Transcription factor Nrf1 mediates the proteasome recovery pathway after proteasome inhibition in mammalian cells

Abstract

In Saccharomyces cerevisiae, chemical or genetic inhibition of proteasome activity induces new proteasome synthesis promoted by the transcription factor RPN4. This ensures that proteasome activity is matched to demand. This transcriptional feedback loop is conserved in mammals, but its molecular basis is not understood. Here, we report that nuclear factor erythroid-derived 2-related factor 1 (Nrf1), a transcription factor of the cap "n" collar basic leucine zipper family, but not the related Nrf2, is necessary for induced proteasome gene transcription in mouse embryonic fibroblasts (MEFs). Promoter-reporter assays revealed the importance of antioxidant response elements in Nrf1-mediated upregulation of proteasome subunit genes. Nrf1(-/-) MEFs were impaired in the recovery of proteasome activity after transient treatment with the covalent proteasome inhibitor YU101, and knockdown of Nrf1 in human cancer cells enhanced cell killing by YU101. Taken together, our results suggest that Nrf1-mediated proteasome homeostasis could be an attractive target for therapeutic intervention in cancer.

Fig 1. Proteasome inhibitors, but not a Nedd8 pathway inhibitor, upregulate RNA levels of PSM genes in cancer cells

Prostate cancer LNCaP and colon cancer HT-29 cells were treated with the indicated concentrations of proteasome inhibitors (MG132, YU101, and Bortezomib) or the Nedd8 pathway inhibitor (MLN4924) for 10 hrs, and mRNA levels of representative PSM genes were analyzed by quantitative RT-PCR. The values were normalized to GAPDH and for each cell line the DMSO treated sample was set to 1. Error bars denote SD (n=3).

Fig 2. Nrf1 but not Nrf2 is required for MG132-mediated upregulation of RNA levels of PSM genes

(A) MEFs of different genotypes (WT, Nrf1^-/-, and Nrf2^-/-) were treated for 10 hrs with MG132 as indicated and the cell lysates were used for immunoblotting to detect protein levels of Nrf1 (with the antibody raised against the N-terminus) and Nrf2. β-actin protein levels were used as loading control. (B) RNA from MEFs under the same treatment conditions as above was used for quantitative RT-PCR to assess the mRNA levels of representative PSM genes. The values were normalized to GAPDH and the DMSO treated WT sample was set to 1. Error bars denote SD (n=3).

Fig 3. Knock-down of Nrf1 in WT MEFs abolishes MG132-mediated upregulation of RNA levels of PSM genes

(A) WT and Nrf1^-/- MEFs were transduced with retrovirus expressing sh-Nrf1 or vector control and 72 hrs later treated with MG132 for 10 hrs as indicated. The cell lysates were then used for immunoblotting to analyze protein levels of Nrf1 with either a rabbit polyconal antibody specific for the N-terminus or a mouse polyclonal antibody specific for the C-terminal region of Nrf1. β-actin protein levels were used as loading control. (B) RNA from MEFs under the same viral transduction and treatment conditions as above was used for quantitative RT-PCR to assess the mRNA levels of representative PSM genes. The values were normalized to GAPDH and for each cell line the vector-transduced DMSO-treated sample was set to 1. Error bars denote SD (n=3).

Fig 4. Forced expression of Nrf1 in Nrf1^-/- MEFs reinstates MG132-mediated upregulation of RNA levels of PSM genes

(A) Nrf1^-/- MEFs were transduced with retrovirus expressing one of Flag-Nrf1, Flag-Nrf1-HA or vector control and 72 hrs later treated with MG132 for 10 hrs as indicated. The cell lysates were used for immunoblotting to detect the levels of exogenous Nrf1 by using tag-specific antibodies. β-actin protein levels were used as loading control. (B) RNA from Nrf1^-/- MEFs under the same viral transduction and treatment conditions as above was used for quantitative RT-PCR to assess the mRNA levels of representative PSM genes. The values were normalized to GAPDH and the vector-transduced DMSO-treated sample was set to 1. Error bars denote SD (n=3).

Fig 5. Nrf1 is necessary and sufficient to activate AREs from PSM genes

(A) Sequence alignment of the genomic region close to the transcription start site (indicated by +1) of the PSMB6 gene in mouse and human. Putative ARE and the start codon are marked. (B) WT and Nrf1^-/- MEFs were transfected with the PSMB6-Luc construct and 24 hrs post-transfection, the cells were treated with the indicated concentration of MG132 for 12 hrs after which luciferase assays were performed as described in Materials and Methods. Error bars denote SD (n=3). (C) Schematic representation of the luciferase reporter constructs – 3xPSMA4-ARE-Luc which has three copies of ARE derived from the first intron of the human PSMA4 gene and 3xPSMA4-mutARE-Luc which is identical to the above except that it has the AREs mutated in key positions indicated by asterisks. (D) LNCaP cells were transiently transfected with the indicated reporter constructs along with either a vector control or Flag-Nrf1 expression construct. Forty-eight hrs after transfection, the cells were further incubated with the indicated concentration of MG132 for 12 hrs after which luciferase assays were performed as described in Materials and Methods. Error bars denote SD (n=3).

Fig 6. Loss of Nrf1 influences recovery of proteasome activity and cancer cell apoptosis after proteasome inhibition

(A) HT29 cells were treated with either MG132 (2 μM), YU101 (100 nM) or Bortezomib (40 nM) for 1 hr after which the drugs were washed off and the cells were allowed to recover in the absence or presence of 50 μg/ml cycloheximide (CHX). Cells were frozen at different time points as indicated and were used for proteasome activity assays as described in Materials and Methods. For each time point, the results are normalized to DMSO-treated control in the case of hatched lines and to CHX-treated control in the case of solid lines. Error bars denote SD (n=3). (B) WT and Nrf1^-/- MEFs were treated with either MG132 (50 μM) or YU101 (300 nM) for an hour after which the drugs were washed off and proteasome activity was measured for cells collected at different time points as indicated. The results were normalized to DMSO-treated control for each cell type. Error bars denote S.E.M. (n=2). (C) MDA-MB-231 and U2OS cells were transduced with retrovirus expressing either sh-Nrf1 or vector control, and 48 hrs later were seeded in to 96-well plates. The next day, the cells were treated with indicated concentrations of YU101 and the pan-caspase inhibitor Z-VAD-FMK, and further incubated for 72 hrs. The cell viability was then assessed using the CellTiter-Glo method. The results were normalized to DMSO-treated control which was set to 100% in each case. Error bars denote S.E.M. (n=2). (D) MDAMB-231 and U2OS cells were transduced with retrovirus expressing either sh-Nrf1 or vector control, and 72 hrs later were treated with indicated concentrations of YU101 for 48 hrs (MDA-MB-231) or 24 hrs (U2OS). The cell lysates were used for immunoblotting to detect the levels of Nrf1 (with the antibody raised against N-terminus) and cleaved caspase-3. β-actin protein levels were used as loading control.