Quantitative proteomics reveals the function of unconventional ubiquitin chains in proteasomal degradation.
All seven lysine residues in ubiquitin contribute to the synthesis of polyubiquitin chains on protein substrates. Whereas K48-linked chains are well established as mediators of proteasomal degradation, and K63-linked chains act in nonproteolytic events, the roles of unconventional polyubiquitin chains linked through K6, K11, K27, K29, or K33 are not well understood. Here, we report that the unconventional linkages are abundant in vivo and that all non-K63 linkages may target proteins for degradation. Ubiquitin with K48 as the single lysine cannot support yeast viability, and different linkages have partially redundant functions. By profiling both the entire yeast proteome and ubiquitinated proteins in wild-type and ubiquitin K11R mutant strains using mass spectrometry, we identified K11 linkage-specific substrates, including Ubc6, a ubiquitin-conjugating enzyme involved in endoplasmic reticulum-associated degradation (ERAD). Ubc6 primarily synthesizes K11-linked chains, and K11 linkages function in the ERAD pathway. Thus, unconventional polyubiquitin chains are critical for ubiquitin-proteasome system function.
Xu
Ping
P
Department of Human Genetics, Center for Neurodegenerative Diseases, Emory University, Atlanta, GA 30322, USA.
Duong
Duc M
DM
Seyfried
Nicholas T
NT
Cheng
Dongmei
D
Xie
Yang
Y
Robert
Jessica
J
Rush
John
J
Hochstrasser
Mark
M
Finley
Daniel
D
Peng
Junmin
J
D004721:Endoplasmic Reticulum / Q000378:metabolism; D008239:Lysine / Q000378:metabolism; D013058:Mass Spectrometry; D046988:Proteasome Endopeptidase Complex / Q000378:metabolism*; D020543:Proteome / Q000032:analysis*; D012441:Saccharomyces cerevisiae / Q000737:chemistry / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism; D025801:Ubiquitin / Q000378:metabolism; D044763:Ubiquitin-Conjugating Enzymes / Q000378:metabolism
D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins; D025801:Ubiquitin; C082461:UBC6 protein, S cerevisiae; D044763:Ubiquitin-Conjugating Enzymes; D046988:Proteasome Endopeptidase Complex; D008239:Lysine