Quantitative Proteomics Reveals the Function of Unconventional Ubiquitin Chains in Proteasomal Degradation

摘要

All seven lysine residues in ubiquitin contribute to the synthesis of polyubiquitin chains on protein substrates. Whereas K48-linked chains are well es_tablished 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 unconven_tional 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. Bу profiling both the entire yeast proteome and ubiquitinated proteins in wild-type and ubiquitin Ki 1 R mutant strains using mass spectrom_etry, we identified K11 linkage-specific substrates, including Ubc6, a ubiquitin-conjugating enzyme involved in endoplasmic reticuJum-associated degra_dation (ERAD). Ubc6 primarily synthesizes Ki 1-linked chains, and K11 linkages function in the ERAD pathway. Thus, unconventional polyubiquitin chains are critical for ubiquitin-proteasome system function.