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The DOI matches its Crossref record; 8 of the 8 references it cites were found in a registry or an index.

Defining the Human Deubiquitinating Enzyme Interaction Landscape

Open access
Sowa, Mathew E., Bennett, Eric J., Gygi, Steven P., Harper, J. Wade·2009·Cell
DOI 10.1016/j.cell.2009.04.042
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Abstract

Summary Deubiquitinating enzymes (Dubs) function to remove covalently attached ubiquitin from proteins, thereby controlling substrate activity and/or abundance. For most Dubs, their functions, targets, and regulation are poorly understood. To systematically investigate Dub function, we initiated a global proteomic analysis of Dubs and their associated protein complexes. This was accomplished through the development of a software platform, called CompPASS, which uses unbiased metrics to assign confidence measurements to interactions from parallel non-reciprocal proteomic datasets. We identified 774 candidate interacting proteins associated with 75 Dubs. Using Gene Ontology, interactome topology classification, sub-cellular localization and functional studies, we link Dubs to diverse processes, including protein turnover, transcription, RNA processing, DNA damage, and endoplasmic reticulum-associated degradation. This work provides the first glimpse into the Dub interaction landscape, places previously unstudied Dubs within putative biological pathways, and identifies previously unknown interactions and protein complexes involved in this increasingly important arm of the ubiquitin-proteasome pathway.

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Show all 8 references

Research works printed but not linked: 36

  1. Bellare, 2008, A role for ubiquitin in the spliceosome assembly pathway, Nat. Struct. Mol. Biol., 15, 444, 10.1038/nsmb.1401 · DOI
  2. Bennett, 2005, Global impairment of the ubiquitin-proteasome system by nuclear or cytoplasmic protein aggregates precedes inclusion body formation, Mol. Cell, 17, 351, 10.1016/j.molcel.2004.12.021 · DOI · Paper page
  3. Braun, 2009, An experimentally derived confidence score for binary protein-protein interactions, Nat. Methods, 6, 91, 10.1038/nmeth.1281 · DOI · Paper page
  4. Cohn, 2007, A UAF1-containing multisubunit protein complex regulates the Fanconi anemia pathway, Mol. Cell, 28, 786, 10.1016/j.molcel.2007.09.031 · DOI · Paper page
  5. Cohn, 2008, UAF1 is a subunit of multiple deubiquitinating enzyme complexes, J. Biol. Chem.
  6. Cusick, 2009, Literature-curated protein interaction datasets, Nat. Methods, 6, 39, 10.1038/nmeth.1284 · DOI · Paper page
  7. DeLaBarre, 2006, Central pore residues mediate the p97/VCP activity required for ERAD, Mol. Cell, 22, 451, 10.1016/j.molcel.2006.03.036 · DOI · Paper page
  8. Ewing, 2007, Large-scale mapping of human protein-protein interactions by mass spectrometry, Mol. Syst. Biol., 3, 89, 10.1038/msb4100134 · DOI · Paper page
  9. Futschik, 2007, Comparison of human protein-protein interaction maps, Bioinformatics, 23, 605, 10.1093/bioinformatics/btl683 · DOI
  10. Gavin, 2002, Functional organization of the yeast proteome by systematic analysis of protein complexes, Nature, 415, 141, 10.1038/415141a · DOI · Paper page
  11. Jeronimo, 2007, Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme, Mol. Cell, 27, 262, 10.1016/j.molcel.2007.06.027 · DOI · Paper page
  12. Kraft, 2008, Mature ribosomes are selectively degraded upon starvation by an autophagy pathway requiring the Ubp3p/Bre5p ubiquitin protease, Nat. Cell Biol., 10, 602, 10.1038/ncb1723 · DOI · Paper page
  13. Krogan, 2006, Global landscape of protein complexes in the yeast Saccharomyces cerevisiae, Nature, 440, 637, 10.1038/nature04670 · DOI · Paper page
  14. Liu, 2004, A model for random sampling and estimation of relative protein abundance in shotgun proteomics, Anal. Chem., 76, 4193, 10.1021/ac0498563 · DOI · Paper page
  15. Lu, 2009, USP19 deubiquitinating enzyme supports cell proliferation by stabilizing KPC1, a ubiquitin ligase for p27Kip1, Mol. Cell. Biol., 29, 547, 10.1128/MCB.00329-08 · DOI
  16. Malhotra, 2007, The endoplasmic reticulum and the unfolded protein response, Semin. Cell Dev. Biol., 18, 716, 10.1016/j.semcdb.2007.09.003 · DOI · Paper page
  17. Mendoza, 2007, PHLPPing it off: phosphatases get in the Akt, Mol. Cell, 25, 798, 10.1016/j.molcel.2007.03.007 · DOI
  18. Nicassio, 2007, Human USP3 is a chromatin modifier required for S phase progression and genome stability, Curr. Biol., 17, 1972, 10.1016/j.cub.2007.10.034 · DOI · Paper page
  19. Nijman, 2005, The deubiquitinating enzyme USP1 regulates the Fanconi anemia pathway, Mol. Cell, 17, 331, 10.1016/j.molcel.2005.01.008 · DOI · Paper page
  20. Nijman, 2005, A genomic and functional inventory of deubiquitinating enzymes, Cell, 123, 773, 10.1016/j.cell.2005.11.007 · DOI · Paper page
  21. Pickart, 2004, Proteasomes and their kin: proteases in the machine age, Nat. Rev. Mol. Cell Biol., 5, 177, 10.1038/nrm1336 · DOI · Paper page
  22. Pijnappel, 2008, Dubbing SAGA unveils new epigenetic crosstalk, Mol. Cell, 29, 152, 10.1016/j.molcel.2008.01.007 · DOI
  23. Rumpf, 2006, Functional division of substrate processing cofactors of the ubiquitin-selective Cdc48 chaperone, Mol. Cell, 21, 261, 10.1016/j.molcel.2005.12.014 · DOI · Paper page
  24. Sardiu, 2008, Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics, Proc. Natl. Acad. Sci. USA, 105, 1454, 10.1073/pnas.0706983105 · DOI · Paper page
  25. Sobhian, 2007, RAP80 targets BRCA1 to specific ubiquitin structures at DNA damage sites, Science, 316, 1198, 10.1126/science.1139516 · DOI · Paper page
  26. Stegmeier, 2007, Anaphase initiation is regulated by antagonistic ubiquitination and deubiquitination activities, Nature, 446, 876, 10.1038/nature05694 · DOI · Paper page
  27. Stegmeier, 2007, The tumor suppressor CYLD regulates entry into mitosis, Proc. Natl. Acad. Sci. USA, 104, 8869, 10.1073/pnas.0703268104 · DOI
  28. Sun, 2008, Deubiquitylation and regulation of the immune response, Nat. Rev. Immunol., 8, 501, 10.1038/nri2337 · DOI · Paper page
  29. Trippe, 2006, Identification, cloning, and functional analysis of the human U6 snRNA-specific terminal uridylyl transferase, RNA, 12, 1494, 10.1261/rna.87706 · DOI
  30. Uchiyama, 2002, VCIP135, a novel essential factor for p97/p47-mediated membrane fusion, is required for Golgi and ER assembly in vivo, J. Cell Biol., 159, 855, 10.1083/jcb.200208112 · DOI · Paper page
  31. Ventii, 2008, Protein partners of deubiquitinating enzymes, Biochem. J., 414, 161, 10.1042/BJ20080798 · DOI · Paper page
  32. Wang, 2006, Regulation of retrotranslocation by p97-associated deubiquitinating enzyme ataxin-3, J. Cell Biol., 174, 963, 10.1083/jcb.200605100 · DOI · Paper page
  33. Wang, 2008, Inhibition of p97-dependent Protein Degradation by Eeyarestatin I, J. Biol. Chem., 283, 7445, 10.1074/jbc.M708347200 · DOI · Paper page
  34. Zhang, 2006, A Role for the Deubiquitinating Enzyme USP28 in Control of the DNA-Damage Response, Cell, 126, 529, 10.1016/j.cell.2006.06.039 · DOI · Paper page
  35. Zhang, 2003, Transcriptional regulation by histone ubiquitination and deubiquitination, Genes Dev., 17, 2733, 10.1101/gad.1156403 · DOI · Paper page
  36. Zhao, 2008, A TFTC/STAGA module mediates histone H2A and H2B deubiquitination, coactivates nuclear receptors, and counteracts heterochromatin silencing, Mol. Cell, 29, 92, 10.1016/j.molcel.2007.12.011 · DOI · Paper page

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Metadata

Authors
Sowa, M. E., Bennett, E. J., Gygi, S. P., & Harper, J. W.
Venue
Cell
Publisher
Elsevier BV
Published
2009-07
Volume
138
Issue
2
Pages
389-403
ISSN
0092-8674 (ISSN-L)
DOI
10.1016/j.cell.2009.04.042
OpenAlex
W2106969933
Cited by
1,512
References
8
FWCI
40.33
Type
journal article
Language
en
Open access
bronze
Licence

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Sowa, M. E., Bennett, E. J., Gygi, S. P., & Harper, J. W. (2009). Defining the Human Deubiquitinating Enzyme Interaction Landscape. Cell. https://doi.org/10.1016/j.cell.2009.04.042

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