A subset of proteins targeted by the N-end rule pathway bear degradation signals called N-degrons, whose determinants include destabilizing N-terminal residues. Our previous work identified mouse UBR1 and UBR2 as E3 ubiquitin ligases that recognize N-degrons. Such E3s are called N-recognins. We report here that while double-mutant UBR1 ؊/؊ UBR2 ؊/؊ mice die as early embryos, the rescued UBR1 ؊/؊ UBR2 ؊/؊ fibroblasts still retain the N-end rule pathway, albeit of lower activity than that of wild-type fibroblasts. An affinity assay for proteins that bind to destabilizing N-terminal residues has identified, in addition to UBR1 and UBR2, a huge (570 kDa) mouse protein, termed UBR4, and also the 300-kDa UBR5, a previously characterized mammalian E3 known as EDD/hHYD. UBR1, UBR2, UBR4, and UBR5 shared a ϳ70-amino-acid zinc finger-like domain termed the UBR box. The mammalian genome encodes at least seven UBR box-containing proteins, which we propose to call UBR1 to UBR7. UBR1 ؊/؊ UBR2 ؊/؊ fibroblasts that have been made deficient in UBR4 as well (through RNA interference) were significantly impaired in the degradation of N-end rule substrates such as the Sindbis virus RNA polymerase nsP4 (bearing N-terminal Tyr) and the human immunodeficiency virus type 1 integrase (bearing N-terminal Phe). Our results establish the UBR box family as a unique class of E3 proteins that recognize N-degrons or structurally related determinants for ubiquitin-dependent proteolysis and perhaps other processes as well.

The conjugation of proteins with ubiquitin plays numerous regulatory roles through both proteasomal-dependent and nonproteasomal-dependent functions. Alterations in ubiquitylation are observed in a wide range of pathologic conditions, including numerous malignancies. For this reason, there is great interest in targeting the ubiquitin-proteasome system in cancer. Several classes of proteasome inhibitors, which block degradation of ubiquitylated proteins, are widely used in research, and one, Bortezomib, is now in clinical use. Despite the well-defined and central role of the ubiquitin-activating enzyme (E1), no cell permeable inhibitors of E1 have been identified. Such inhibitors should, in principle, block all functions of ubiquitylation. We now report 4[4-(5-nitro-furan-2-ylmethylene)-3,5-dioxo-pyrazolidin-1-yl]-benzoic acid ethyl ester (PYR-41) as the first such inhibitor. Unexpectedly, in addition to blocking ubiquitylation, PYR-41 increased total sumoylation in cells. The molecular basis for this is unknown; however, increased sumoylation was also observed in cells harboring temperature-sensitive E1. Functionally, PYR-41 attenuates cytokine-mediated nuclear factor-KB activation. This correlates with inhibition of nonproteasomal (Lys-63) ubiquitylation of TRAF6, which is essential to IKB kinase activation. PYR-41 also prevents the downstream ubiquitylation and proteasomal degradation of IKBA. Furthermore, PYR-41 inhibits degradation of p53 and activates the transcriptional activity of this tumor suppressor. Consistent with this, it differentially kills transformed p53-expressing cells. Thus, PYR-41 and related pyrazones provide proof of principle for the capacity to differentially kill transformed cells, suggesting the potential for E1 inhibitors as therapeutics in cancer. These inhibitors can also be valuable tools for studying ubiquitylation. [Cancer Res 2007;67(19):9472-81]

Addendum to the main text (i) ATE1-/-embryos from ATE1 +/-intercrosses were present at the expected (~25%) frequency up to ~E13.5, but virtually no ATE1 -/-embryos were recovered alive by E17. Specifically, no ATE1 -/-mice were recovered amongst either 954 F 2 -generation pups of the C57BL/6J-129SvEv (mixed) background or 267 F 2 -generation pups of the 129SvEv (inbred) background. Timed intercrosses of ATE1 +/-mice were used to determine that ATE1 -/-embryos were present at approximately the expected (25%) frequency up to ~E13.5, but no ATE1 -/-embryos were recovered alive by E17.Until E12.5, ATE1 -/-embryos appeared to be morphologically normal; however, their growth stopped during E13.5-E15.5. By E14.5-E15.5, ~50% of ATE1 -/-embryos were still alive, but growth-retarded. Live E14.5-E15.5 embryos were capable of opening their mouths and flexing their bodies, suggesting the absence of gross neuromuscular defects. Sections through E13.5 ATE1-/-embryos indicated the presence and apparently normal appearance of major organs, except for the phenotypes described in the main text and below.(ii) We examined the expression of ATE1 mRNA during embryogenesis using Northern hybridization with total RNA from +/+ embryos ranging in age from E4.5 to E18.5. ATE1 mRNA was present at least as early as E4.5, and a strong spike of ATE1 expression was observed during E7.5-9.5 (Fig. S1E). The ~2 kb ATE1 transcript detected in adult mouse testis (1) was also clearly present during the spike of ATE1 expression in E7.5-E9.5 embryos (Fig. S1E). The ATE1 -allele was marked with NLS-β-galactosidase (hereafter βgal), expressed from the ATE1 promoter

The ATE1-encoded Arg-transferase mediates conjugation of Arg to N-terminal Asp, Glu, and Cys of certain eukaryotic proteins, yielding N-terminal Arg that can act as a degradation signal for the ubiquitin-dependent N-end rule pathway. We have previously shown that mouse ATE1 ؊/؊ embryos die with defects in heart development and angiogenesis. Here, we report that the ATE1 Arg-transferase mediates the in vivo degradation of RGS4 and RGS5, which are negative regulators of specific G proteins whose functions include cardiac growth and angiogenesis. The proteolysis of these regulators of G protein signaling (RGS) proteins was perturbed either by hypoxia or in cells lacking ubiquitin ligases UBR1 and͞or UBR2. Mutant RGS proteins in which the conserved Cys-2 residue could not become N-terminal were long-lived in vivo. We propose a model in which the sequential modifications of RGS4, RGS5, and RGS16 (N-terminal exposure of their Cys-2, its oxidation, and subsequent arginylation) act as a licensing mechanism in response to extracellular and intracellular signals before the targeting for proteolysis by UBR1 and UBR2. We also show that ATE1 ؊/؊ embryos are impaired in the activation of extracellular signal-regulated kinase mitogen-activated protein kinases and in the expression of G protein-induced downstream effectors such as Jun, cyclin D1, and ␤-myosin heavy chain. These results establish RGS4 and RGS5 as in vivo substrates of the mammalian N-end rule pathway and also suggest that the O2-ATE1-UBR1͞UBR2 proteolytic circuit plays a role in RGS-regulated G protein signaling in the cardiovascular system. ATE1 R-transferase ͉ G protein signaling ͉ oxidation ͉ ubiquitin ͉ UBR T he ubiquitin (Ub)-dependent N-end rule pathway relates the in vivo half-life of a protein to the identity of its N-terminal residue (1) (Fig. 1A). We previously identified the mouse ATE1 gene encoding Arg-transferase, which conjugates Arg to Nterminal Asp, Glu, and Cys of engineered N-end rule substrates (2, 3), yielding N-terminal Arg that can act as an essential component of N-degron (N-terminal degradation signal). Ndegrons can be recognized by Ub ligases (E3s) for protein ubiquitylation. Mouse ATE1 Ϫ/Ϫ embryos died with cardiovascular defects, including ventricular hypoplasia, ventricular septal defect, and impaired late angiogenesis (3), suggesting that the ATE1-dependent proteolysis of unknown substrate(s) is a crucial regulatory mechanism for myocardial growth and blood vessel integrity͞maturation. One aim of this study was to identify in vivo ATE1 substrates that are important for cardiovascular functions.We previously reported that RGS4, a G protein-specific GTPase-activating protein (4), is N-terminally arginylated and degraded by the Ub system in ATP-supplemented reticulocyte extract and that its in vitro degradation is inhibited by the Arg-Ala dipeptide inhibitor of the N-end rule pathway (5). However, previous attempts to verify the functional connection between RGS4 and the N-end rule pathway in vivo (in mammalian cells) were unsuccessful....

The p53 tumor suppressor protein is regulated by its interaction with HDM2, which serves as a ubiquitin ligase (E3) to target p53 for degradation. We have identified a family of small molecules (HLI98) that inhibits HDM2's E3 activity. These compounds show some specificity for HDM2 in vitro, although at higher concentrations effects on unrelated RING and HECT domain E3s are detectable, which could be due, at least in part, to effects on E2-ubiquitin thiol-ester levels. In cells, the compounds allow the stabilization of p53 and HDM2 and activation of p53-dependent transcription and apoptosis, although other p53-independent toxicity was also observed.

Substrates of the ubiquitin-dependent N-end rule pathway include proteins with destabilizing N-terminal residues. UBR1 ؊/؊ mice, which lacked the pathway's ubiquitin ligase E3␣, were viable and retained the N-end rule pathway. The present work describes the identification and analysis of mouse UBR2, a homolog of UBR1. We demonstrate that the substrate-binding properties of UBR2 are highly similar to those of UBR1, identifying UBR2 as the second E3 of the mammalian N-end rule pathway. UBR2 ؊/؊ mouse strains were constructed, and their viability was found to be dependent on both gender and genetic background. In the strain 129 (inbred) background, the UBR2 ؊/؊ genotype was lethal to most embryos of either gender. In the 129/B6 (mixed) background, most UBR2 ؊/؊ females died as embryos, whereas UBR2 ؊/؊ males were viable but infertile, owing to the postnatal degeneration of the testes. The gross architecture of UBR2 ؊/؊ testes was normal and spermatogonia were intact as well, but UBR2 ؊/؊ spermatocytes were arrested between leptotene/zygotene and pachytene and died through apoptosis. A conspicuous defect of UBR2 ؊/؊ spermatocytes was the absence of intact synaptonemal complexes. We conclude that the UBR2 ubiquitin ligase and, hence, the N-end rule pathway are required for male meiosis and spermatogenesis and for an essential aspect of female embryonic development.

The N-end rule relates the in vivo half-life of a protein to the identity of its N-terminal residue. In the yeast Saccharomyces cerevisiae, the UBR1-encoded ubiquitin ligase (E3) of the N-end rule pathway mediates the targeting of substrate proteins in part through binding to their destabilizing N-terminal residues. The functions of the yeast N-end rule pathway include fidelity of chromosome segregation and the regulation of peptide import. Our previous work described the cloning of cDNA and a gene encoding the 200-kDa mouse UBR1 (E3␣). Here we show that mouse UBR1, in the presence of a cognate mouse ubiquitin-conjugating (E2) enzyme, can rescue the N-end rule pathway in ubr1⌬ S. cerevisiae. We also constructed UBR1 ؊/؊ mouse strains that lacked the UBR1 protein. UBR1؊/؊ mice were viable and fertile but weighed significantly less than congenic ؉/؉ mice. The decreased mass of UBR1 ؊/؊ mice stemmed at least in part from smaller amounts of the skeletal muscle and adipose tissues. The skeletal muscle of UBR1 ؊/؊ mice apparently lacked the N-end rule pathway and exhibited abnormal regulation of fatty acid synthase upon starvation. By contrast, and despite the absence of the UBR1 protein, UBR1 ؊/؊ fibroblasts contained the N-end rule pathway. Thus, UBR1 ؊/؊ mice are mosaics in regard to the activity of this pathway, owing to differential expression of proteins that can substitute for the ubiquitin ligase UBR1 (E3␣). We consider these UBR1-like proteins and discuss the functions of the mammalian N-end rule pathway.

The N-end rule relates the in vivo half-life of a protein to the identity of its N-terminal residue. We used an expression-cloning screen to search for mouse proteins that are degraded by the ubiquitin/proteasome-dependent N-end rule pathway in a reticulocyte lysate. One substrate thus identified was RGS4, a member of the RGS family of GTPase-activating proteins that downregulate specific G proteins. A determinant of the RGS4 degradation signal (degron) was located at the N terminus of RGS4, because converting cysteine 2 to either glycine, alanine, or valine completely stabilized RGS4. Radiochemical sequencing indicated that the N-terminal methionine of the lysate-produced RGS4 was replaced with arginine. Since N-terminal arginine is a destabilizing residue not encoded by RGS4 mRNA, we conclude that the degron of RGS4 is generated through the removal of N-terminal methionine and enzymatic arginylation of the resulting N-terminal cysteine. RGS16, another member of the RGS family, was also found to be an N-end rule substrate. RGS4 that was transiently expressed in mouse L cells was short-lived in these cells. However, the targeting of RGS4 for degradation in this in vivo setting involved primarily another degron, because N-terminal variants of RGS4 that were stable in reticulocyte lysate remained unstable in L cells.