A novel modification pathway related to the ubiquitin system

ZMBH, Zentrum für Molekulare Biologie der Universität Heidelberg, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany.
The EMBO Journal (Impact Factor: 10.43). 04/1998; 17(8):2208-14. DOI: 10.1093/emboj/17.8.2208
Source: PubMed


Ubiquitin conjugation is known to target protein substrates primarily to degradation by the proteasome or via the endocytic route. Here we describe a novel protein modification pathway in yeast which mediates the conjugation of RUB1, a ubiquitin-like protein displaying 53% amino acid identity to ubiquitin. We show that RUB1 conjugation requires at least three proteins in vivo. ULA1 and UBA3 are related to the N- and C-terminal domains of the E1 ubiquitin-activating enzyme, respectively, and together fulfil E1-like functions for RUB1 activation. RUB1 conjugation also requires UBC12, a protein related to E2 ubiquitin-conjugating enzymes, which functions analogously to E2 enzymes in RUB1-protein conjugate formation. Conjugation of RUB1 is not essential for normal cell growth and appears to be selective for a small set of substrates. Remarkably, CDC53/cullin, a common subunit of the multifunctional SCF ubiquitin ligase, was found to be a major substrate for RUB1 conjugation. This suggests that the RUB1 conjugation pathway is functionally affiliated to the ubiquitin-proteasome system and may play a regulatory role.

Download full-text


Available from: Kai Matuschewski, Apr 30, 2014
24 Reads
  • Source
    • "Nedd8 is a ubiquitin-like protein (UBL) that covalently modifies the cullin subunits of the cullin-RING complexes to turn on their activities as E3 ubiquitin (UB) ligases (Figure 1a) [1], [2], [3], [4], [5], [6]. The E1 enzyme specific for Nedd8, also known as Nedd8 activating enzyme (NAE), catalyzes the condensation of ATP with the C-terminal carboxylate of Nedd8 to form a Nedd8-AMP conjugate [5], [7], [8]. The activated Nedd8 is then captured by a catalytic Cys residue of NAE to form a Nedd8∼NAE thioester conjugate (“∼” designates the thioester linkage). "
    [Show abstract] [Hide abstract]
    ABSTRACT: The C-terminal peptides of ubiquitin (UB) and UB-like proteins (UBLs) play a key role in their recognition by the specific activating enzymes (E1s) to launch their transfer through the respective enzymatic cascades thus modifying cellular proteins. UB and Nedd8, a UBL regulating the activity of cullin-RING UB ligases, only differ by one residue at their C-termini; yet each has its specific E1 for the activation reaction. It has been reported recently that UAE can cross react with Nedd8 to enable its passage through the UB transfer cascade for protein neddylation. To elucidate differences in UB recognition by UAE and NAE, we carried out phage selection of a UB library with randomized C-terminal sequences based on the catalytic formation of UB∼NAE thioester conjugates. Our results confirmed the previous finding that residue 72 of UB plays a "gate-keeping" role in E1 selectivity. We also found that diverse sequences flanking residue 72 at the UB C-terminus can be accommodated by NAE for activation. Furthermore heptameric peptides derived from the C-terminal sequences of UB variants selected for NAE activation can function as mimics of Nedd8 to form thioester conjugates with NAE and the downstream E2 enzyme Ubc12 in the Nedd8 transfer cascade. Once the peptides are charged onto the cascade enzymes, the full-length Nedd8 protein is effectively blocked from passing through the cascade for the critical modification of cullin. We have thus identified a new class of inhibitors of protein neddylation based on the profiles of the UB C-terminal sequences recognized by NAE.
    PLoS ONE 08/2013; 8(8):e70312. DOI:10.1371/journal.pone.0070312 · 3.23 Impact Factor
  • Source
    • "In the fission yeast Schizosaccharomyces pombe[6,7], as in mammals [8], the null mutation of either Nedd8 itself or components of its conjugation pathway, i.e. its E1 or E2 enzymes, are lethal to the cell. Curiously, the Nedd8 system is not essential for viability of the budding yeast Saccharomyces cerevisiae[9,10]. The reason for this difference is unknown, but could reflect differences in Nedd8 substrates between these organisms. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Background Conjugation of the ubiquitin-like modifier Nedd8 to cullins is critical for the function of SCF-type ubiquitin ligases and thus facilitates ubiquitin conjugation and ultimately degradation of SCF substrates, including several cell cycle regulators. Like ubiquitin, Nedd8 is produced as a precursor that must first be processed before it becomes active. In Saccharomyces cerevisiae this is carried out exclusively by the enzyme Yuh1. Results Here we show that in the fission yeast, Schizosaccharomyces pombe, the Yuh1 orthologue, Uch1, is not the sole Nedd8 processing enzyme. Instead it appears that deubiquitylating enzymes can efficiently process the Nedd8 precursor in vivo. Conclusions Several enzymes contribute to Nedd8 precursor processing including a number of deubiquitylating enzymes.
    BMC Biochemistry 03/2013; 14(1):8. DOI:10.1186/1471-2091-14-8 · 1.44 Impact Factor
  • Source
    • "Dissection of DNA Damage Response Pathways are targeted by the neddylation pathway, which in turn may affect cell-cycle progression. The best-studied NEDD8/Rub1 targets are cullin proteins, which are scaffolds for the assembly of multisubunit cullin-RING ubiquitin ligases (Laplaza et al., 2004; Liakopoulos et al., 1998). These ubiquitin ligases are responsible for the turnover of a vast majority of proteins and consequently play a major role in maintaining cellular homeostasis (Soucy et al., 2010). "
    [Show abstract] [Hide abstract]
    ABSTRACT: To protect the genome, cells have evolved a diverse set of pathways designed to sense, signal, and repair multiple types of DNA damage. To assess the degree of coordination and crosstalk among these pathways, we systematically mapped changes in the cell's genetic network across a panel of different DNA-damaging agents, resulting in ∼1,800,000 differential measurements. Each agent was associated with a distinct interaction pattern, which, unlike single-mutant phenotypes or gene expression data, has high statistical power to pinpoint the specific repair mechanisms at work. The agent-specific networks revealed roles for the histone acetyltranferase Rtt109 in the mutagenic bypass of DNA lesions and the neddylation machinery in cell-cycle regulation and genome stability, while the network induced by multiple agents implicates Irc21, an uncharacterized protein, in checkpoint control and DNA repair. Our multiconditional genetic interaction map provides a unique resource that identifies agent-specific and general DNA damage response pathways.
    Molecular cell 12/2012; 49(2). DOI:10.1016/j.molcel.2012.11.023 · 14.02 Impact Factor
Show more