Functional diversification of the RING finger and other binuclear treble clef domains in prokaryotes and the early evolution of the ubiquitin system

Abstract

Recent studies point to a diverse assemblage of prokaryotic cognates of the eukaryotic ubiquitin (Ub) system. These systems span an entire spectrum, ranging from those catalyzing cofactor and amino acid biosynthesis, with only adenylating E1-like enzymes and ubiquitin-like proteins (Ubls), to those that are closer to eukaryotic systems by virtue of possessing E2 enzymes. Until recently E3 enzymes were unknown in such prokaryotic systems. Using contextual information from comparative genomics, we uncover a diverse group of RING finger E3s in prokaryotes that are likely to function with E1s, E2s, JAB domain peptidases and Ubls. These E1s, E2s and RING fingers suggest that features hitherto believed to be unique to eukaryotic versions of these proteins emerged progressively in such prokaryotic systems. These include the specific configuration of residues associated with oxyanion-hole formation in E2s and the C-terminal UFD in the E1 enzyme, which presents the E2 to its active site. Our study suggests for the first time that YukD-like Ubls might be conjugated by some of these systems in a manner similar to eukaryotic Ubls. We also show that prokaryotic RING fingers possess considerable functional diversity and that not all of them are involved in Ub-related functions. In eukaryotes, other than RING fingers, a number of distinct binuclear (chelating two Zn atoms) and mononuclear (chelating one zinc atom) treble clef domains are involved in Ub-related functions. Through detailed structural analysis we delineated the higher order relationships and interaction modes of binuclear treble clef domains. This indicated that the FYVE domain acquired the binuclear state independently of the other binuclear forms and that different treble clef domains have convergently acquired Ub-related functions independently of the RING finger. Among these, we uncover evidence for notable prokaryotic radiations of the ZF-UBP, B-box, AN1 and LIM clades of treble clef domains and present contextual evidence to support their role in functions unrelated to the Ub-system in prokaryotes. In particular, we show that bacterial ZF-UBP domains are part of a novel cyclic nucleotide-dependent redox signaling system, whereas prokaryotic B-box, AN1 and LIM domains have related functions as partners of diverse membrane-associated peptidases in processing proteins. This information, in conjunction with structural analysis, suggests that these treble clef domains might have been independently recruited to the eukaryotic Ub-system due to an ancient conserved mode of interaction with peptides.

A Conserved Protein with AN1 Zinc Finger and Ubiquitin-like Domains Modulates Cdc48 (p97) Function in the Ubiquitin-Proteasome Pathway

“…presumably due to lateral gene transfer (39). Most remarkably, this domain is part of many highly divergent multidomain proteins, but most, if not all, are linked to membrane-localized proteolytic systems.…”

“…The presence of upstream proteasomeassociated control elements was our original search criterion. Both YNL155W and YOR052C encode predicted proteins with AN1-type zinc finger (Zf_AN1) domains, which coordinate a pair of zinc ions and are part of a widespread structural motif known as the treble-clef domain (39). Treble-clef domains include the RING and IBR domains, both sequence signatures of ubiquitin ligases.…”

Ubiquitylation activates a peptidase that promotes cleavage and destabilization of its activating E3 ligases and diverse growth regulatory proteins to limit cell proliferation in Arabidopsis

“…Alignments revealed high similarity to predicted protein sequences from the photosynthetic bacteria Roseiflexus sp (Supplemental Fig. S7; Burroughs et al 2011) that included four pairs of CxxC/H motifs with the potential to bind zinc similar to those in canonical LIM domains (Kadrmas and Beckerle 2004). The chs3-2d mutation changes a cysteine to a tyrosine in the third pair of conserved CxxC/H motifs ( Supplemental Figs.…”

“…6A,B), suggesting a functional role for this ancient conserved LIM-like domain (Supplemental Fig. S7; Burroughs et al 2011) in peptidase activation. Analyses of conformational changes caused by DA1 ubiquitylation and their influence on peptidase activity are required to establish this potential mechanism.…”

A Rhomboid Protease Gene Deletion Affects a Novel Oligosaccharide N-Linked to the S-layer Glycoprotein of Haloferax volcanii

“…1A, inset). The occurrence of the AN1 zinc finger-Rho arrangement has been reported in haloarchaea and some methanogens (37). In this work, we expanded the search and found that this combination only occurs in members of Euryarchaeota, including all of the haloarchaea and Archaeoglobus fulgidus, Archaeoglobus veneficus, Ferroglobus placidus, Methanococcoides burtonii, Methanohalophilus mahii, Methanocelea paludicola, Methanohalobium evestigatum, and the uncultured methanogenic archaeon RC-1.…”