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Perturbations to the Ubiquitin Conjugate Proteome in Yeast Δubx Mutants Identify Ubx2 as a Regulator of Membrane Lipid Composition

Kolawa, Natalie and Sweredoski, Michael J. and Graham, Robert L. J. and Oania, Robert and Hess, Sonja and Deshaies, Raymond J. (2013) Perturbations to the Ubiquitin Conjugate Proteome in Yeast Δubx Mutants Identify Ubx2 as a Regulator of Membrane Lipid Composition. Molecular and Cellular Proteomics, 12 (10). pp. 2791-2803. ISSN 1535-9476. PMCID PMC3790291. https://resolver.caltech.edu/CaltechAUTHORS:20140306-101045851

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Abstract

Yeast Cdc48 (p97/VCP in human cells) is a hexameric AAA ATPase that is thought to use ATP hydrolysis to power the segregation of ubiquitin-conjugated proteins from tightly bound partners. Current models posit that Cdc48 is linked to its substrates through adaptor proteins, including a family of seven proteins (13 in human) that contain a Cdc48-binding UBX domain. However, few substrates for specific UBX proteins are known, and hence the generality of this hypothesis remains untested. Here, we use mass spectrometry to identify ubiquitin conjugates that accumulate in cdc48 and ubx mutants. Different ubx mutants exhibit unique patterns of conjugate accumulation that point to functional specialization of individual Ubx proteins. To validate our findings, we examined in detail the endoplasmic reticulum-bound transcription factor Spt23, which we identified as a putative Ubx2 substrate. Mutant ubx2Δ cells are deficient in both cleaving the ubiquitinated 120 kDa precursor of Spt23 to form active p90 and in localizing p90 to the nucleus, resulting in reduced expression of the target gene OLE1, which encodes fatty acid desaturase. Our findings provide a resource for future investigations on Cdc48, illustrate the utility of proteomics to identify ligands for specific ubiquitin receptor pathways, and uncover Ubx2 as a key player in the regulation of membrane lipid biosynthesis.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1074/mcp.M113.030163 DOIArticle
http://www.mcponline.org/content/12/10/2791PublisherArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3790291/PubMed CentralArticle
ORCID:
AuthorORCID
Sweredoski, Michael J.0000-0003-0878-3831
Hess, Sonja0000-0002-5904-9816
Deshaies, Raymond J.0000-0002-3671-9354
Additional Information:© 2013 The American Society for Biochemistry and Molecular Biology, Inc. Received April 22, 2013, and in revised form, May 31, 2013; published, MCP Papers in Press, June 22, 2013. We thank S. Jentsch, L. Hicke, T. Sommer, E. Jarosch, and C.-W. Wang for gifts of strains, plasmids, antibodies, and W. den Besten for help with strain construction and valuable discussions. We also thank R. Ernst for communicating results before publication and M. Mann for hosting N.K. for a visit. This work was supported by the Howard Hughes Medical Institute, of which R.J.D. is an Investigator. The Proteome Exploration Laboratory is supported by the Gordon and Betty Moore Foundation through Grant GBMF775 and the Beckman Institute.
Funders:
Funding AgencyGrant Number
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
Gordon and Betty Moore FoundationGBMF775
Caltech Beckman InstituteUNSPECIFIED
Issue or Number:10
PubMed Central ID:PMC3790291
Record Number:CaltechAUTHORS:20140306-101045851
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20140306-101045851
Official Citation:Kolawa, N., Sweredoski, M. J., Graham, R. L. J., Oania, R., Hess, S., & Deshaies, R. J. (2013). Perturbations to the Ubiquitin Conjugate Proteome in Yeast Δubx Mutants Identify Ubx2 as a Regulator of Membrane Lipid Composition. Molecular & Cellular Proteomics, 12(10), 2791-2803. doi: 10.1074/mcp.M113.030163
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:44176
Collection:CaltechAUTHORS
Deposited By: Jason Perez
Deposited On:06 Mar 2014 23:23
Last Modified:03 Oct 2019 06:15

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