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

Volume 3, Issue 11   November 2004
Pages 1440 - 1450
http://dx.doi.org/10.4161/cc.3.11.1206
Authors: Lakshminarayan M. Iyer, Eugene V. Koonin and L. Aravind

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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 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 alpha-helical Ub-associated domain (the PLAP, Ufd3p and Lub1p or PUL domain) amongst different members of the PPPDE supefamily. The presence of the PPPDE superfamily proteins in most eukaryotic lineages, including basal ones, such as Giardia, suggest 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 Zincin-like superfamily of Zn-dependent peptidases, which are linked to the Ub -system by virtue of fusions with the UB-binding PUG (PUB), ubiquitin-like and Little Finger domains. More specifically on the basis of genetic evidence the WLM family is implicated in de-SUMOylation. If validated experimentally, the WLM family proteins will represent the first case of a Zincin-like metalloprotease involvement in Ub-signaling.

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