Polyubiquitin Linkage Profiles in Three Models of Proteolytic Stress Suggest the Etiology of Alzheimer Disease

Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322, USA.
Journal of Biological Chemistry (Impact Factor: 4.57). 03/2011; 286(12):10457-65. DOI: 10.1074/jbc.M110.149633
Source: PubMed


Polyubiquitin chains on substrates are assembled through any of seven lysine residues or the N terminus of ubiquitin (Ub),
generating diverse linkages in the chain structure. PolyUb linkages regulate the fate of modified substrates, but their abundance
and function in mammalian cells are not well studied. We present a mass spectrometry-based method to measure polyUb linkages
directly from total lysate of mammalian cells. In HEK293 cells, the level of polyUb linkages was found to be 52% (Lys48), 38% (Lys63), 8% (Lys29), 2% (Lys11), and 0.5% or less for linear, Lys6, Lys27, and Lys33 linkages. Tissue specificity of these linkages was examined in mice fully labeled by heavy stable isotopes (i.e. SILAC mice). Moreover, we profiled the Ub linkages in brain tissues from patients of Alzheimer disease with or without concurrent
Lewy body disease as well as three cellular models of proteolytic stress: proteasome deficiency, lysosome deficiency, and
heat shock. The data support that polyUb chains linked through Lys6, Lys11, Lys27, Lys29, and Lys48 mediate proteasomal degradation, whereas Lys63 chains are preferentially involved in the lysosomal pathway. Mixed linkages, including Lys48, may also contribute to lysosomal targeting, as both Lys63 and Lys48 linkages are colocalized in LC3-labeled autophagosomes. Interestingly, heat shock treatment augments Lys11, Lys48, and Lys63 but not Lys29 linkages, and this unique pattern is similar to that in the profiled neurodegenerative cases. We conclude that different
polyUb linkages play distinct roles under the three proteolytic stress conditions, and protein folding capacity in the heat
shock responsive pathway might be more affected in Alzheimer disease.

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    • "Chains that are linked through K48 are the principal signal for degradation by the proteasome [30] [31]. Recent studies, based on mass spectrometry have shown that homogeneous chains consisting of K29, K11, K27 and K6- linkages, heterogeneous chains with mixed lysine linkages, as well as multiple nearby monoubiquitination and, in cases of substrates up to 150 amino acids, even monoubiquitination can promote proteasomal degradation [32] [33]. Chain elongation of ubiquitinated substrates is mediated via another class of ubiquitin ligases, "
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    • "Moreover, they show that the K11 specificity of the APC/C is not essential for the turnover of anaphase substrates , whereas K48-linked chains are not a prerequisite for substrate targeting to the proteasome. Our observations thus support studies that found most linkages to accumulate in response to proteasome inhibition, indicative of a proteolytic role for the majority of chain topologies (Dammer et al., 2011; Peng et al., 2003; Xu et al., 2009). "
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