<?xml version="1.0" ?> <tei> <teiHeader> <fileDesc xml:id="0"/> </teiHeader> <text xml:lang="en"> <p>The UPS is a fundamental component of normal cell growth and<lb/> proliferation. The UPS is also important for cancer cell growth, as<lb/> highlighted by the recent approval of the proteasome inhibitor,<lb/> Velcade, for the treatment of relapsed multiple myeloma <ref type="biblio">8</ref> . Recent<lb/> studies have investigated the mechanism of Velcade action by<lb/> examining the transcriptional response to the drug in human and<lb/> yeast cells <ref type="biblio">9,10</ref> . These studies indicate that proteasome inhibition does<lb/> not substantially alter bulk transcription of the genome in myeloma<lb/> cells or in Saccharomyces cerevisiae. However, a group of genes are<lb/> repressed by Velcade, including human growth and survival genes<lb/> and yeast genes involved in the biosynthesis of amino acids <ref type="biblio">9,10</ref> . These<lb/> yeast genes are regulated by the b-ZIP transcriptional activator Gcn4,<lb/> which promotes the expression of more than 500 genes <ref type="biblio">11</ref> . Gcn4 is a<lb/> target for UPS-mediated degradation <ref type="biblio">12</ref> through the E3-ubiquitin<lb/> ligase SCF Cdc4 . Ligases comprise the final, substrate recognition step<lb/> of the ubiquitination cascade. SCF Cdc4 ubiquitinates and targets for<lb/> proteolysis Gcn4 molecules that have been phosphorylated by the<lb/> cyclin-dependent kinases (CDKs) Srb10 and Pho85 <ref type="biblio">(refs 5, 7)</ref>. We<lb/> have attempted to explain the role of the UPS in the function of Gcn4<lb/> and other activators.<lb/></p> <p>To assess the impact of proteolysis on Gcn4 function, we treated a<lb/> yeast strain (pdr5D) that is sensitive to proteasome inhibitors <ref type="biblio">10</ref> with<lb/> the Velcade analogue MG132 <ref type="biblio">(ref. 4)</ref>. Reverse transcriptase-mediated<lb/> polymerase chain reaction (RT–PCR) analyses confirmed that, as<lb/> for Velcade <ref type="biblio">10</ref> , treatment with MG132 substantially reduced the<lb/> transcription of several Gcn4 targets, including HIS4 and CPA2, in<lb/> minimal medium, in comparison with dimethylsulphoxide (DMSO)<lb/> alone <ref type="figure">(Fig. 1a and Supplementary Fig. S1a)</ref>. Similar results were<lb/> obtained when Gcn4 was highly induced by amino acid starvation<lb/> (<ref type="figure" >Fig. 1a</ref>, 2Leu; see Supplementary Information for discussion of<lb/> media). These effects were largely dependent on Gcn4, because we<lb/> observed similar decreases in the transcription of a reporter driven<lb/> exclusively by six Gcn4-binding sites 13 (<ref type="figure">Fig. 1a</ref>, GCRE6–LacZ).<lb/></p> <figure>Figure 1 | UPS-dependent proteolysis positively regulates inducible<lb/> transcriptional activators. a, Indicated strains were grown in minimal or<lb/> starvation (2Leu) medium, treated with MG132 (50 mM) or DMSO, and<lb/> processed for RT–PCR of the indicated transcripts. pdr5D enables the uptake<lb/> of MG132 into yeast. b, A pdr5D strain was induced with galactose, treated<lb/> with MG132 and prepared for RT–PCR of GAL1 and ACT1. c, wild-type<lb/> (WT) and pre1-1, pre4-1 strains were grown in minimal medium at 27 8C<lb/> and processed for RT–PCR of HIS4 and ACT1. d, Conditionally expressed<lb/> ubiquitin was depleted from strains while expression from a complementing<lb/> plasmid encoding either WT ubiquitin, no ubiquitin (D) or K48R-ubiquitin<lb/> was induced (see Supplementary Information). Samples were prepared for<lb/> RT–PCR as above. e, WT (white bars), cdc34-2 (grey bars) and gcn4D (black<lb/> bars) strains expressing LacZ from the HIS3 or GCRE6 promoter were<lb/> grown in minimal or starvation medium (3-AT) at 30 8C and then processed<lb/> to test b-galactosidase (b-gal) activity. Standard deviations are from three<lb/> replicates. n.d., not detectable. f, WT, cdc34-2 and cdc4-1 strains were grown<lb/> at 27 8C or shifted to 30 8C for 1 h. RT–PCR was performed for HIS4, ARG1<lb/> and ACT1.<lb/></figure> <p>We also tested the proteasome dependence of two regulons (GAL<lb/> and INO) that might have eluded the Velcade microarray analysis<lb/> because they were not expressed under the growth conditions that<lb/> were employed. MG132 substantially decreased induction of the Gal4<lb/> target, GAL1, on the addition of galactose <ref type="figure">(Fig. 1b)</ref>. Similarly, on the<lb/> removal of inositol, transcription of INO1, a target of the activators<lb/> Ino2 and Ino4, was largely abrogated by MG132 <ref type="figure">(Supplementary<lb/> Fig. S1b)</ref>. In all cases treatment with MG132 did not affect the<lb/> constitutive transcription of ACT1.<lb/></p> <p>These findings indicate that the 26S proteasome might promote<lb/> the function of some inducible transcriptional activators. Focusing<lb/> on Gcn4, we tested additional components of the UPS for their<lb/> impact on transcription. A strain (pre1-1 and pre4-1) mutated for the<lb/> peptidase activity of the proteasome showed reduced transcription of<lb/> HIS4 in comparison with a wild-type (WT) strain <ref type="figure" >(Fig. 1c)</ref> <ref type="biblio">14</ref> . We also<lb/> tested transcription of HIS4 in strains that conditionally express<lb/> alternative versions of ubiquitin <ref type="biblio">6</ref> . When endogenous ubiquitin was<lb/> depleted in the presence of a vector plasmid (UbD) or depleted in a<lb/> cell expressing K48R ubiquitin, HIS4 messenger RNA levels were<lb/> sharply decreased in comparison with a depleted strain that<lb/> expressed WT ubiquitin <ref type="figure">(Fig. 1d)</ref>. Again, the ACT1 mRNA remained<lb/> constant. These findings confirm that ubiquitination and proteolysis<lb/> are important for Gcn4 function. Importantly, because the<lb/> K48R mutant cannot form chains that target substrates to the<lb/> proteasome, these findings also indicate that, in contrast to<lb/> the regulation proposed for Gal4–VP16 <ref type="biblio">(ref. 15)</ref> and c-Myc <ref type="biblio">16,17</ref> ,<lb/> mono-ubiquitination might not be able to sustain Gcn4 activity.<lb/></p> <p>We next examined the impact of Cdc34–SCF Cdc4 , the specific<lb/> E2–E3 ubiquitin ligase for Gcn4 <ref type="biblio">(refs 5, 7)</ref>, on activator function.<lb/> Gcn4-dependent expression of b-galactosidase was evaluated in WT,<lb/> temperature-sensitive cdc34-2, and gcn4D strains. After growth at the<lb/> semi-permissive temperature of 30 8C, the cdc34-2 strain exhibited a<lb/> fourfold decrease (relative to WT) in reporter expressed from the<lb/> HIS3 promoter (HIS3P) in minimal medium and a roughly 15-fold<lb/> reduction on starvation by 3-aminotriazole (3-AT, <ref type="biblio">ref. 11</ref>) <ref type="figure">(Fig. 1e)</ref>.<lb/> Expression from GCRE6–LacZ was also compromised about 10-fold<lb/> in cdc34-2 <ref type="figure">(Fig. 1e)</ref>. In addition, expression from both promoters was<lb/> extinguished in gcn4D cells under all conditions <ref type="figure">(Fig. 1e)</ref>. RT–PCR<lb/> analysis was then used to assess effects on endogenous targets.<lb/> Gcn4-dependent transcription of HIS4 and ARG1 was defective in<lb/> both cdc34-2 and cdc4-1 (a thermosensitive allele of the SCF F-box<lb/> protein Cdc4) strains at 30 8C <ref type="figure">(Fig. 1f)</ref>. In contrast, ACT1 transcript<lb/> levels in all strains were similar. These results point to a stimulatory<lb/> role for Cdc34–SCF Cdc4 in Gcn4-mediated transcription.<lb/></p> <p>To explore the molecular basis of the stimulation of Gcn4 function<lb/> by the UPS, we examined the effect that proteasome inhibition has on<lb/> the abundance and ubiquitination of Gcn4. Western blotting showed<lb/> that MG132 increased the abundance of chromosomally encoded<lb/> Gcn4–Myc9 and led to the appearance of a high-molecular-mass<lb/> ladder <ref type="figure">(Fig. 2a, lanes 1 and 2)</ref>. Immunoprecipitation and western<lb/> analysis with anti-ubiquitin antibodies confirmed that this ladder<lb/> was ubiquitinated Gcn4 <ref type="figure">(Fig. 2a, lanes 5, 6, 9 and 10)</ref>. Because<lb/> transcription mediated by Gcn4 was strongly repressed by MG132<lb/> <ref type="figure">(Fig. 1)</ref>, ubiquitination was presumably insufficient to sustain Gcn4<lb/> activity. To confirm the specificity of Gcn4 ubiquitination, we<lb/> repeated the analysis with a gcn4–3T2S strain. Gcn4–3T2S lacks<lb/> five phosphorylation sites, is no longer phosphorylated by Srb10 or<lb/> Pho85 nor ubiquitinated by SCF Cdc4 in vitro, and is stabilized <ref type="biblio">7</ref> . As<lb/> predicted, the 3T2S strain had much lower levels of ubiquitinated<lb/> Gcn4 <ref type="figure">(Fig. 2a, lanes 3, 4, 7, 8, 11 and 12)</ref>.<lb/></p> <p>We next investigated promoter occupancy by Gcn4 and Gal4 and<lb/> recruitment of RNA polymerase II (polII) to target genes. Chromatin<lb/> immunoprecipitation (ChIP) assays <ref type="biblio">18</ref> revealed a substantial increase<lb/> in the association of Gcn4–Myc9 with the HIS4 promoter in cells<lb/> treated with MG132 <ref type="figure" >(Fig. 2b, 9E10)</ref>. Similar experiments showed<lb/> little change in levels of TAP-tagged Gal4 at the GAL1 promoter on<lb/> treatment with MG132 <ref type="figure" >(Fig. 2c, IgG)</ref>. The galactose-dependent<lb/> decrease in promoter-bound Gal80–TAP was also unaffected by<lb/> MG132 <ref type="figure">(Supplementary Fig. S3)</ref>. When the ChIP was performed<lb/> with polII, MG132 reduced the signal for the promoter, open reading<lb/> frame (ORF) and terminator regions of the Gcn4 target HIS4,<lb/> whereas the signal for the ACT1 ORF was unaffected <ref type="figure">(Fig. 2b,<lb/> polII)</ref>. MG132 also decreased the polII ChIP signal for the GAL1<lb/> promoter and ORF <ref type="figure">(Fig. 2c, polII)</ref> and the INO1 promoter (data not<lb/> shown).<lb/></p> <p>The ChIP analysis was extended to cdc34-2 and cdc4-1 strains. At<lb/> 30 8C, more Gcn4–Myc9 <ref type="figure">(Fig. 2d, 9E10)</ref> but less polII was associated<lb/> with the HIS4 promoter in the SCF mutants than in the WT.<lb/> Recruitment of polII to ACT1 was unaffected in the SCF mutants.<lb/> Results from all the ChIP analyses closely parallel the transcription<lb/> results and imply that the UPS is important for sustaining the<lb/> interaction of RNA polymerase II with the targets of some activators<lb/> despite the increased accumulation of activator (for Gcn4) at the<lb/> promoter.<lb/></p> <figure>Figure 2 | Defects in the UPS lead to the accumulation of ubiquitinated<lb/> Gcn4 and impair the association of RNA polymerase II with Gcn4 and Gal4<lb/> targets. a, pdr5D strains expressing Gcn4–Myc9 (WT) or Gcn4–3T2S–<lb/> Myc9 (3T2S) were grown in minimal medium and treated with MG132 or<lb/> DMSO. Immunoprecipitations (IPs) were performed with 9E10 antibodies<lb/> recognizing Myc9, and subsequent western blots of the input (lanes 1–4) or<lb/> immunoprecipitation (IP; lanes 5–12) samples were probed with 9E10 (lanes<lb/> 1–8) or anti-Ub antibodies (lanes 9–12). b, A WT strain, as above, was<lb/> processed for ChIP analysis with 9E10 and anti-polII antibodies. PCR was<lb/> performed to amplify the promoter, ORF and terminator regions of HIS4<lb/> and the ORF of ACT1. c, ChIP analysis of Gal4–TAP and polII was<lb/> performed with galactose-induced strains treated with MG132 or DMSO.<lb/> The promoter and ORF regions of GAL1 were amplified. IgG was used to<lb/> retrieve Gal4–TAP. d, ChIP analysis of Gcn4–Myc9 and polII was performed,<lb/> as in b, with WT, cdc34-2 and cdc4-1 strains that were grown at 27 8C, then<lb/> shifted to 30 8C for 1 h. kb, kilobases; n.d., not done.<lb/></figure> <p>To test whether turnover of the activator itself can promote<lb/> function, we evaluated the stabilized Gcn4–3T2S <ref type="biblio">(ref. 7)</ref>. In minimal<lb/> medium the levels of total protein <ref type="figure">(Fig. 3a)</ref> and promoter-associated<lb/> Gcn4–Myc9 <ref type="figure">(Fig. 3b)</ref> were about twofold to threefold higher in the<lb/> gcn4–3T2S strain. Despite such increases, gcn4–3T2S did not alter the<lb/> expression of Gcn4 targets in minimal <ref type="figure">(Fig. 3c, SM þ ; Fig. 3e,<lb/> CDC34)</ref> or starvation medium <ref type="figure">(Fig. 3c, 2Leu)</ref>, indicating a<lb/> possible decrease in specific activity. Most importantly, gcn4–3T2S<lb/> partly alleviated the deleterious effects of an impaired UPS on<lb/> Gcn4-dependent transcription. For example, MG132 inhibited<lb/> HIS4 transcription in gcn4–3T2S much less than in GCN4 <ref type="figure">(Fig. 3d)</ref>.<lb/> In addition, cdc34-2 diminished HIS3P–LacZ expression only about<lb/> 1.2-fold in gcn4–3T2S, in comparison with more than 2.5-fold in<lb/> GCN4 <ref type="figure">(Fig. 3e)</ref>. The cdc34-2 mutation had no impact on gcn4D<lb/> <ref type="figure">(Fig. 3e)</ref>. A similar epistatic relationship was seen on deletion of<lb/> SRB10 and PHO85, which stabilizes Gcn4 to a similar extent to the<lb/> gcn4–3T2S mutation <ref type="biblio">7</ref> . Deletion of both CDKs (DD) slightly increased<lb/> LacZ expression (1.2-fold) and, as with gcn4–3T2S, cdc34-2 only<lb/> mildly affected expression (1.2-fold) in the DD strain <ref type="figure">(Fig. 3f)</ref>. The<lb/> suppression of cdc34-2 required the deletion of both kinases, because<lb/> srb10D and pho85D single mutants remained relatively sensitive to<lb/> cdc34-2 <ref type="figure">(Fig. 3f)</ref>. We note that gcn4–3T2S is not completely refrac-<lb/>tory to UPS inhibition, indicating that, in addition to Gcn4, the UPS<lb/> might also promote transcription through other factors. Neverthe-<lb/>less, these findings indicate that proteolysis of CDK-phosphorylated<lb/> Gcn4 by means of the UPS might be important in sustaining<lb/> maximal expression of Gcn4 targets and that, in the absence of<lb/> phosphorylation, Gcn4 activity is less dependent on its turnover.<lb/></p> <p>Components of the UPS have been posited to activate transcrip-<lb/>tion by multiple mechanisms <ref type="biblio">2,3</ref> . In numerous examples, including<lb/> the activation of Gcn4 in response to ultraviolet radiation <ref type="biblio">19</ref> and<lb/> transcription of NF-kB <ref type="biblio">(ref. 2)</ref> and oestrogen receptor targets <ref type="biblio">20</ref> , the<lb/> UPS seems to mediate signalling upstream of the activator. As<lb/> discussed in <ref type="figure">Supplementary Fig. S3</ref>, this mechanism probably does<lb/> not account for our findings. Meanwhile, subunits of the 19S cap of<lb/> the proteasome have been suggested to have a positive role in<lb/> transcription that is independent of their proteolytic function <ref type="biblio" >21,22</ref> .<lb/> In addition, it has been proposed that the ubiquitination of<lb/> Gal4–VP16 and c-Myc transiently increases the activity of these<lb/> factors before proteolysis <ref type="biblio">15–17</ref> . Our results differ substantively from<lb/> these examples, in that neither the 19S cap (whose activity is not<lb/> known to be affected by inhibition of the 20S proteases <ref type="biblio">23</ref> ) nor<lb/> ubiquitination was sufficient to achieve maximal transcription of<lb/> Gcn4 targets <ref type="figure">(Figs 1d and 2a)</ref>. Instead, we found that inhibition of<lb/> the proteasome and genetic manipulations of the UPS, the CDKs for<lb/> Gcn4, and Gcn4 itself all provided evidence that turnover of Gcn4<lb/> normally enhances its function.<lb/></p> <p>Proteasome activity also seems to sustain inducible transcription<lb/> mediated by Gal4 and Ino2/4. Interestingly, activation of promoter-<lb/>associated Gal4 in galactose medium requires Srb10-dependent<lb/> phosphorylation <ref type="biblio">24,25</ref> , and this activated form has a short half-life <ref type="biblio">24</ref> .<lb/> This indicates that Gal4 might be regulated by degradation in a<lb/> manner similar to that of Gcn4. We previously proposed a model<lb/> consistent with these current findings in which proteolysis is required<lb/> to remove 'spent' activators and to reset the promoter <ref type="biblio">3</ref> . The initial<lb/> 'pioneer round(s)' of transcription would not involve the UPS, but<lb/> subsequent rounds would be stimulated by turnover of the spent,<lb/> promoter-bound activator to allow binding of a fresh molecule. This<lb/> mechanism places Gcn4, Gal4 and Ino2/4 into a class of regulatory<lb/> factors—including securin, p21 and p27—whose activity is required<lb/> early in a process but whose subsequent turnover or removal<lb/> promotes completion of the process or subsequent reaction cycles.<lb/> We call this phenomenon 'activation by destruction' and believe that,<lb/> given the diversity of the examples listed in Supplementary Table S2,<lb/> it might represent a regulatory mechanism for a large class of factors<lb/> and might be an important determinant of infection and disease.<lb/></p> <head>METHODS<lb/></head> <p>Yeast strains, growth conditions and extract preparation. A complete list of<lb/> yeast strains used in this study is provided in Supplementary Table S1. All strains<lb/> were derived from the S288C background, except RJD 2505 and RJD 3137–3141,<lb/> which were derived from the W303 background. Strains were constructed and<lb/> grown in accordance with standard protocols <ref type="biblio">26</ref> . A description of the various<lb/> media used in the study is given in Supplementary Information. MG132<lb/> (American Peptide) was added to cultures of pdr5D strains to a final concen-<lb/>tration of 50 mM. All extracts were prepared by lysis with glass beads (Sigma) in a<lb/> Fast Prep (Bio 101) device. Ubiquitin derivative analysis <ref type="figure">(Fig. 1d)</ref> is described in<lb/> the Supplementary Methods.<lb/></p> <p>RT–PCR analysis. mRNA was prepared using RNeasy kits (Qiagen). Total<lb/> mRNA (200 ng) and 10 pmol of oligo(dT) were used to reverse-transcribe<lb/> complementary DNA (Stratagene). One-tenth of the cDNA reaction was then<lb/> used for 20–22 cycles of PCR and products were resolved on 2% agarose gels.<lb/> Primer sequences are available from the authors on request.<lb/></p> <p>b-Galactosidase assays. The HIS3P–LacZ, HIS4P–LacZ and GCRE–LacZ repor-<lb/>ter constructs and the protocol to measure b-galactosidase activity were as<lb/> described previously <ref type="biblio">27</ref> . Reported activity was normalized to total extract protein<lb/> as measured by bicinchoninic acid assay (Pierce). Relative activities are reported<lb/> with average WT activity set to 1.<lb/></p> <p>Western blots. Except as noted, extracts were prepared by immediate boiling of<lb/> cell pellets in 2 £ Laemmli SDS sample buffer followed by lysis with glass beads.<lb/> Equal amounts of total protein (as judged by Coomassie staining) were resolved<lb/> by SDS–PAGE. Blots were probed with 9E10 antibodies to recognize Gcn4–Myc9<lb/> or FK1 antibodies (Affiniti) to recognize ubiquitin. Horseradish peroxidase-<lb/>coupled goat anti-mouse secondary antibodies (Bio-Rad) were used for<lb/> detection.<lb/></p> <figure>Figure 3 | The UPS has little effect on the activity of stable,<lb/> non-phosphorylated versions of Gcn4. a, GCN4 (WT), gcn4–3T2S or<lb/> gcn4D strains were grown in minimal medium and processed for western<lb/> blotting with 9E10 antibodies. Protein half-life data (t 1/2 ) were reported<lb/> previously 7 . n.a., not applicable. b, ChIP analysis of the above strains was<lb/> performed for the HIS4 promoter. c, RT–PCR of the indicated transcripts<lb/> were performed with WTand gcn4–3T2S strains grown in minimal (Min) or<lb/> starvation (2Leu) medium. d, RT–PCR analysis of HIS4 and ACT1 was<lb/> performed with WTand 3T2S strains in the presence and absence of MG132.<lb/> e, CDC34 (open bars) and cdc34-2 (filled bars) strains with the HIS3P-LacZ<lb/> reporter and expressing either WT, 3T2S or null (gcn4D) versions of<lb/> GCN4 were grown in minimal medium and processed for b-galactosidase<lb/> (b-gal) activity. Standard deviations were calculated from three replicates.<lb/> f, WTand cdc34-2 strains with a HIS4P-LacZ reporter and harbouring WTor<lb/> deleted versions of SRB10 and/or PHO85 were treated as in e.<lb/></figure> <p>Immunoprecipitations and detection of ubiquitinated Gcn4. DMSO-treated<lb/> or MG132-treated cultures were treated with formaldehyde (final concentration<lb/> 1%) for 20 min to trap ubiquitinated intermediates. Crosslinking was quenched<lb/> and extracts were made in ChIP buffer <ref type="biblio">18</ref> . A 10% sample of the extract (whole cell<lb/> extract) was removed and boiled in SDS sample buffer. The remainder of<lb/> the extract was incubated at 4 8C with 9E10 antibodies coupled to Protein A–<lb/> Sepharose (Sigma) beads. Proteins were eluted and crosslinks were reversed by<lb/> being boiled in SDS sample buffer. Proteins samples were then processed for<lb/> western blotting. For FK1 (anti-ubiquitin) western blots, the nitrocellulose was<lb/> boiled before incubation with the antibody.<lb/></p> <p>ChIP assays. ChIP assays were performed as described <ref type="biblio">18</ref> ; 9E10 antibodies were<lb/> used to immunoprecipitate chromatin fragments associated with Gcn4–Myc9 and<lb/> antibodies against the carboxy-terminal domain of the largest subunit of RNA<lb/> polymerase II (anti-polII; Covance) were used to immunoprecipitate fragments<lb/> associated with polII. Protein G–Sepharose beads (Amersham Biosciences)<lb/> were used to precipitate antibody–antigen complexes. Rabbit immunoglobulin<lb/> (Ig) G–agarose (Sigma) was used to immunoprecipitate Gal4-associated<lb/> fragments. Primer sequences are available from the authors on request.<lb/></p> </text> </tei>