title: Mixed-linkage ubiquitin chains send mixed messages.
abstract: Research on ubiquitin (Ub) signaling has focused primarily on homogeneously linked polyUb. Although polyUb containing different linkages within the same chain exist, their structures and signaling properties are unknown. These mixed-linkage chains could be unbranched (i.e., no more than one lysine or methionine linkage per Ub) or branched. Here, we examined the structure, dynamics, receptor selectivity, and disassembly of branched and unbranched tri-Ub containing both K48 and K63 linkages. Each linkage was virtually indistinguishable from its counterpart in homogeneously linked polyUb. Linkage-selective receptors from hHR23A and Rap80 preferentially bound to the K48 or K63 linkages in the branched trimer. Linkage-selective deubiquitinases specifically cleaved their cognate Ub-Ub linkages in mixed-linkage chains, and the 26S proteasome recognized and processed branched tri-Ub. We conclude that mixed-linkage chains retain the distinctive signaling properties of their K48 and K63 components and that these multiple signals can be recognized by multiple linkage-specific receptors. Finally, we propose a new, comprehensive notation for Ub and Ub-like polymers.
authors.affiliation: Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA.
authors.forename: Mark A
authors.initials: MA
authors.lastname: Nakasone
authors.forename: Nurit
authors.initials: N
authors.lastname: Livnat-Levanon
authors.forename: Michael H
authors.initials: MH
authors.lastname: Glickman
authors.forename: Robert E
authors.initials: RE
authors.lastname: Cohen
authors.forename: David
authors.initials: D
authors.lastname: Fushman
mesh_terms: D002384:Catalysis; D008239:Lysine / Q000737:chemistry; D008958:Models, Molecular; D046988:Proteasome Endopeptidase Complex / Q000737:chemistry; D011487:Protein Conformation; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry; D025801:Ubiquitin / Q000737:chemistry*; D054875:Ubiquitination
chemical_list: D029701:Saccharomyces cerevisiae Proteins; D025801:Ubiquitin; D046988:Proteasome Endopeptidase Complex; C061553:ATP dependent 26S protease; D008239:Lysine
references.citation: J Cell Sci. 2012 Feb 1;125(Pt 3):539-48
references.pmid: 22389393
references.citation: J Biol Chem. 1990 May 25;265(15):8354-7
references.pmid: 2160452
references.citation: Curr Opin Chem Biol. 2004 Dec;8(6):610-6
references.pmid: 15556404
references.citation: Mol Cell Proteomics. 2011 May;10(5):R110.003871
references.pmid: 20823120
references.citation: J Mol Biol. 2009 Mar 6;386(4):1011-23
references.pmid: 19211026
references.citation: Cell. 2008 Aug 22;134(4):668-78
references.pmid: 18724939
references.citation: EMBO J. 2009 Aug 19;28(16):2461-8
references.pmid: 19536136
references.citation: J Biol Chem. 2007 Jun 15;282(24):17375-86
references.pmid: 17426036
references.citation: J Biol Chem. 2008 Sep 26;283(39):26436-43
references.pmid: 18599482
references.citation: Mol Cell Proteomics. 2011 May;10(5):M111.009753
references.pmid: 21427232
references.citation: J Biol Chem. 2009 Dec 18;284(51):35485-94
references.pmid: 19858201
references.citation: Mol Cell. 2006 Dec 8;24(5):701-711
references.pmid: 17157253
references.citation: Mol Cell Proteomics. 2010 Apr;9(4):705-18
references.pmid: 20047951
references.citation: Methods Enzymol. 2005;399:177-92
references.pmid: 16338356
references.citation: Mol Cell. 2009 Mar 27;33(6):775-83
references.pmid: 19328070
references.citation: J Mol Biol. 2002 Dec 6;324(4):637-47
references.pmid: 12460567
references.citation: J Biol Chem. 2010 Nov 12;285(46):35311-9
references.pmid: 20833710
references.citation: J Biol Chem. 2011 Mar 25;286(12):10457-65
references.pmid: 21278249
references.citation: Mol Cell. 2005 Jun 10;18(6):687-98
references.pmid: 15949443
references.citation: Nat Cell Biol. 2006 Jul;8(7):700-10
references.pmid: 16799550
references.citation: Methods Mol Biol. 2012;832:639-52
references.pmid: 22350918
references.citation: EMBO J. 2009 Mar 18;28(6):621-31
references.pmid: 19214193
references.citation: J Am Chem Soc. 2012 Apr 25;134(16):6916-9
references.pmid: 22497214
references.citation: J Am Chem Soc. 2007 Mar 21;129(11):3315-27
references.pmid: 17319663
references.citation: F1000 Biol Rep. 2011;3:26
references.pmid: 22162729
references.citation: Cell. 2009 Apr 3;137(1):133-45
references.pmid: 19345192
references.citation: PLoS Biol. 2004 Jan;2(1):E13
references.pmid: 14737189
references.citation: Cell. 2006 Dec 29;127(7):1401-13
references.pmid: 17190603
references.citation: J Cell Biol. 2004 Aug 16;166(4):487-92
references.pmid: 15314065
references.citation: Nat Protoc. 2010 May;5(5):883-97
references.pmid: 20431534
references.citation: J Biol Chem. 2004 Feb 20;279(8):7055-63
references.pmid: 14645257
references.citation: EMBO J. 2009 Jul 8;28(13):1867-77
references.pmid: 19387488
references.citation: Annu Rev Biochem. 1998;67:425-79
references.pmid: 9759494