Diverse fate of ubiquitin chain moieties: The proximal is degraded with the target, and the distal protects the proximal from removal and recycles

Significance The canonical targeting signal for degrading proteins by the ubiquitin (Ub) system—a chain composed of multiple Ub moieties—has remained a mystery. The structure of the proteasome, the enzyme that recognizes the signal and degrades the target substrate cannot explain why such a long chain is needed. To better understand this problem, we synthesized α-globin to which chains with different number of Ubs were attached. In long adducts, the proximal Ub remains on the substrate, likely securing its attachment to the proteasome, and is degraded with it. The distal Ub protects the proximal from removal by deubiquitinating enzymes and is then removed and recycled. In short adducts, the Ub moieties are rapidly removed, and the substrate remains stable.