Overlapping function of Hrd1 and Ste24 in translocon quality control provides robust channel surveillance
Avery M. Runnebohm, Kyle A. Richards, Courtney Broshar Irelan, Samantha M. Turk, Halie E. Vitali, Christopher J. Indovina, Eric M. Rubenstein
Abstract
Translocation of proteins across biological membranes is essential for life. Proteins that clog the endoplasmic reticulum (ER) translocon prevent the movement of other proteins into the ER. Eukaryotes have multiple translocon quality control (TQC) mechanisms to detect and destroy proteins that persistently engage the translocon. TQC mechanisms have been defined using a limited panel of substrates that aberrantly occupy the channel. The extent of substrate overlap among TQC pathways is unknown. In this study, we found that two TQC enzymes, the ER-associated degradation ubiquitin ligase Hrd1 and zinc metalloprotease Ste24, promote degradation of characterized translocon-associated substrates of the other enzyme in Saccharomyces cerevisiae. Although both enzymes contribute to substrate turnover, our results suggest a prominent role for Hrd1 in TQC. Yeast lacking both Hrd1 and Ste24 exhibit a profound growth defect, consistent with overlapping function. Remarkably, two mutations that mildly perturb post-translational translocation and reduce the extent of aberrant translocon engagement by a model substrate diminish cellular dependence on TQC enzymes. Our data reveal previously unappreciated mechanistic complexity in TQC substrate detection and suggest that a robust translocon surveillance infrastructure maintains functional and efficient translocation machinery. Translocation of proteins across biological membranes is essential for life. Proteins that clog the endoplasmic reticulum (ER) translocon prevent the movement of other proteins into the ER. Eukaryotes have multiple translocon quality control (TQC) mechanisms to detect and destroy proteins that persistently engage the translocon. TQC mechanisms have been defined using a limited panel of substrates that aberrantly occupy the channel. The extent of substrate overlap among TQC pathways is unknown. In this study, we found that two TQC enzymes, the ER-associated degradation ubiquitin ligase Hrd1 and zinc metalloprotease Ste24, promote degradation of characterized translocon-associated substrates of the other enzyme in Saccharomyces cerevisiae. Although both enzymes contribute to substrate turnover, our results suggest a prominent role for Hrd1 in TQC. Yeast lacking both Hrd1 and Ste24 exhibit a profound growth defect, consistent with overlapping function. Remarkably, two mutations that mildly perturb post-translational translocation and reduce the extent of aberrant translocon engagement by a model substrate diminish cellular dependence on TQC enzymes. Our data reveal previously unappreciated mechanistic complexity in TQC substrate detection and suggest that a robust translocon surveillance infrastructure maintains functional and efficient translocation machinery. Approximately one-third of eukaryotic proteins enter the endoplasmic reticulum (ER) en route to their final destinations (1Chen Y. Zhang Y. Yin Y. Gao G. Li S. Jiang Y. Gu X. Luo J. SPD: a web-based secreted protein database.Nucleic Acids Res. 2004; 33 (15608170): D169-D17310.1093/nar/gki093Crossref Scopus (153) Google Scholar, 2Choi J. Park J. Kim D. Jung K. Kang S. Lee Y.H. Fungal secretome database: integrated platform for annotation of fungal secretomes.BMC Genomics. 2010; 11 (20146824): 10510.1186/1471-2164-11-105Crossref PubMed Scopus (132) Google Scholar). Many of these proteins use the conserved Sec61 translocon protein channel to cross the ER membrane (3Aviram N. Schuldiner M. Targeting and translocation of proteins to the endoplasmic reticulum at a glance.J. Cell Sci. 2017; 130 (29246967): 4079-408510.1242/jcs.204396Crossref PubMed Scopus (62) Google Scholar). Translocation is essential to cellular viability (4Stirling C.J. Rothblatt J. Hosobuchi M. Deshaies R. Schekman R. 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The protease Ste24 clears clogged translocons.Cell. 2016; 164 (26771486): 103-11410.1016/j.cell.2015.11.053Abstract Full Text Full Text PDF PubMed Scopus (58) Google Scholar). The importance of protein translocation is underscored by the fact that cells have evolved at least three translocon quality control (TQC) mechanisms to detect and destroy such aberrant proteins (11Izawa T. Tsuboi T. Kuroha K. Inada T. Nishikawa S. Endo T. Roles of dom34:hbs1 in nonstop protein clearance from translocators for normal organelle protein influx.Cell Rep. 2012; 2 (22981232): 447-45310.1016/j.celrep.2012.08.010Abstract Full Text Full Text PDF PubMed Scopus (40) Google Scholar, 12Ast T. Michaelis S. Schuldiner M. The protease Ste24 clears clogged translocons.Cell. 2016; 164 (26771486): 103-11410.1016/j.cell.2015.11.053Abstract Full Text Full Text PDF PubMed Scopus (58) Google Scholar, 13Arakawa S. Yunoki K. Izawa T. Tamura Y. Nishikawa S. Endo T. Quality control of nonstop membrane proteins at the ER membrane and in the cytosol.Sci. Rep. 2016; 6 (27481473): 3079510.1038/srep30795Crossref PubMed Scopus (20) Google Scholar, 14Crowder J.J. Geigges M. Gibson R.T. Fults E.S. Buchanan B.W. Sachs N. Schink A. Kreft S.G. Rubenstein E.M. Rkr1/Ltn1 ubiquitin ligase-mediated degradation of translationally stalled endoplasmic reticulum proteins.J. Biol. Chem. 2015; 290 (26055716): 18454-1846610.1074/jbc.M115.663559Abstract Full Text Full Text PDF PubMed Scopus (29) Google Scholar, 15Rubenstein E.M. Kreft S.G. Greenblatt W. Swanson R. Hochstrasser M. Aberrant substrate engagement of the ER translocon triggers degradation by the Hrd1 ubiquitin ligase.J. Cell Biol. 2012; 197 (22689655): 761-77310.1083/jcb.201203061Crossref PubMed Scopus (48) Google Scholar, 16Voorhees R.M. Hegde R.S. Toward a structural understanding of co-translational protein translocation.Curr. Opin. Cell Biol. 2016; 41 (27155805): 91-9910.1016/j.ceb.2016.04.009Crossref PubMed Scopus (56) Google Scholar). Conserved TQC mechanisms have been most intensively studied in yeast. ER-associated degradation (ERAD) of translocon-associated proteins (ERAD-T) is mediated by the ER-resident ubiquitin ligase Hrd1 (15Rubenstein E.M. Kreft S.G. Greenblatt W. Swanson R. Hochstrasser M. Aberrant substrate engagement of the ER translocon triggers degradation by the Hrd1 ubiquitin ligase.J. Cell Biol. 2012; 197 (22689655): 761-77310.1083/jcb.201203061Crossref PubMed Scopus (48) Google Scholar). Mammalian apolipoprotein B (the major protein component of low-density lipoproteins) is targeted for degradation by the Hrd1 homolog gp78 if its translocation arrests (17Fisher E.A. Khanna N.A. McLeod R.S. Ubiquitination regulates the assembly of VLDL in HepG2 cells and is the committing step of the apoB-100 ERAD pathway.J. Lipid Res. 2011; 52 (21421992): 1170-118010.1194/jlr.M011726Abstract Full Text Full Text PDF PubMed Scopus (26) Google Scholar). In ERAD of ribosome-associated proteins (ERAD-RA), the cytosolic ubiquitin ligase Ltn1/Rkr1 (listerin in mammals) promotes destruction of yeast proteins that simultaneously arrest in the ribosome and translocon (14Crowder J.J. Geigges M. Gibson R.T. Fults E.S. Buchanan B.W. Sachs N. Schink A. Kreft S.G. Rubenstein E.M. Rkr1/Ltn1 ubiquitin ligase-mediated degradation of translationally stalled endoplasmic reticulum proteins.J. Biol. Chem. 2015; 290 (26055716): 18454-1846610.1074/jbc.M115.663559Abstract Full Text Full Text PDF PubMed Scopus (29) Google Scholar). In vitro data indicate that ERAD-RA is conserved in mammalian systems (18von der Malsburg K. Shao S. Hegde R.S. The ribosome quality control pathway can access nascent polypeptides stalled at the Sec61 translocon.Mol. Biol. Cell. 2015; 26 (25877867): 2168-218010.1091/mbc.E15-01-0040Crossref PubMed Scopus (36) Google Scholar). In a third TQC mechanism, the ER-localized zinc metalloprotease Ste24 (ZMPSTE24 in mammals) promotes the degradation of proteins engineered to clog the translocon, likely via substrate cleavage (12Ast T. Michaelis S. Schuldiner M. The protease Ste24 clears clogged translocons.Cell. 2016; 164 (26771486): 103-11410.1016/j.cell.2015.11.053Abstract Full Text Full Text PDF PubMed Scopus (58) Google Scholar). The extent of overlap of TQC pathways in substrate selection is not known. We investigated the functional redundancy between Hrd1 and Ste24. We found that two model TQC substrates are targeted for destruction, to different extents, by both Hrd1 and Ste24. Cells lacking both enzymes exhibit a synthetic growth defect, consistent with overlapping function. This phenotype is rescued by two mutations that preferentially impair PTT and reduce the extent of aberrant engagement by a model TQC substrate. We speculate that many naturally occurring TQC substrates engage the translocon that impair PTT are likely to reduce the of the cellular dependence on enzymes for translocon Our results indicate that TQC is a robust characterized by functional redundancy of and protein the of Hrd1 and Ste24 to we yeast lacking both enzymes. We the growth of and yeast. Yeast lacking or to cells However, yeast a profound growth defect, consistent with Hrd1 and Ste24 function. yeast lacking and the enzyme that with or yeast We previously in that yeast to yeast (14Crowder J.J. Geigges M. Gibson R.T. Fults E.S. Buchanan B.W. Sachs N. Schink A. Kreft S.G. Rubenstein E.M. Rkr1/Ltn1 ubiquitin ligase-mediated degradation of translationally stalled endoplasmic reticulum proteins.J. Biol. Chem. 2015; 290 (26055716): 18454-1846610.1074/jbc.M115.663559Abstract Full Text Full Text PDF PubMed Scopus (29) Google Scholar). We yeast lacking and and results reveal a between and Roles for Hrd1 and Ste24 in TQC have been by their to model substrates engineered to aberrantly engage the translocon. Hrd1 substrates are in mechanisms J.J. S.G. C.J. Rubenstein E.M. of and two is for degradation of a protein that aberrantly the endoplasmic reticulum 2017; PubMed Scopus Google Scholar). their in we Hrd1 and Ste24 can characterized substrates of the other The Hrd1 substrate is (15Rubenstein E.M. Kreft S.G. Greenblatt W. Swanson R. Hochstrasser M. Aberrant substrate engagement of the ER translocon triggers degradation by the Hrd1 ubiquitin ligase.J. Cell Biol. 2012; 197 (22689655): 761-77310.1083/jcb.201203061Crossref PubMed Scopus (48) Google Scholar). co-translational insertion of the cytosolic into the translocon via PTT (15Rubenstein E.M. Kreft S.G. Greenblatt W. Swanson R. Hochstrasser M. Aberrant substrate engagement of the ER translocon triggers degradation by the Hrd1 ubiquitin ligase.J. Cell Biol. 2012; 197 (22689655): 761-77310.1083/jcb.201203061Crossref PubMed Scopus (48) Google Scholar). This engagement is by an between and the of Sec61 (15Rubenstein E.M. Kreft S.G. Greenblatt W. Swanson R. Hochstrasser M. Aberrant substrate engagement of the ER translocon triggers degradation by the Hrd1 ubiquitin ligase.J. Cell Biol. 2012; 197 (22689655): 761-77310.1083/jcb.201203061Crossref PubMed Scopus (48) Google Scholar, Schekman R. of Sec61p in the ER-associated degradation of proteins.J. Cell Biol. PubMed Scopus Google Scholar). Hrd1 targets for degradation following this aberrant translocation (15Rubenstein E.M. Kreft S.G. Greenblatt W. Swanson R. Hochstrasser M. Aberrant substrate engagement of the ER translocon triggers degradation by the Hrd1 ubiquitin ligase.J. Cell Biol. 2012; 197 (22689655): 761-77310.1083/jcb.201203061Crossref PubMed Scopus (48) Google Scholar). We investigated the of Hrd1 and Ste24 to In post-translational and degradation and (15Rubenstein E.M. Kreft S.G. Greenblatt W. Swanson R. Hochstrasser M. Aberrant substrate engagement of the ER translocon triggers degradation by the Hrd1 ubiquitin ligase.J. Cell Biol. 2012; 197 (22689655): 761-77310.1083/jcb.201203061Crossref PubMed Scopus (48) Google Scholar). of Hrd1 consistent with the of Cells lacking Ste24 with However, of in the of of This is by the fact that for and results indicate that both Hrd1 and Ste24 contribute to with Hrd1 the prominent We Hrd1 promotes degradation of the model Ste24 In the protein is to a of (12Ast T. Michaelis S. Schuldiner M. The protease Ste24 clears clogged translocons.Cell. 2016; 164 (26771486): 103-11410.1016/j.cell.2015.11.053Abstract Full Text Full Text PDF PubMed Scopus (58) Google Scholar). are and of the The of to the ER membrane can on by with the are and have been into the ER with the are cytosolic that have not the translocon. We to the that is clogged or cytosolic the of in both and cells with yeast and This in cells A and (12Ast T. Michaelis S. Schuldiner M. 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Cell Biol. 2012; 197 (22689655): 761-77310.1083/jcb.201203061Crossref PubMed Scopus (48) Google in cells The of the protein the translocon. A on Sec61 the extent of consistent with of aberrant translocon engagement B and We investigated the of the Sec61 on translocation of model and the ER via can engineered to CTT by its with that of protein the protein is (14Crowder J.J. Geigges M. Gibson R.T. Fults E.S. Buchanan B.W. Sachs N. Schink A. Kreft S.G. Rubenstein E.M. Rkr1/Ltn1 ubiquitin ligase-mediated degradation of translationally stalled endoplasmic reticulum proteins.J. Biol. Chem. 2015; 290 (26055716): 18454-1846610.1074/jbc.M115.663559Abstract Full Text Full Text PDF PubMed Scopus (29) Google Scholar, M. C.J. Sec61p is for of the translocation and of using of Biol. Chem. Full Text Full Text PDF PubMed Scopus Google Scholar). ER and and exhibit by (14Crowder J.J. Geigges M. Gibson R.T. Fults E.S. Buchanan B.W. Sachs N. Schink A. Kreft S.G. Rubenstein E.M. 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Protein translocation is essential for life. of of cells lacking TQC enzymes likely a robust translocon surveillance infrastructure by functional we found of Ste24 and Hrd1 its enzyme with our between and have been in multiple M. A. J. Kim Y. H. K. S. J. T. of a 2010; PubMed Scopus Google Scholar, S. A. E. R.M. Schuldiner M. J.S. J. A a complex for membrane in Cell Biol. 2011; PubMed Scopus Google Scholar, M. A. C. G. W. M. J. Lee M. J. N. network a of cellular 2016; PubMed Scopus Google Scholar, M. A. T. J. C. Greenblatt J.S. of the and of the yeast pathway an Full Text Full Text PDF PubMed Scopus Google Scholar). we that Hrd1 and Ste24 are to different extents, of model substrates of the other Hrd1 and Ste24 not overlap in with of with or not reduce that Hrd1 not model translationally and stalled substrates (14Crowder J.J. Geigges M. Gibson R.T. Fults E.S. Buchanan B.W. Sachs N. Schink A. Kreft S.G. Rubenstein E.M. Rkr1/Ltn1 ubiquitin ligase-mediated degradation of translationally stalled endoplasmic reticulum proteins.J. Biol. Chem. 2015; 290 (26055716): 18454-1846610.1074/jbc.M115.663559Abstract Full Text Full Text PDF PubMed Scopus (29) Google Scholar). This a in the TQC of with that of Hrd1 and Ste24. in TQC is likely a of its role in ribosome quality control of a ribosome-associated ubiquitin ligase in protein quality 2010; PubMed Scopus Google Scholar, Mechanisms and of ribosome-associated protein quality Rev. Cell Biol. 2019; PubMed Scopus Google Scholar). by the protein promotes degradation of translationally stalled mammalian proteins Y. H. Li H. Y. of quality control to endoplasmic reticulum protein Res. PubMed Scopus Google Scholar). is not conserved in other ribosome quality control of translationally and stalled yeast proteins in to In to the characterized TQC substrates of Hrd1 and Ste24 aberrantly engage the translocon (12Ast T. Michaelis S. Schuldiner M. 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Rapoport T.A. mechanisms the protein translocation complex with proteins.J. Biol. Chem. 2017; Full Text Full Text PDF PubMed Scopus Google Scholar). the or of the PTT degradation is of Hrd1 that are for of Hrd1 substrates with or degradation (15Rubenstein E.M. Kreft S.G. Greenblatt W. Swanson R. Hochstrasser M. Aberrant substrate engagement of the ER translocon triggers degradation by the Hrd1 ubiquitin ligase.J. Cell Biol. 2012; 197 (22689655): 761-77310.1083/jcb.201203061Crossref PubMed Scopus (48) Google Scholar). Hrd1 is of or these proteins are for TQC to of the to degradation of Hrd1 of to (12Ast T. Michaelis S. Schuldiner M. The protease Ste24 clears clogged translocons.Cell. 2016; 164 (26771486): 103-11410.1016/j.cell.2015.11.053Abstract Full Text Full Text PDF PubMed Scopus (58) Google and of an engineered protein in yeast C. A. G. J. S. D. D. J. M. Ste24 Full Text Full Text PDF PubMed Scopus (31) Google Scholar). In these been to to substrates from the translocon. Our that Hrd1 to degradation the that a Hrd1 in TQC. to Hrd1 and its or of Although both Hrd1 and Ste24 contribute to destruction of two model aberrant translocon-associated the of these enzymes in TQC are not Hrd1 is the to a role for Ste24 is Hrd1 is a on the of degradation of these these results suggest that Hrd1 a prominent role in TQC substrate Ste24. the cytosolic of most in yeast. a of protein is in suggest previously unappreciated mechanistic complexity in TQC substrate Ste24 aberrant proteins to or in of Hrd1 proteins that have Ste24 detection and clog the model in detection by Ste24 is by data that Ste24 with both clogged and cytosolic (12Ast T. Michaelis S. Schuldiner M. The protease Ste24 clears clogged translocons.Cell. 2016; 164 (26771486): 103-11410.1016/j.cell.2015.11.053Abstract Full Text Full Text PDF PubMed Scopus (58) Google Scholar). of an of and on is consistent with a model in Hrd1 and Ste24 in a However, of a of degradation and to the The via translocation to of the or in a that of the translocon is the of in cells to the of TQC mechanisms or the degradation of that have the ER a growth is both and are consistent with at least function. of for Hrd1 and Ste24 in TQC and of these enzymes in a or pathways by of substrates that clog the translocon. We both and are by ER B.W. Hochstrasser M. Rubenstein E.M. reticulum endoplasmic reticulum and membrane protein quality control degradation Biol. Chem. 2019; Full Text Full Text PDF PubMed Scopus Google Scholar). The extent to substrate by ER of Hrd1 or Ste24 is not known. In the study, we of the clogged of we to preferentially in consistent with of Hrd1 by ER We speculate that of TQC ER is an to protein into an ER. Hrd1 and Ste24. Yeast lacking or exhibit of ER E. E.M. J. J.S. Schuldiner M. of for protein in the endoplasmic PubMed Scopus Google and to ER N. C. A. J. D. R.S. conserved of Biol. 2010; 6 PubMed Scopus Google Scholar, H. Li Zhang C. C. of and data to cellular 2004; PubMed Scopus Google Scholar). of and to ER and to the synthetic phenotype of yeast. both and exhibit a with M. A. J. Kim Y. H. K. S. J. T. of a 2010; PubMed Scopus Google and M. A. C. G. W. M. J. Lee M. J. N. network a of cellular 2016; PubMed Scopus Google and a post-translational translocon In the of of and on cellular the complex role of the translocon in the of different have on cellular from in translocation of a of proteins or in the or of other translocon Our and data indicate that Hrd1 and Ste24 overlapping at the translocon. Our results reveal complexity in TQC mediated by these enzymes. in of Hrd1 and Ste24 in and suggest that these enzymes detect different of proteins or of clogged Hrd1 and Ste24 with the translocon (12Ast T. Michaelis S. Schuldiner M. The protease Ste24 clears clogged translocons.Cell. 2016; 164 (26771486): 103-11410.1016/j.cell.2015.11.053Abstract Full Text Full Text PDF PubMed Scopus (58) Google Scholar, H. Y. H. of ER quality control of the translocon, and Rep. PubMed Scopus Google Scholar, A. Sec61p is of the endoplasmic degradation J. PubMed Scopus Google Ste24 with the translocon (12Ast T. Michaelis S. Schuldiner M. The protease Ste24 clears clogged translocons.Cell. 2016; 164 (26771486): 103-11410.1016/j.cell.2015.11.053Abstract Full Text Full Text PDF PubMed Scopus (58) Google Scholar). to the TQC substrate Yeast and in this are in of yeast and in this is in the by in the of cells to yeast by C. to Yeast and and Cell Scholar). Yeast in growth C. to Yeast and and Cell Scholar). of D. or two to membrane protein Cell Biol. 2015; Full Text Full Text PDF PubMed Scopus (58) Google yeast in containing the in containing and to B.W. Rubenstein E.M. of protein degradation in Saccharomyces 2016; and protein from 2000; PubMed Scopus Google Scholar, S.G. J.J. Rubenstein E.M. and of for protein degradation in Saccharomyces 2015; and Endo J.J. S.G. C.J. Rubenstein E.M. of and two is for degradation of a protein that aberrantly the endoplasmic reticulum 2017; PubMed Scopus Google The following at to detect at to detect and at by with at to detect the protein A H. K. J. Protein A from its by and its use an for of PubMed Scopus Google at the of and using an and data are the We and of the and Hochstrasser for We and for in and We and for We and for and We and Schuldiner for yeast We and Kreft for of this with co-translational translocation endoplasmic reticulum ER-associated degradation ERAD of translocon-associated proteins ERAD of ribosome-associated proteins a of engineered to the from post-translational translocation translocon quality