In this study we demonstrate that the Deg1 degradation signal of the transcriptional repressor Matα2 confers compartment-specific turnover to a reporter protein. Rapid degradation of a Deg1-containing fusion protein is observed only when the reporter is efficiently imported into the nucleus. In contrast, a reporter that is constantly exported from the nucleus exhibits an extended half-life. Furthermore, nuclear import functions are crucial for both Deg1-induced degradation as well as for the turnover of the endogenous Matα2 protein. The conjugation of ubiquitin to a Deg1-containing reporter protein is abrogated in mutants affected in nuclear import. Obviously, the Deg1 signal initiates rapid proteolysis within the nucleoplasm, whereas in the cytosol it mediates turnover via a slower pathway. In both pathways the ubiquitin-conjugating enzymes Ubc6p/Ubc7p play a pivotal role. These observations imply that both the cellular targeting of a substrate and the compartment-specific activity of components of the ubiquitin-proteasome system define the half-life of naturally short-lived proteins. In this study we demonstrate that the Deg1 degradation signal of the transcriptional repressor Matα2 confers compartment-specific turnover to a reporter protein. Rapid degradation of a Deg1-containing fusion protein is observed only when the reporter is efficiently imported into the nucleus. In contrast, a reporter that is constantly exported from the nucleus exhibits an extended half-life. Furthermore, nuclear import functions are crucial for both Deg1-induced degradation as well as for the turnover of the endogenous Matα2 protein. The conjugation of ubiquitin to a Deg1-containing reporter protein is abrogated in mutants affected in nuclear import. Obviously, the Deg1 signal initiates rapid proteolysis within the nucleoplasm, whereas in the cytosol it mediates turnover via a slower pathway. In both pathways the ubiquitin-conjugating enzymes Ubc6p/Ubc7p play a pivotal role. These observations imply that both the cellular targeting of a substrate and the compartment-specific activity of components of the ubiquitin-proteasome system define the half-life of naturally short-lived proteins. ubiquitin-activating enzyme ubiquitin-conjugating enzyme ubiquitin-protein ligase endoplasmic reticulum-associated protein degradation nuclear localization signal classic NLS polymerase chain reaction green fluorescence protein nuclear export signal Rapid inactivation of regulatory factors is an essential step in many central biological processes including cell cycle control and signal transduction (1Hood J.K. Silver P. Curr. Opin. Cell Biol. 1999; 11: 241-247Crossref PubMed Scopus (114) Google Scholar, 2Görner W. Schüller C. Ruis H. Biol. Chem. 1999; 380: 147-150Crossref PubMed Google Scholar). Down-regulation of these factors often occurs by specific proteolysis mediated by the ubiquitin system. In a brief and simplified view, the conjugation of substrates with ubiquitin involves the successive action of three classes of enzymes: The E11 or ubiquitin-activating enzyme, E2s or ubiquitin-conjugating enzymes (Ubc), and occasionally E3s or ubiquitin-protein ligases. In most cases described in vivo, complexes of E2 and E3 enzymes mediate the specificity of the system. These enzymes catalyze the formation of polyubiquitin chain, which is subsequently recognized by the 26 S proteasome (3Hershko A. Ciechanover A. Annu. Rev. Biochem. 1998; 67: 425-479Crossref PubMed Scopus (6792) Google Scholar, 4Hochstrasser M. Annu. Rev. Genet. 1996; 30: 405-439Crossref PubMed Scopus (1452) Google Scholar). Specific protein degradation also relies on features contained in the proteolytic substrate itself. First, a degradation signal has to be present. These signals are transferable sequences or structural features of the target protein, which are in some cases activated by phosphorylation (5Laney J.D. M. 1999; PubMed Scopus Google Scholar). within the substrates the for the polyubiquitin of the and degradation signals is in the transcriptional repressor Matα2 of and Deg1 M. A. PubMed Scopus Google Scholar). signal the of the Matα2 protein, and involves the E2 enzymes and P. P. M. PubMed Scopus Google Scholar). has that a of an in Deg1 is the structural of this signal M. 1998; PubMed Scopus Google Scholar). is that the Deg1 signal also a nuclear localization signal C. A. PubMed Scopus Google it that the components of the ubiquitin system are the for the of the system is 11: PubMed Scopus Google Scholar, Annu. Rev. Cell Biol. 1998; PubMed Scopus Google Scholar). and and are also crucial components of PubMed Scopus Google Scholar, C. 1996; PubMed Scopus Google Scholar, A. M. 1996; PubMed Scopus Google Scholar, C. PubMed Scopus Google Scholar). proteolytic which to be to a specific is the degradation of In the of the E3 or are in the W. M. 1996; PubMed Scopus Google Scholar). Furthermore, it has that the 26 S proteasome is in and the nucleus in C. A. 1998; PubMed Scopus Google Scholar). it to be in which proteolysis we demonstrate for the that rapid and specific proteolysis of a short-lived protein is to a cellular the Matα2 is an nuclear protein that is the Deg1 signal confers localization to a reporter protein and is with slower a NLS PubMed Scopus Google is to Deg1 turnover the of Matα2 a degradation signal has to be with localization signals it to to proteolysis by the Deg1 signal with to nuclear this we fusion of the Deg1 signal with a of PubMed Scopus Google which in and the of short-lived fusion proteins. is a protein, which is the cell of the reporter the nuclear a of localization of fusion with a fluorescence and protein in by In is of that the of as well as the degradation of the fusion protein to of a described both in the reporter to be a substrate to study we the Deg1 degradation signal to exhibits the nuclear localization as the Matα2 protein. observed that the endogenous NLS of Deg1 is to the fusion protein to the which is in with C. A. PubMed Scopus Google Scholar). In to a of the Matα2 and to a reporter protein both of which are nuclear a of in the we the half-life of be by this this we the Deg1 and the in this fusion protein in the nucleus turnover that observed for that the we this by a PubMed Scopus Google Scholar). this is to the nucleus these the that nuclear import of a proteolytic substrate be a for degradation via the ubiquitin-proteasome we the of a in nuclear import on proteolysis of C. P. 11: PubMed Scopus Google Scholar, W. Cell Biol. Google PubMed Scopus Google Scholar, M. Silver 1996; PubMed Scopus Google in which nuclear import is affected of in components of the nuclear to the to the nuclear both and and turnover to the of with degradation of an substrate 11: PubMed Scopus Google Scholar, Annu. Rev. Cell Biol. 1998; PubMed Scopus Google in these mutants that nuclear import of the proteolytic system. Furthermore, we the that the nuclear import of the NLS J.D. Silver A. 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The fusion and in the nucleus and the fusion protein is whereas the reporter exhibits an half-life with turnover of the substrate with nuclear localization whereas proteolysis with we that the Deg1 degradation signal mediates proteolysis only in the nucleus. for this is by the that proteolysis of the fusion protein as well as is in mutants in nuclear import it that proteolysis in is in these mutants the degradation of a substrate as from the with the Deg1 signal are of for the degradation of the Matα2 transcriptional repressor of the First, turnover of the endogenous Matα2 also in nuclear import the of a on Matα2 degradation that of or a exported fusion protein a half-life with a fusion protein the The and on the fusion protein the that the half-life of Matα2 is a of the the protein in the we observed and nuclear turnover of Deg1-containing fusion proteins. The of Deg1 by a of Ubc6p/Ubc7p is in the cytosol in the nucleus. the of on Deg1-induced proteolysis to be in the whereas in the cytosol a crucial role. The of observed in is most to the that the of is in these C. PubMed Scopus Google Scholar). The turnover of in the cytosol most the endoplasmic it that degradation of a fusion protein on the of and on the of to the endoplasmic C. PubMed Scopus Google Scholar). degradation of and and from that of a substrate turnover in the cytosol and in the nucleus are most of the rapid Matα2 system M. A. PubMed Scopus Google also be in the cytosol many of the be of demonstrate that the half-life of a protein is by specific degradation and localization The on localization signals is by the of components of the ubiquitin system to a E3 enzyme be in the nucleus and rapid turnover in this this the Ubc6p/Ubc7p are to the signal with imply that the nucleus is a crucial for Matα2 in which nuclear export is also a specific for rapid proteolysis M. 1998; PubMed Scopus Google Scholar, 1999; PubMed Scopus Google Scholar, Biol. Chem. 1999; PubMed Scopus Google Scholar). In cell biological a to a half-life. a protein into a the turnover be or components of the are to within an Rapid inactivation of regulatory factors is an essential step in many central biological processes including cell cycle control and signal transduction (1Hood J.K. Silver P. Curr. Opin. Cell Biol. 1999; 11: 241-247Crossref PubMed Scopus (114) Google Scholar, 2Görner W. Schüller C. Ruis H. Biol. Chem. 1999; 380: 147-150Crossref PubMed Google Scholar). Down-regulation of these factors often occurs by specific proteolysis mediated by the ubiquitin system. In a brief and simplified view, the conjugation of substrates with ubiquitin involves the successive action of three classes of enzymes: The E11 or ubiquitin-activating enzyme, E2s or ubiquitin-conjugating enzymes (Ubc), and occasionally E3s or ubiquitin-protein ligases. In most cases described in vivo, complexes of E2 and E3 enzymes mediate the specificity of the system. These enzymes catalyze the formation of polyubiquitin chain, which is subsequently recognized by the 26 S proteasome (3Hershko A. Ciechanover A. Annu. Rev. Biochem. 1998; 67: 425-479Crossref PubMed Scopus (6792) Google Scholar, 4Hochstrasser M. Annu. Rev. Genet. 1996; 30: 405-439Crossref PubMed Scopus (1452) Google Scholar). Specific protein degradation also relies on features contained in the proteolytic substrate itself. First, a degradation signal has to be present. These signals are transferable sequences or structural features of the target protein, which are in some cases activated by phosphorylation (5Laney J.D. M. 1999; PubMed Scopus Google Scholar). within the substrates the for the polyubiquitin of the and degradation signals is in the transcriptional repressor Matα2 of and Deg1 M. A. PubMed Scopus Google Scholar). signal the of the Matα2 protein, and involves the E2 enzymes and P. P. M. PubMed Scopus Google Scholar). has that a of an in Deg1 is the structural of this signal M. 1998; PubMed Scopus Google Scholar). is that the Deg1 signal also a nuclear localization signal C. A. PubMed Scopus Google Scholar). it that the components of the ubiquitin system are the for the of the system is 11: PubMed Scopus Google Scholar, Annu. Rev. Cell Biol. 1998; PubMed Scopus Google Scholar). and and are also crucial components of PubMed Scopus Google Scholar, C. 1996; PubMed Scopus Google Scholar, A. M. 1996; PubMed Scopus Google Scholar, C. PubMed Scopus Google Scholar). proteolytic which to be to a specific is the degradation of In the of the E3 or are in the W. M. 1996; PubMed Scopus Google Scholar). Furthermore, it has that the 26 S proteasome is in and the nucleus in C. A. 1998; PubMed Scopus Google Scholar). it to be in which proteolysis we demonstrate for the that rapid and specific proteolysis of a short-lived protein is to a cellular the Matα2 is an nuclear protein that is the Deg1 signal confers localization to a reporter protein and is with slower a NLS PubMed Scopus Google is to Deg1 turnover the of Matα2 a degradation signal has to be with localization signals it to to proteolysis by the Deg1 signal with to nuclear this we fusion of the Deg1 signal with a of PubMed Scopus Google which in and the of short-lived fusion proteins. is a protein, which is the cell of the reporter the nuclear a of localization of fusion with a fluorescence and protein in by In is of that the of as well as the degradation of the fusion protein to of a described both in the reporter to be a substrate to study we the Deg1 degradation signal to exhibits the nuclear localization as the Matα2 protein. observed that the endogenous NLS of Deg1 is to the fusion protein to the which is in with C. A. PubMed Scopus Google Scholar). In to a of the Matα2 and to a reporter protein both of which are nuclear a of in the we the half-life of be by this this we the Deg1 and the in this fusion protein in the nucleus turnover that observed for that the we this by a PubMed Scopus Google Scholar). this is to the nucleus these the that nuclear import of a proteolytic substrate be a for degradation via the ubiquitin-proteasome we the of a in nuclear import on proteolysis of C. P. 11: PubMed Scopus Google Scholar, W. Cell Biol. Google PubMed Scopus Google Scholar, M. Silver 1996; PubMed Scopus Google in which nuclear import is affected of in components of the nuclear to the to the nuclear both and and turnover to the of with degradation of an substrate 11: PubMed Scopus Google Scholar, Annu. Rev. Cell Biol. 1998; PubMed Scopus Google in these mutants that nuclear import of the proteolytic system. Furthermore, we the that the nuclear import of the NLS J.D. Silver A. PubMed Scopus Google Scholar). In this to the cytosol and turnover In contrast, proteolysis of which the as in for a specific degradation of the nucleus we the of this we an of ubiquitin M. Biol. Chem. PubMed Google in and W. C. PubMed Scopus Google the of which is affected in In the from or the we observed of we to in that ubiquitin conjugation pathways are for the proteolysis of substrates to this described with fusion the Deg1 the of observations for the degradation of the endogenous Matα2 protein we the proteolysis of this in In both a in Matα2 turnover observed The of with that of in that nuclear import a proteolytic of the Matα2 protein. In the are with with the reporter protein and the of a proteolytic specific for Matα2 in the described to the that nuclear import be a for rapid proteolysis by Deg1 a NLS the fusion of it imported into the nucleus. half-life when import into the nucleus is this we the endogenous NLS in the Deg1 In to in the PubMed Scopus Google we and with In into In the turnover of this fusion protein slower that of an localization of observed of into the nucleus by an of a to turnover of this protein slower that of Obviously, the in the of Deg1 to with of the degradation signal or with of the of the Deg1 signal and endogenous we an a nuclear export signal specific for the C. PubMed Scopus Google into to the imported into the a we a W. 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A. PubMed Scopus Google Scholar). In to a of the Matα2 and to a reporter protein both of which are nuclear a of in the we the half-life of be by this this we the Deg1 and the in this fusion protein in the nucleus turnover that observed for that the we this by a PubMed Scopus Google Scholar). this is to the nucleus these the that nuclear import of a proteolytic substrate be a for degradation via the ubiquitin-proteasome pathway. we the of a in nuclear import on proteolysis of C. P. 11: PubMed Scopus Google Scholar, W. Cell Biol. Google PubMed Scopus Google Scholar, M. Silver 1996; PubMed Scopus Google in which nuclear import is affected of in components of the nuclear to the to the nuclear both and and turnover to the of with degradation of an substrate 11: PubMed Scopus Google Scholar, Annu. Rev. Cell Biol. 1998; PubMed Scopus Google in these mutants that nuclear import of the proteolytic system. Furthermore, we the that the nuclear import of the NLS J.D. Silver A. PubMed Scopus Google Scholar). In this to the cytosol and turnover In contrast, proteolysis of which the as in for a specific degradation of the nucleus we the of this we an of ubiquitin M. Biol. Chem. PubMed Google in and W. C. PubMed Scopus Google the of which is affected in In the from or the we observed of we to in that ubiquitin conjugation pathways are for the proteolysis of substrates to this described with fusion the Deg1 the of observations for the degradation of the endogenous Matα2 protein we the proteolysis of this in In both a in Matα2 turnover observed The of with that of in that nuclear import a proteolytic of the Matα2 protein. In the are with with the reporter protein and the of a proteolytic specific for Matα2 in the nucleus. described to the that nuclear import be a for rapid proteolysis by Deg1 a NLS the fusion of it imported into the nucleus. half-life when import into the nucleus is this we the endogenous NLS in the Deg1 In to in the PubMed Scopus Google we and with In into In the turnover of this fusion protein slower that of an localization of observed of into the nucleus by an of a to turnover of this protein slower that of Obviously, the in the of Deg1 to with of the degradation signal or with of the of the Deg1 signal and endogenous we an a nuclear export signal specific for the C. PubMed Scopus Google into to the imported into the a we a W. 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The fusion and in the nucleus and the fusion protein is whereas the reporter exhibits an half-life with turnover of the substrate with nuclear localization whereas proteolysis with we that the Deg1 degradation signal mediates proteolysis only in the nucleus. for this is by the that proteolysis of the fusion protein as well as is in mutants in nuclear import it that proteolysis in is in these mutants the degradation of a substrate as from the with the Deg1 signal are of for the degradation of the Matα2 transcriptional repressor of the First, turnover of the endogenous Matα2 also in nuclear import the of a on Matα2 degradation that of or a exported fusion protein a half-life with a fusion protein the The and on the fusion protein the that the half-life of Matα2 is a of the the protein in the we observed and nuclear turnover of Deg1-containing fusion proteins. The of Deg1 by a of Ubc6p/Ubc7p is in the cytosol in the nucleus. the of on Deg1-induced proteolysis to be in the whereas in the cytosol a crucial role. The of observed in is most to the that the of is in these C. PubMed Scopus Google Scholar). The turnover of in the cytosol most the endoplasmic it that degradation of a fusion protein on the of and on the of to the endoplasmic C. PubMed Scopus Google Scholar). degradation of and and from that of a substrate turnover in the cytosol and in the nucleus are most of the rapid Matα2 system M. A. PubMed Scopus Google also be in the cytosol many of the be of demonstrate that the half-life of a protein is by specific degradation and localization The on localization signals is by the of components of the ubiquitin system to a E3 enzyme be in the nucleus and rapid turnover in this this the Ubc6p/Ubc7p are to the signal with imply that the nucleus is a crucial for Matα2 in which nuclear export is also a specific for rapid proteolysis M. 1998; PubMed Scopus Google Scholar, 1999; PubMed Scopus Google Scholar, Biol. Chem. 1999; PubMed Scopus Google Scholar). In cell biological a to a half-life. a protein into a the turnover be or components of the are to within an The of this study to and proteolysis of a short-lived protein only on the of a degradation signal also a specific localization of the this we fusion of and the degradation signal contained in Matα2 or for the to to the nucleus or to the the specific localization of the substrate in in which in on the ubiquitin-proteasome pathway. The fusion and in the nucleus and the fusion protein is whereas the reporter exhibits an half-life with turnover of the substrate with nuclear localization whereas proteolysis with we that the Deg1 degradation signal mediates proteolysis only in the nucleus. for this is by the that proteolysis of the fusion protein as well as is in mutants in nuclear import it that proteolysis in is in these mutants the degradation of a substrate as The from the with the Deg1 signal are of for the degradation of the Matα2 transcriptional repressor of the First, turnover of the endogenous Matα2 also in nuclear import the of a on Matα2 degradation that of or a exported fusion protein a half-life with a fusion protein the The and on the fusion protein the that the half-life of Matα2 is a of the the protein in the nucleus. In we observed and nuclear turnover of Deg1-containing fusion proteins. The of Deg1 by a of Ubc6p/Ubc7p is in the cytosol in the nucleus. the of on Deg1-induced proteolysis to be in the whereas in the cytosol a crucial role. The of observed in is most to the that the of is in these C. PubMed Scopus Google Scholar). The turnover of in the cytosol most the endoplasmic it that degradation of a fusion protein on the of and on the of to the endoplasmic C. PubMed Scopus Google Scholar). degradation of and and from that of a substrate These turnover in the cytosol and in the nucleus are most of the rapid Matα2 system M. A. 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