A1 for the indicated time. (C) Immunoblots with phospho-T398-S6K1 or S6K1 antibodies of lysates of cells mock transfected or transfected with dominant negative forms of RagB (RagB-DN, FLAG-tagged). (D) Immunoblots with phospho-T398-S6K1 or S6K1 antibodies of lysates of 293T cells either left untreated or treated with 10 μM MG-132 with or without 100 μM cycloheximide (CHX) for 1 hr. (E) Changes in the content of cellular free cysteine (Cys) or asparagine/aspartate (Asx) in cells treated with 10 μM MG-132 with or without 50 μM cycloheximide (CHX) for 4 hr. (F) Viability of NIH 3T3 cells, assessed by the reduction of WST-8 into formazan, after 2 days of growth, following treatment with 10 μM MG-132 with or without 50 μM cycloheximide (CHX) for 8 hr. Data are means ± SD (n = 4), normalized to cell number. ^∗∗∗p ≤ 0.0001. Representative results of at least three independent experiments are shown.

Figure 6

Amino Acid Imbalance Mediates the Lethality Resulting from Proteasome Inhibition in Drosophila (A) Changes in the content of free amino acids in Drosophila treated with or without 50 μM Bortezomib for 3 days. Asx, asparagine/aspartate; Glx, glutamine/glutamate. Data are means ± SEM (30 flies per conditions, from six independent experiments). ^∗∗p ≤ 0.005; ^∗∗∗p ≤ 0.001. (B) Survival of Drosophila either untreated or treated with 50 μM Bortezomib, with or without additional amino acids (AA), at the concentration used in Grandison et al. (2009). Data are means ± SEM (400 flies per condition, from four independent experiments). ^∗∗p ≤ 0.005; ^∗∗∗p ≤ 0.001. (C) Polyubiquitin (Ubⁿ) immunoblots from lysates of flies treated with 50 μM Bortezomib and additional amino acids, where indicated. Ponceau staining of the membrane. Representative results of at least three independent experiments are shown.

Figure 7

Proteasome Inhibition Causes an Intolerable Amino Acid Imbalance and the Resulting Lethality Is Rescued upon Supplementation with Amino Acids The amino acid shortage resulting from proteasome inhibition is the signal that induces eIF2α phosphorylation and autophagy, in a vain attempt to replenish to pool of amino acid and sustain vital protein synthesis rates. In yeast, mammalian cells, and Drosophila, the lethality resulting from proteasome inhibition is rescued upon amino acid supplementation. This rescuing effect occurs without a detectable decrease in the levels of proteasome substrates in proteasome-inhibited cells.