Ubiquitin is double-phosphorylated by PINK1 for enhanced pH-sensitivity of conformational switch

The pros and cons of ubiquitination on the formation of protein condensates

Ubiquitination, a post-translational modification that attaches one or more ubiquitin (Ub) molecules to another protein, plays a crucial role in the phase-separation processes. Ubiquitination can modulate the formation of membrane-less organelles in two ways. First, a scaffold protein drives phase separation, and Ub is recruited to the condensates. Second, Ub actively phase-separates through the interactions with other proteins. Thus, the role of ubiquitination and the resulting polyUb chains ranges from bystanders to active participants in phase separation. Moreover, long polyUb chains may be the primary driving force for phase separation. We further discuss that the different roles can be determined by the lengths and linkages of polyUb chains which provide preorganized and multivalent binding platforms for other client proteins. Together, ubiquitination adds a new layer of regulation for the flow of material and information upon cellular compartmentalization of proteins.

Kinetic Constraints in the Specific Interaction between Phosphorylated Ubiquitin and Proteasomal Shuttle Factors

Ubiquitin (Ub) specifically interacts with the Ub-associating domain (UBA) in a proteasomal shuttle factor, while the latter is involved in either proteasomal targeting or self-assembly coacervation. PINK1 phosphorylates Ub at S65 and makes Ub alternate between C-terminally relaxed (pUb_RL) and retracted conformations (pUb_RT). Using NMR spectroscopy, we show that pUb_RL but not pUb_RT preferentially interacts with the UBA from two proteasomal shuttle factors Ubqln2 and Rad23A. Yet discriminatorily, Ubqln2-UBA binds to pUb more tightly than Rad23A does and selectively enriches pUb_RL upon complex formation. Further, we determine the solution structure of the complex between Ubqln2-UBA and pUb_RL and uncover the thermodynamic basis for the stronger interaction. NMR kinetics analysis at different timescales further suggests an indued-fit binding mechanism for pUb-UBA interaction. Notably, at a relatively low saturation level, the dissociation rate of the UBA-pUb_RL complex is comparable with the exchange rate between pUb_RL and pUb_RT. Thus, a kinetic constraint would dictate the interaction between Ub and UBA, thus fine-tuning the functional state of the proteasomal shuttle factors.

The 'dark matter' of ubiquitin-mediated processes: opportunities and challenges in the identification of ubiquitin-binding domains

Ubiquitin modifications of target proteins act to localise, direct and specify a diverse range of cellular processes, many of which are biomedically relevant. To allow this diversity, ubiquitin modifications exhibit remarkable complexity, determined by a combination of polyubiquitin chain length, linkage type, numbers of ubiquitin chains per target, and decoration of ubiquitin with other small modifiers. However, many questions remain about how different ubiquitin signals are specifically recognised and transduced by the decoding ubiquitin-binding domains (UBDs) within ubiquitin-binding proteins. This review briefly outlines our current knowledge surrounding the diversity of UBDs, identifies key challenges in their discovery and considers recent structural studies with implications for the increasing complexity of UBD function and identification. Given the comparatively low numbers of functionally characterised polyubiquitin-selective UBDs relative to the ever-expanding variety of polyubiquitin modifications, it is possible that many UBDs have been overlooked, in part due to limitations of current approaches used to predict their presence within the proteome. Potential experimental approaches for UBD discovery are considered; web-based informatic analyses, Next-Generation Phage Display, deubiquitinase-resistant diubiquitin, proximity-dependent biotinylation and Ubiquitin-Phototrap, including possible advantages and limitations. The concepts discussed here work towards identifying new UBDs which may represent the 'dark matter' of the ubiquitin system.

How Phosphorylation by PINK1 Remodels the Ubiquitin System: A Perspective from Structure and Dynamics

Ubiquitin is an important signaling protein in cells. It functions by covalent attachment to substrate proteins and by noncovalent interactions with target proteins. Ubiquitins are also concatenated, and the resulting polyubiquitins recognize target proteins multivalently with enhanced specificity. The function of ubiquitin is enabled by the conformational dynamics of ubiquitin and polyubiquitins, which spans over 12 orders of magnitude in a time scale. Recently, it was found that ubiquitin can be phosphorylated by PINK1 at residues S65 and T66. Only sparsely populated for the unmodified ubiquitin, a C-terminally retracted conformation is stabilized for phosphorylated ubiquitin and is further enriched at an increasing pH. The modulation of tertiary structure further impacts the quaternary arrangements of ubiquitin subunits in polyubiquitins. Additionally, ubiquitin phosphorylation inhibits the activities of many enzymes responsible for attaching and removing polyubiquitins, thus remodeling the composition and length of polyubiquitins. The phosphorylation-remolded polyubiquitins can then recognize different target proteins. As PINK1 and ubiquitin phosphorylation levels are up-regulated under certain pathophysiological conditions, the remodeled ubiquitin system may be involved in the divergence of cell fate.