THE UNIQUE PROPERTIES OF BRANCHED K11/K48-LINKED POLYUBIQUITIN, AND THE PROTEASOMAL RECOGNITION OF (POLY)UBIQUITIN AND UBIQUITIN-LIKE SIGNALS BY RPN1

Abstract

Post-translational modification of substrates with ubiquitin (Ub) is an essential process across all eukaryotes, responsible for regulating a myriad of cellular pathways. Many aspects of ubiquitination are extensively studied, and its role in proteasomal degradation is of significant therapeutic interest. This degradation pathway relies upon the coordinated interplay among Ub, shuttle proteins containing Ub-like (UBL) domains, and the proteasome. Substrates are tagged with polymeric Ub (polyUb) and shuttle proteins; these signals are recognized by the proteasome, which subsequently degrades the substrate.The diversity of polyUb signaling reflects Ub’s ability to form a covalent linkage between the C-terminus of one Ub and any of seven lysines or the N-terminus of another Ub. Furthermore, polyUb may contain homogeneous, heterogeneous, unbranched, or branched linkages. Thus, polyUb can be assembled with numerous specific architectures, each of which may convey distinct signaling outcomes. Notably, branched K11/K48-linked polyUb was recently shown to enhance proteasomal degradation during mitosis. Here, we determined the crystal and NMR structures of branched K11/K48-linked Ub3 and discovered a previously unobserved interface between the distal Ubs. Additional techniques corroborated this interfacial effect, which we hypothesized to be influential in the physiological role of branched K11/K48-linked polyUb. Although initial probing of polyUb interactions – binding to the shuttle protein hHR23A; deubiquitination assays – resulted in negligible differences between branched K11/K48-linked Ub3 and related Ub2 moieties, stronger binding affinity for branched K11/K48-linked Ub3 was observed with proteasomal subunit Rpn1, thereby suggesting a functional impact of this interdomain interface and pinpointing the mechanistic site of enhanced degradation. We devoted further attention to Rpn1, the largest and least characterized proteasomal subunit. We confirmed that Rpn1 associates with UBL-containing proteins and polyUbs, while exhibiting a preference for shuttle protein Rad23. Moreover, our results suggested that Rpn1 contains multiple Ub/UBL-binding sites. These sites are shared among polyUb and Ub-like moieties, thereby ruling out the possibility of exclusive recognition sites for individual signals. Finally, we identified the location of a novel Ub/UBL-binding site in Rpn1, which exhibits relatively strong affinity for polyUb and Ub-like signals. Surprisingly, this site is situated in a region of Rpn1 previously surmised to be devoid of functionality.