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The natural history of ubiquitin and ubiquitin-related domains #MMPMID22201813
Burroughs AM; Iyer LM; Aravind L
Front Biosci (Landmark Ed) 2012[Jan]; 17 (ä): 1433-60 PMID22201813show ga
The ubiquitin (Ub) system, which is centered on the conjugation and deconjugation of Ub and Ub-like (Ubls) proteins to proteins or lipids by a system of ligases and peptidases, respectively, regulates practically all aspects of eukaryotic biology. Ub/Ubls contain the beta-grasp fold (beta-GF) that is also found in Ub-related domains of several other proteins of the Ub-system and numerous proteins with biochemically distinct roles unrelated to the conventional Ub-system. Taken together, domains displaying the beta-grasp include versions performing catalytic roles, scaffolding of iron-sulfur clusters, binding of RNA and other biomolecules such as co-factors and sulfur transfer in biosynthesis of diverse metabolites. The beta-GF appears to have undergone an early radiation spawning at least seven clades prior to the divergence of extant organisms from their last universal common ancestor. The beta-GF appears to have first emerged in the context of translation-related RNA-interactions and subsequently exploded to occupy various functional niches. Most structural and biochemical diversification of the beta-GF occurred in prokaryotes, with the Ubl clade showing a dramatic expansion in the eukaryotic phase of its evolution. Hence, at least 70 distinct Ubl families are observed in eukaryotes, of which nearly 20 families were probably present in the last eukaryotic common ancestor. Diversification of Ubl families early in eukaryotic evolution played a major role in emergence of characteristic eukaryotic cellular sub-structures and systems pertaining to nucleo-cytoplasmic compartmentalization and dynamics, vesicular trafficking, autophagy and different protein degradation systems. Recent comparative genomics studies indicate that precursors of the eukaryotic Ub-system emerged first in prokaryotes. The simplest of these combine an Ubl and an E1-like enzyme involved in metabolic pathways related metallopterin, thiamine, cysteine, siderophore and perhaps modified base biosynthesis. Sampylation in archaea and Urmylation in eukaryotes appear to represent direct recruitment of such systems as simple protein-tagging apparatuses. However, other prokaryotic systems incorporated further components that more or less mirror the eukaryotic condition in possessing an E2, a RING-type E3 or both of these components. Additionally, prokaryotes have evolved conjugation systems that are independent of Ub ligases, such as the Pup system.
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Front+Biosci+(Landmark+Ed) 2012 ; 17 (ä): 1433-60
