Biochemical properties of K11,48-branched ubiquitin chains

As one of the most widely existing post-translational modification models, ubiquitination regulates diverse cellular activities. In eukaryotes, K_11,48-branched ubiquitin chains play key roles in cell cycle and protein quality control. However, the structural and biochemical properties of K_11,48-branched ubiquitin chains have not been well examined. Here we employed the synthetic linkage- and length-defined K_11,48-branched ubiquitin chains to examine their binding and hydrolysis properties in vitro. Quantitatively affinity determination of ubiquitin chains to the proteasome ubiquitin receptor S5a indicated that the S5a exhibited preference binding to K_11,48-branched chains over K₁₁-linked chains, but not K₄₈-conjugated chains. In addition, deubiquitination experiments were carried out and the results showed that K_11,48-branched chains were preferably hydrolyzed by proteasome-associated deubiquitinase Rpn11 than homotypic K₁₁ or K₄₈-linked chains.