The natural history of ubiquitin and ubiquitin-related domains

Abstract

The ubiquitin (Ub) system is centered on conjugation and deconjugation of Ub and Ub-like (Ubls) proteins by a system of ligases and peptidases, respectively. Ub/Ubls contain the beta-grasp fold, also found in numerous proteins with biochemically distinct roles unrelated to the conventional Ub-system. The beta-GF underwent an early radiation spawning at least seven clades prior to the divergence of extant organisms from their last universal common ancestor, first emerging in the context of translation-related RNA-interactions and subsequently exploding to occupy various functional niches. Most beta-GF diversification occurred in prokaryotes, with the Ubl clade showing dramatic expansion in the eukaryotes. Diversification of Ubl families in eukaryotes played a major role in emergence of characteristic eukaryotic cellular sub-structures and systems. Recent comparative genomics studies indicate precursors of the eukaryotic Ub-system emerged in prokaryotes. The simplest of these combine an Ubl and an E1-like enzyme in metabolic pathways. Sampylation in archaea and Urmylation in eukaryotes appear to represent recruitment of such systems as simple protein-tagging apparatuses. However, other prokaryotic systems incorporated further components and mirror the eukaryotic condition in possessing an E2, a RING-type E3 or both of these components. Additionally, prokaryotes have evolved conjugation systems independent of Ub ligases, such as the Pup system.

Figure 1

Topology diagrams of selected beta-GF members. A generalized representation of the beta-GF depicting the conserved secondary structure elements, and key structural features found in certain lineages of the fold, is shown in (A). Shown in (B) are idealized versions of specific lineages, the names of which are given above the diagrams. Strands are illustrated as arrows with the arrowhead pointing to the C-terminal end and helices as rectangles. Strands belonging to the 4-stranded beta-GF core are colored green, the additional strand found in the 5-stranded assemblage is colored yellow, strands forming a conserved insert within the beta-GF scaffold are colored magenta, and other strands specific to a certain lineage are colored grey and outlined with a broken line. The absolutely conserved core helix is colored orange and other helices specific to a certain lineage colored grey and outlined with a broken line. Topologies are grouped and labeled in a manner consistent with the structural classes described in the text, with members of the eukaryotic UB-like superfamily nested within other members of the 5-stranded assemblage. The 2Fe-2S cluster of the ferredoxins is shown as four small ovals bound to cysteine residues represented by the letter "C".

Figure 2

Cartoon depictions of distinct beta-GF domains. The core conserved strands and helices are colored blue and red respectively. Also shown are the critical residues in MutT responsible for catalytic activity.

Figure 3

Reconstructed evolutionary history of the beta-grasp fold. Individual lineages, listed to the right of the figure, are grouped according to classification given in the text. The inferred evolutionary depth of the lineages is traced by solid horizontal lines across the relative temporal epochs representing major evolutionary transitional periods shown as vertical lines. Horizontal lines are colored according to their observed phyletic distributions; the key for this coloring scheme is given at the bottom of the figure. Dashed lines indicate an uncertainty in terms of the origins of a lineage, while grey ellipses group lineages of relatively restricted phyletic distribution with more broadly distributed ones, indicating that the former likely underwent rapid divergence from the latter. The major structural and functional transitions of the fold are marked by green ellipses along with a brief description. Colored, labeled squares immediately to the left of the lineage names represent broad functional categories: E, enzymatic activity; LMB, ligand or metal-binding; CO, conjugated versions; AD, mediator of protein-protein interactions; RNA, RNA metabolism-related.

Figure 4

Reconstructed evolutionary history of the eukaryotic ubiquitin superfamily. In contrast to Figure 3, major evolutionary transitions are now shown as horizontal lines and the maximum depth to which these individual lineages can be traced is shown with solid vertical lines. The rest of the details that includes functional categories are as in Figure 3.

Figure 5

A) Architectural complexity plot of beta-grasp domains found in eukaryotes and prokaryotes. The complexity quotient (CQ) for a given species (y-axis) is plotted against the total number of beta-grasp domain containing proteins in the same species. Species abbreviations are given next to plot points. B) Domain architectures of selected beta-grasp domains. Proteins are denoted by their gene names, species abbreviations and genbank index numbers. Proteins are not drawn to scale. The conserved cysteine clusters observed in the NPL4-N family are shown as orange ellipses. Expansion of domain abbreviations: B3, DNA-binding domain; Auxin response, auxin-responsive transcription factor domain, also called Aux-RF; OTU, OTU-like family of cysteine proteases; Znf, zinc-finger; Znf_LF, little finger family of zinc finger domains; beta-P, beta-propeller domain; X, previously uncharacterized BofC C-terminal domain. Species abbreviations are as follows: Aaeo, Aquifex aeolicus; Ath, Arabidopsis thaliana; Bfra, Bacteroides fragilis; Cele, Caenorhabditis elegans; Cneo, Cryptococcus neoformans; Cpneu, Chlamydophila pneumoniae.; Cpar, Cryptosporidium parva; Ctet, Clostridium tetani; Ctep, Chlorobium tepidum; Ddis, Dictyostelium discoideum; Dmel, Drosophila melonogaster; Drad, Deinococcus radiodurans; Drer, Danio rerio; Ecol, Escherichia cioli; Ehis, Entamoeba histolytica; Glam, Giardia lamblia; Hpyl, Helicobacter pylori; Hsap, Homo sapiens; Lmaj, Leishmania major; Mpne, Mycoplasma pneumoniae; Msp., Mesorhizobium sp.; Mtub, Mycobacterium tuberculosis; Ncra, Neurospora crassa; Nmen, Neisseria meningitides; Nsp., Nostoc sp.; Otau, Ostreococcus tauri; Pfal, Plasmodium falciparum; Rnor, Rattus norvegicus; Save, Streptomyces avermitilis; Scer, Saccharomyces cerevisiae; Spom, Schizosaccharomyces pombe; Ssp., Synecococcus sp.; Tcru, Trypanosoma cruzi; Tden, Treponema denticola; Tmar, Thermotoga maritima; Tthe, Tetrahymena thermophila; Tvag, Trichomonas vaginalis; Uma, Ustilago maydis; Vcho, Vibrio cholerae.

Figure 6

Relative location of beta-grasp interacting partners. The strands and core helix of an idealized beta-GF domain have been sectored into interaction zones, and the names of representatives of the beta-GF that interact using each of these zones are listed. The top view depicts the exposed face while the bottom view depicts the obscured face.