Novel Predicted Peptidases with a Potential Role in the Ubiquitin Signaling Pathway

Abstract

A multi-pronged strategy including extensive sequence searches, structural modeling, and analysis of contextual information extracted from domain architectures, genetic screens, and large-scale protein-protein interaction analyses was employed to predict previously undetected components of the eukaryotic ubiquitin (Ub) signaling system. Two novel groups of proteins that are likely to function as de-ubiquitinating and de-SUMOylating peptidases (DUBs) were identified. The first group of putative DUBs, designated PPPDE superfamily (after Permuted Papain fold Peptidases of DsRNA viruses and Eukaryotes), consists of predicted thiol peptidases with a circularly permuted papain-like fold. The inference of the likely DUB function of the PPPDE superfamily proteins is based on the fusions of the catalytic domain to Ub-binding PUG (PUB)/UBA domains and a novel α-helical Ub-associated domain (the PUL domain, after PLAP, Ufd3p and Lub1p). The presence of the PPPDE superfamily proteins in most eukaryotic lineages, including basal ones, such as Giardia, suggests a role in deubiquitination of highly conserved proteins involved in key cellular functions, such as cell cycle control. In addition to eukaryotic proteins, the PPPDE superfamily includes predicted proteases from several groups of double-stranded RNA viruses and one single-stranded DNA virus. The apparent recruitment of DUBs for viral polyprotein processing seems to represent a common theme in evolution of viruses. The second group of putative DUBs identified in this study is the WLM (Wss1p-like metalloproteases) family of the Zincin-like superfamily of Zn-dependent peptidases, which are linked to the Ub-system by virtue of fusions with the UB-binding PUG (PUB), Ub-like, and Little Finger domains. More specifically, genetic evidence implicates the WLM family in de-SUMOylation. If validated experimentally, the WLM family proteins will represent the first case of a Zincin-like metalloprotease involvement in Ub-signaling.

Doa1 Is a Cdc48 Adapter That Possesses a Novel Ubiquitin Binding Domain

“…Using a bioinformatics approach, Iyer et al identified a conserved domain (the PUL domain, present in PLAA, Ufd3, and Lub1) within the PLAA family (Doa1 residues 465 to 715) and speculated that it is a ubiquitin binding domain (19). In part, they based this analysis on previous biochemical data from our lab that also suggested the presence of a ubiquitin binding domain in Doa1 (38).…”

“…We show that the C-terminal PUL domain of Doa1 directly binds to Cdc48 and that this interaction facilitates the recruitment of Cdc48 to ubiquitin (19). Moreover, we demonstrate that DOA1 and CDC48 are genetically linked.…”

Control of p97 function by cofactor binding

“…Both modules had originally been linked to the ubiquitin system based on bioinformatic analyses [82][83][84].…”

Wss1 Is a SUMO-Dependent Isopeptidase That Interacts Genetically with the Slx5-Slx8 SUMO-Targeted Ubiquitin Ligase

“…The loss of WSS1 alone does not result in an obvious growth defect; however, the cells are sensitive to continuous UV irradiation (36), and the sgs1⌬ wss1⌬ double mutant displays a slow-growth phenotype (37,49). Bioinformatic analysis of ubiquitination factors by Iyer and colleagues identified Wss1 as the founding member of the "WLM" family of metalloproteases (Wss1p-like metalloproteases) (18). The WLM metalloprotease domain is characterized by the Zn-binding consensus sequence HEXsHX6H (where s is a small amino acid).…”