RecR-mediated Modulation of RecF Dimer Specificity for Single- and Double-stranded DNA

RecF pathway proteins play an important role in the restart of stalled replication and DNA repair in prokaryotes. Following DNA damage, RecF, RecR, and RecO initiate homologous recombination (HR) by loading of the RecA recombinase on single-stranded (ss) DNA, protected by ssDNA-binding protein. The specific role of RecF in this process is not well understood. Previous studies have proposed that RecF directs the RecOR complex to boundaries of damaged DNA regions by recognizing single-stranded/double-stranded (ss/ds) DNA junctions. RecF belongs to ABC-type ATPases, which function through an ATP-dependent dimerization. Here, we demonstrate that the RecF of Deinococcus radiodurans interacts with DNA as an ATP-dependent dimer, and that the DNA binding and ATPase activity of RecF depend on both the structure of DNA substrate, and the presence of RecR. We found that RecR interacts as a tetramer with the RecF dimer. RecR increases the RecF affinity to dsDNA without stimulating ATP hydrolysis but destabilizes RecF binding to ssDNA and dimerization, likely due to increasing the ATPase rate. The DNA-dependent binding of RecR to the RecF-DNA complex occurs through specific protein-protein interactions without significant contributions from RecR-DNA interactions. Finally, RecF neither alone nor in complex with RecR preferentially binds to the ss/dsDNA junction. Our data suggest that the specificity of the RecFOR complex toward the boundaries of DNA damaged regions may result from a network of protein-protein and DNA-protein interactions, rather than a simple recognition of the ss/dsDNA junction by RecF.Homologous recombination (HR)² is one of the primary mechanisms by which cells repair dsDNA breaks (DSBs) and ssDNA gaps (SSGs), and is important for restart of stalled DNA replication (1). HR is initiated when RecA-like recombinases bind to ssDNA forming an extended nucleoprotein filament, referred to as a presynaptic complex (2). The potential for genetic rearrangements dictates that HR initiation is tightly regulated at multiple levels (1). During replication, the ssDNA-binding protein (SSB) protects transiently unwound DNA chains, preventing interactions with recombinases. Following DNA damage, recombination mediator proteins (RMPs) initiate HR by facilitating the formation of the recombinase filaments with ssDNA, while removing SSB (3, 4). Mutations in human proteins involved in HR initiation are linked to cancer predisposition, chromosome instability, UV sensitivity, and premature aging diseases (4–8). To date, little is known about the mechanism by which RMPs regulate the formation of the recombinase filaments on the SSB-protected ssDNA.In Escherichia coli, there are two major recombination pathways, RecBCD and RecF (9, 10). A helicase/nuclease RecBCD complex processes DSBs and recruits RecA on ssDNA in a sequence-specific manner (11–13). The principle players in the RecF pathway are the RecF, RecO, and RecR proteins, which form an epistatic group that is important for SSG repair, for restart of stalled DNA replication, and under specific conditions, can also process DSBs (14–20). Homologs of RecF, -O, and -R are present in the majority of known bacteria (21), including Deinococcus radiodurans, extremely radiation-resistant bacteria that lacks the RecBCD pathway, yet is capable of repairing thousands of DSBs (22, 23). In addition, the sequence or functional homologs of RecF pathway proteins are involved in similar pathways in eukaryotes that include among others WRN, BLM, RAD52, and BRCA2 proteins (4–8).The involvement of all three RecF, -O, and -R proteins in HR initiation is well documented by genetic and cellular approaches (18, 24–30), yet their biochemical functions in the initiation process remain unclear, particularly with respect to RecF. RecO and RecR proteins are sufficient to promote formation of the RecA filament on SSB-bound ssDNA in vitro (27). The UV-sensitive phenotype of recF mutants can be suppressed by RecOR overexpression, suggesting that RecF may direct the RMP complex to DNA-damaged regions where HR initiation is required (31). In agreement with this hypothesis, RecF dramatically increases the efficiency of the RecA loading at ds/ssDNA junctions with a 3′ ssDNA extension under specific conditions (32). RecF and RecR proteins also prevent the RecA filaments from extending into dsDNA regions adjacent to SSGs (33). These data suggest that RecF may directly recognize an ss/dsDNA junction structure (34). However, DNA binding experiments have not provided clear evidence to support such a hypothesis (11).The targeting promoted by RecF may also occur through more complex processes. RecF shares a high structural similarity with the head domain of Rad50, an ABC-type ATPase that recognizes DSBs and initiates repair in archaea and eukaryotes (35). All known ABC-type ATPases function as oligomeric complexes in which a sequence of inter- and intra-molecular interactions is triggered by the ATP-dependent dimerization and the dimer-dependent ATP hydrolysis (36–39). RecF is also an ATP-dependent DNA-binding protein and a weak DNA-dependent ATPase (11, 40). RecF forms an ATP-dependent dimer and all three conserved motifs (Walker A, Walker B, and “signature”) of RecF are important for ATP-dependent dimerization, ATP hydrolysis, and functional resistance to DNA damage (35). Thus, RecF may function in recombination initiation through a complex pathway of protein-protein and DNA-protein interactions regulated by ATP-dependent RecF dimerization.In this report, we present a detailed characterization of the RecF dimerization, and its role in the RecF interaction with various DNA substrates, with RecR, and in ATP hydrolysis. Our data outline the following key findings. First, RecF interacts with DNA as a dimer. Second, neither RecF alone nor the RecFR complex preferentially binds the ss/dsDNA junction. Finally, RecR changes the ATPase activity and the DNA binding of RecF by destabilizing the interaction with ssDNA, and greatly enhancing the interaction with dsDNA. Our results suggest that the specificity of RecF for the boundaries of SSGs is likely to result from a sequence of protein-protein interaction events rather than a simple RecF ss/dsDNA binding, underlining a highly regulated mechanism of the HR initiation by the RecFOR proteins.     

Selective Inhibition of Carotenoid Cleavage Dioxygenases: PHENOTYPIC EFFECTS ON SHOOT BRANCHING*S?

Members of the carotenoid cleavage dioxygenase family catalyze the oxidative cleavage of carotenoids at various chain positions, leading to the formation of a wide range of apocarotenoid signaling molecules. To explore the functions of this diverse enzyme family, we have used a chemical genetic approach to design selective inhibitors for different classes of carotenoid cleavage dioxygenase. A set of 18 arylalkyl-hydroxamic acids was synthesized in which the distance between an iron-chelating hydroxamic acid and an aromatic ring was varied; these compounds were screened as inhibitors of four different enzyme classes, either in vitro or in vivo. Potent inhibitors were found that selectively inhibited enzymes that cleave carotenoids at the 9,10 position; 50% inhibition was achieved at submicromolar concentrations. Application of certain inhibitors at 100 μm to Arabidopsis node explants or whole plants led to increased shoot branching, consistent with inhibition of 9,10-cleavage.Carotenoids are synthesized in plants and micro-organisms as photoprotective molecules and are key components in animal diets, an example being β-carotene (pro-vitamin A). The oxidative cleavage of carotenoids occurs in plants, animals, and micro-organisms and leads to the release of a range of apocarotenoids that function as signaling molecules with a diverse range of functions (1). The first gene identified as encoding a carotenoid cleavage dioxygenase (CCD)² was the maize Vp14 gene that is required for the formation of abscisic acid (ABA), an important hormone that mediates responses to drought stress and aspects of plant development such as seed and bud dormancy (2). The VP14 enzyme cleaves at the 11,12 position (Fig. 1) of the epoxycarotenoids 9′-cis-neoxanthin and/or 9-cis-violaxanthin and is now classified as a 9-cis-epoxycarotenoid dioxygenase (NCED) (3), a subclass of the larger CCD family.Open in a separate windowFIGURE 1.Reactions catalyzed by the carotenoid cleavage dioxygenases. a, 11,12-oxidative cleavage of 9′-cis-neoxanthin by NCED; b, oxidative cleavage reactions on β-carotene and zeaxanthin.Since the discovery of Vp14, many other CCDs have been shown to be involved in the production of a variety of apocarotenoids (Fig. 1). In insects, the visual pigment retinal is formed by oxidative cleavage of β-carotene by β-carotene-15,15′-dioxygenase (4). Retinal is produced by an orthologous enzyme in vertebrates, where it is also converted to retinoic acid, a regulator of differentiation during embryogenesis (5). A distinct mammalian CCD is believed to cleave carotenoids asymmetrically at the 9,10 position (6) and, although its function is unclear, recent evidence suggests a role in the metabolism of dietary lycopene (7). The plant volatiles β-ionone and geranylacetone are produced from an enzyme that cleaves at the 9,10 position (8) and the pigment α-crocin found in the spice saffron results from an 7,8-cleavage enzyme (9).Other CCDs have been identified where biological function is unknown, for example, in cyanobacteria where a variety of cleavage specificities have been described (10-12). In other cases, there are apocarotenoids with known functions, but the identity or involvement of CCDs have not yet been described: grasshopper ketone is a defensive secretion of the flightless grasshopper Romalea microptera (13), mycorradicin is produced by plant roots during symbiosis with arbuscular mycorrhyza (14), and strigolactones (15) are plant metabolites that act as germination signals to parasitic weeds such as Striga and Orobanche (16).Recently it was discovered that strigolactones also function as a branching hormone in plants (17, 18). The existence of such a branching hormone has been known for some time, but its identity proved elusive. However, it was known that the hormone was derived from the action of at least two CCDs, max3 and max4 (more axillary growth) (19), because deletion of either of these genes in Arabidopsis thaliana, leads to a bushy phenotype (20, 21). In Escherichia coli assays, AtCCD7 (max3) cleaves β-carotene at the 9,10 position and the apocarotenoid product (10-apo-β-carotene) is reported to be further cleaved at 13,14 by AtCCD8 (max4) to produce 13-apo-β-carotene (22). Also recent evidence suggests that AtCCD8 is highly specific, cleaving only 10-apo-β-carotene (23). How the production of 13-apo-β-carotene leads to the synthesis of the complex strigolactone is unknown. The possibility remains that the enzymes may have different specificities and cleavage activities in planta. In addition, a cytochrome P450 enzyme (24) is believed to be involved in strigolactone synthesis and acts in the pathway downstream of the CCD genes. Strigolactone is thought to effect branching by regulating auxin transport (25). Because of the involvement of CCDs in strigolactone synthesis, the possibility arises that plant architecture and interaction with parasitic weeds and mycorrhyza could be controlled by the manipulation of CCD activity.Although considerable success has been obtained using genetic approaches to probe function and substrate specificity of CCDs in their native biological contexts, particularly in plant species with simple genetic systems or that are amenable to transgenesis, there are many systems where genetic approaches are difficult or impossible. Also, when recombinant CCDs are studied either in vitro or in heterologous in vivo assays, such as in E. coli strains engineered to accumulate carotenoids (26), they are often active against a broad range of substrates (5, 21, 27), and in many cases the true in vivo substrate of a particular CCD remains unknown. Therefore additional experimental tools are needed to investigate both apocarotenoid and CCD functions in their native cellular environments.In the reverse chemical genetics approach, small molecules are identified that are active against known target proteins; they are then applied to a biological system to investigate protein function in vivo (28, 29). This approach is complementary to conventional genetics since the small molecules can be applied easily to a broad range of species, their application can be controlled in dose, time, and space to provide detailed studies of biological functions, and individual proteins or whole protein classes may be targeted by varying the specificity of the small molecules. Notably, functions of the plant hormones gibberellin, brassinosteroid, and abscisic acid have been successfully probed using this approach by adapting triazoles to inhibit specific cytochrome P450 monooxygenases involved in the metabolism of these hormones (30).In the case of the CCD family, the tertiary amines abamine (31) and the more active abamineSG (32) were reported as specific inhibitors of NCED, and abamine was used to show new functions of abscisic acid in legume nodulation (33). However, no selective inhibitors for other types of CCD are known. Here we have designed a novel class of CCD inhibitor based on hydroxamic acids, where variable chain length was used to direct inhibition of CCD enzymes that cleave carotenoids at specific positions. We demonstrate the use of such novel inhibitors to control shoot branching in a model plant.     

The Mei5-Sae3 Protein Complex Mediates Dmc1 Activity in Saccharomyces cerevisiae

During homologous recombination, a number of proteins cooperate to catalyze the loading of recombinases onto single-stranded DNA. Single-stranded DNA-binding proteins stimulate recombination by coating single-stranded DNA and keeping it free of secondary structure; however, in order for recombinases to load on single-stranded-DNA-binding protein-coated DNA, the activity of a class of proteins known as recombination mediators is required. Mediator proteins coordinate the handoff of single-stranded DNA from single-stranded DNA-binding protein to recombinase. Here we show that a complex of Mei5 and Sae3 from Saccharomyces cerevisiae preferentially binds single-stranded DNA and relieves the inhibition of the strand assimilation and DNA binding abilities of the meiotic recombinase Dmc1 imposed by the single-stranded DNA-binding protein replication protein A. Additionally, we demonstrate the physical interaction of Mei5-Sae3 with replication protein A. Our results, together with previous in vivo studies, indicate that Mei5-Sae3 is a mediator of Dmc1 assembly during meiotic recombination in S. cerevisiae.During meiosis, recombination between homologous chromosomes ensures proper segregation into haploid products. Recombination events are initiated by the formation of double strand breaks (DSBs)² in DNA (1). This is followed by resection of free DNA ends to yield 3′ single-stranded tails, upon which recombinase assembles to form nucleoprotein filaments. Following recombinase assembly, the nucleoprotein filament engages a donor chromatid, searches for homologous DNA sequences on that chromatid, and promotes strand exchange to yield a heteroduplex DNA intermediate often referred to as a joint molecule. Although recombinase alone is capable of promoting homology search and strand exchange in vitro, genetic and biochemical studies have demonstrated that normal recombinase function in vivo requires the activity of a number of accessory factors (2). These factors enhance the assembly of nucleoprotein filaments, target capture, homology search, and dissociation of recombinase from duplex DNA.Most eukaryotes possess two recombinases, both homologues of the Escherichia coli recombinase RecA: Rad51, which is the major recombinase in mitotic cells and is also important during meiotic recombination, and Dmc1, which functions only in meiosis. Dmc1 and Rad51 have been shown to assemble at DSBs by immunofluorescence and chromatin immunoprecipitation (3–6), and both proteins oligomerize on single-stranded DNA (ssDNA) to form nucleofilaments that catalyze strand invasion (7–9).A number of biochemical studies have defined the role of accessory factors in stimulating the activity of Rad51 (10–12). Replication protein A (RPA), the yeast ssDNA-binding protein (SSB), removes secondary structure in ssDNA that otherwise prevents formation of fully functional nucleoprotein filaments (13). Both Rad52 protein (11, 12) and the heterodimeric protein Rad55/Rad57 (14) can overcome the inhibitory effect of RPA on Rad51 nucleoprotein filament formation in purified systems, mediating a handoff between RPA and Rad51. It is thought that the mechanism for the mediator activity of Rad52 involves Rad52 recognizing and binding to RPA-coated ssDNA, where it provides nucleation sites for the recruitment of free molecules of Rad51 (15). The tumor suppressor protein BRCA2 also serves as an assembly factor for Rad51 during mitosis in a variety of species that encode orthologues of this protein, including mice (16), corn smut (17), and humans (18).The meiosis-specific recombinase Dmc1 is stimulated by a distinct set of accessory factors. Immunostaining studies suggest that the Rad51 mediators Rad52 and Rad55/Rad57 are not required for assembly of Dmc1 foci in vivo, although Rad51 itself promotes Dmc1 foci (19–21). More recently, immunostaining and chromatin immunoprecipitation experiments demonstrated a role for the Mei5 and Sae3 proteins of Saccharomyces cerevisiae in assembly of Dmc1 at sites of DSBs in vivo (22, 23). Consistent with these observations, mei5 and sae3 mutants display markedly similar meiotic defects as compared with dmc1 mutants, including defects in sporulation, spore viability, crossing over, DSB repair, progression through meiosis, and synaptonemal complex formation (19, 22–24). Finally, the three proteins have been shown to physically interact; Mei5 and Sae3 have been co-purified and co-immunoprecipitated, and an N-terminal portion of Mei5 has been shown to interact with Dmc1 in a two-hybrid assay (22).The fission yeast Schizosaccharomyces pombe encodes two proteins, Swi5 and Sfr1, which share sequence homology with Sae3 and Mei5, respectively (22). Swi5 and Sfr1 have been shown to stimulate the strand exchange activity of Rhp51 (the S. pombe Rad51 homologue) and Dmc1 (25). Although some results indicate functional similarity of Swi5-Sfr1 and Mei5-Sae3, there are also clear differences. The Mei5-Sae3 complex of budding yeast is expressed solely during meiosis, and no mitotic phenotypes have been reported for mei5 or sae3 mutants (22, 24, 26). In contrast, the Swi5-Sfr1 complex of fission yeast is expressed in mitotic and meiotic cells, and mutations in SWI5 have been shown to cause defects in mitotic recombination (27). Furthermore, although mei5 and sae3 mutants are phenotypically similar to dmc1 mutants, swi5 and sfr1 mutants display more severe meiotic defects during fission yeast meiosis than do dmc1 mutants (27–29). These data suggest that although Swi5-Sfr1 clearly contributes to Rad51 activity in fission yeast, it is possible that the activity of Mei5-Sae3 is restricted to stimulating Dmc1 in budding yeast.In this study, a biochemical approach is used to test the budding yeast Mei5-Sae3 complex for properties expected of a recombinase assembly mediator. We show that Mei5-Sae3 binds both ssDNA and double-stranded DNA (dsDNA) but binds ssDNA preferentially. We also show that Mei5-Sae3 can overcome the inhibitory effects of RPA on the ssDNA binding and strand assimilation activities of Dmc1. Finally, we show that Mei5-Sae3 and RPA bind one another directly. These results indicate that Mei5-Sae3 acts directly as a mediator protein for assembly of Dmc1.     

Analysis of Intracellular Substrates and Products of Thimet Oligopeptidase in Human Embryonic Kidney 293 Cells

Thimet oligopeptidase (EC 3.4.24.15; EP24.15) is an intracellular enzyme that has been proposed to metabolize peptides within cells, thereby affecting antigen presentation and G protein-coupled receptor signal transduction. However, only a small number of intracellular substrates of EP24.15 have been reported previously. Here we have identified over 100 peptides in human embryonic kidney 293 (HEK293) cells that are derived from intracellular proteins; many but not all of these peptides are substrates or products of EP24.15. First, cellular peptides were extracted from HEK293 cells and incubated in vitro with purified EP24.15. Then the peptides were labeled with isotopic tags and analyzed by mass spectrometry to obtain quantitative data on the extent of cleavage. A related series of experiments tested the effect of overexpression of EP24.15 on the cellular levels of peptides in HEK293 cells. Finally, synthetic peptides that corresponded to 10 of the cellular peptides were incubated with purified EP24.15 in vitro, and the cleavage was monitored by high pressure liquid chromatography and mass spectrometry. Many of the EP24.15 substrates identified by these approaches are 9–11 amino acids in length, supporting the proposal that EP24.15 can function in the degradation of peptides that could be used for antigen presentation. However, EP24.15 also converts some peptides into products that are 8–10 amino acids, thus contributing to the formation of peptides for antigen presentation. In addition, the intracellular peptides described here are potential candidates to regulate protein interactions within cells.Intracellular protein turnover is a crucial step for cell functioning, and if this process is impaired, the elevated levels of aged proteins usually lead to the formation of intracellular insoluble aggregates that can cause severe pathologies (1). In mammalian cells, most proteins destined for degradation are initially tagged with a polyubiquitin chain in an energy-dependent process and then digested to small peptides by the 26 S proteasome, a large proteolytic complex involved in the regulation of cell division, gene expression, and other key processes (2, 3). In eukaryotes, 30–90% of newly synthesized proteins may be degraded by proteasomes within minutes of synthesis (3, 4). In addition to proteasomes, other extralysosomal proteolytic systems have been reported (5, 6). The proteasome cleaves proteins into peptides that are typically 2–20 amino acids in length (7). In most cases, these peptides are thought to be rapidly hydrolyzed into amino acids by aminopeptidases (8–10). However, some intracellular peptides escape complete degradation and are imported into the endoplasmic reticulum where they associate with major histocompatibility complex class I (MHC-I)³ molecules and traffic to the cell surface for presentation to the immune system (10–12). Additionally, based on the fact that free peptides added to the intracellular milieu can regulate cellular functions mediated by protein interactions such as gene regulation, metabolism, cell signaling, and protein targeting (13, 14), intracellular peptides generated by proteasomes that escape degradation have been suggested to play a role in regulating protein interactions (15). Indeed, oligopeptides isolated from rat brain tissue using the catalytically inactive EP24.15 (EC 3.4.24.15) were introduced into Chinese hamster ovarian-S and HEK293 cells and were found capable of altering G protein-coupled receptor signal transduction (16). Moreover, EP24.15 overexpression itself changed both angiotensin II and isoproterenol signal transduction, suggesting a physiological function for its intracellular substrates/products (16).EP24.15 is a zinc-dependent peptidase of the metallopeptidase M3 family that contains the HEXXH motif (17). This enzyme was first described as a neuropeptide-degrading enzyme present in the soluble fraction of brain homogenates (18). Whereas EP24.15 can be secreted (19, 20), its predominant location in the cytosol and nucleus suggests that the primary function of this enzyme is not the extracellular degradation of neuropeptides and hormones (21, 22). EP24.15 was shown in vivo to participate in antigen presentation through MHC-I (23–25) and in vitro to bind (26) or degrade (27) some MHC-I associated peptides. EP24.15 has also been shown in vitro to degrade peptides containing 5–17 amino acids produced after proteasome digestion of β-casein (28). EP24.15 shows substrate size restriction to peptides containing from 5 to 17 amino acids because of its catalytic center that is located in a deep channel (29). Despite the size restriction, EP24.15 has a broad substrate specificity (30), probably because a significant portion of the enzyme-binding site is lined with potentially flexible loops that allow reorganization of the active site following substrate binding (29). Recently, it has also been suggested that certain substrates may be cleaved by an open form of EP24.15 (31). This characteristic is supported by the ability of EP24.15 to accommodate different amino acid residues at subsites S4 to S3′, which even includes the uncommon post-proline cleavage (30). Such biochemical and structural features make EP24.15 a versatile enzyme to degrade structurally unrelated oligopeptides.Previously, brain peptides that bound to catalytically inactive EP24.15 were isolated and identified using mass spectrometry (22). The majority of peptides captured by the inactive enzyme were intracellular protein fragments that efficiently interacted with EP24.15; the smallest peptide isolated in these assays contained 5 and the largest 17 amino acids (15, 16, 22, 32), which is within the size range previously reported for natural and synthetic substrates of EP24.15 (18, 30, 33, 34). Interestingly, the peptides released by the proteasome are in the same size range of EP24.15 competitive inhibitors/substrates (7, 35, 36). Taken altogether, these data suggest that in the intracellular environment EP24.15 could further cleave proteasome-generated peptides unrelated to MHC-I antigen presentation (15).Although the mutated inactive enzyme “capture” assay was successful in identifying several cellular protein fragments that were substrates for EP24.15, it also found some interacting peptides that were not substrates. In this study, we used several approaches to directly screen for cellular peptides that were cleaved by EP24.15. The first approach involved the extraction of cellular peptides from the HEK293 cell line, incubation in vitro with purified EP24.15, labeling with isotopic tags, and analysis by mass spectrometry to obtain quantitative data on the extent of cleavage. The second approach examined the effect of EP24.15 overexpression on the cellular levels of peptides in the HEK293 cell line. The third set of experiments tested synthetic peptides with purified EP24.15 in vitro, and examined cleavage by high pressure liquid chromatography and mass spectrometry. Collectively, these studies have identified a large number of intracellular peptides, including those that likely represent the endogenous substrates and products of EP24.15, and this original information contributes to a better understanding of the function of this enzyme in vivo.     

Phosphorylation of p53 Is Regulated by TPX2-Aurora A in Xenopus Oocytes

p53 is an important tumor suppressor regulating the cell cycle at multiple stages in higher vertebrates. The p53 gene is frequently deleted or mutated in human cancers, resulting in loss of p53 activity. This leads to centrosome amplification, aneuploidy, and tumorigenesis, three phenotypes also observed after overexpression of the oncogenic kinase Aurora A. Accordingly, recent studies have focused on the relationship between these two proteins. p53 and Aurora A have been reported to interact in mammalian cells, but the function of this interaction remains unclear. We recently reported that Xenopus p53 can inhibit Aurora A activity in vitro but only in the absence of TPX2. Here we investigate the interplay between Xenopus Aurora A, TPX2, and p53 and show that newly synthesized TPX2 is required for nearly all Aurora A activation and for full p53 synthesis and phosphorylation in vivo during oocyte maturation. In vitro, phosphorylation mediated by Aurora A targets serines 129 and 190 within the DNA binding domain of p53. Glutathione S-transferase pull-down studies indicate that the interaction occurs via the p53 transactivation domain and the Aurora A catalytic domain around the T-loop. Our studies suggest that targeting of TPX2 might be an effective strategy for specifically inhibiting the phosphorylation of Aurora A substrates, including p53.Aurora A is an oncogenic protein kinase that is active in mitosis and plays important roles in spindle assembly and centrosome function (1). Overexpression of either human or Xenopus Aurora A transforms mammalian cells, but only when the p53 pathway is altered (2–4). Aurora A is localized on centrosomes during mitosis, and overexpression of the protein leads to centrosome amplification and aneuploidy (2, 3, 5, 6), two likely contributors to genomic instability (7, 8). Because of its oncogenic potential and amplification in human tumors, considerable attention has been focused on the mechanism of Aurora A activation in mitosis. Evidence from several laboratories indicates that activation occurs as a result of phosphorylation of a threonine residue in the T-loop of the kinase (4, 9, 10). Purification of Aurora A-activating activity from M phase Xenopus egg extracts led to an apparent activation mechanism in which autophosphorylation at the T-loop is stimulated by binding of the targeting protein for Xklp2 (TPX2) (11–14). On the other hand, it has been shown that Aurora A activity can be inhibited by interaction with several proteins, including PP1 (protein phosphatase 1), AIP (Aurora A kinase-interacting protein), and, more recently, p53 (9, 15–17).p53 is a well known tumor suppressor able to drive cell cycle arrest, apoptosis, or senescence when DNA is damaged or cell integrity is threatened (18, 19). In human cancers, the p53 gene is frequently deleted or mutated, leading to inactivation of p53 functions (20). p53 protein is almost undetectable in “normal cells,” mainly due to its instability. Indeed, during a normal cell cycle, p53 associates with Mdm2 in the nucleus and thereafter undergoes nuclear exclusion, allowing its ubiquitination and subsequent degradation (21). In cells under stress, p53 is stabilized through the disruption of its interaction with Mdm2 (21), leading to p53 accumulation in the nucleus and triggering different responses, as described above.Although p53 has mostly been characterized as a nuclear protein, it has also been shown to localize on centrosomes (22–24) and regulate centrosome duplication (23, 24). Centrosomes are believed to act as scaffolds that concentrate many regulatory molecules involved in signal transduction, including multiple protein kinases (25). Thus, centrosomal localization of p53 might be important for its own regulation by phosphorylation/dephosphorylation, and one of its regulators could be the mitotic kinase Aurora A. Indeed, phenotypes associated with the misexpression of these two proteins are very similar. For example, overexpression of Aurora A kinase leads to centrosome amplification, aneuploidy, and tumorigenesis, and the same effects are often observed after down-regulation of p53 transactivation activity or deletion/mutation of its gene (26, 27).Several recent studies performed in mammalian models show interplay between p53 and Aurora A, with each protein having the ability to inhibit the other, depending on the stage of the cell cycle and the stress level of the cell (17, 28, 29). These studies reported that p53 is a substrate of Aurora A, and serines 215 and 315 were demonstrated to be the two major Aurora A phosphorylation sites in human p53 in vitro and in vivo. Phosphorylation of Ser-215 within the DNA binding domain of human p53 inhibited both p53 DNA binding and transactivation activities (29). Recently, our group showed that Xenopus p53 is able to inhibit Aurora A kinase activity in vitro, but this inhibitory effect can be suppressed by prior binding of Aurora A to TPX2 (9). Contrary to somatic cells, where p53 is nuclear, unstable, and expressed at a very low level, p53 is highly expressed in the cytoplasm of Xenopus oocytes and stable until later stages of development (30, 31). The high concentration of both p53 and Aurora A in the oocyte provided a suitable basis for investigating p53-Aurora A interaction and also evaluating Xenopus p53 as a substrate of Aurora A.     

Recombination Activator Function of the Novel RAD51- and RAD51B-binding Protein, Human EVL

The RAD51 protein is a central player in homologous recombinational repair. The RAD51B protein is one of five RAD51 paralogs that function in the homologous recombinational repair pathway in higher eukaryotes. In the present study, we found that the human EVL (Ena/Vasp-like) protein, which is suggested to be involved in actin-remodeling processes, unexpectedly binds to the RAD51 and RAD51B proteins and stimulates the RAD51-mediated homologous pairing and strand exchange. The EVL knockdown cells impaired RAD51 assembly onto damaged DNA after ionizing radiation or mitomycin C treatment. The EVL protein alone promotes single-stranded DNA annealing, and the recombination activities of the EVL protein are further enhanced by the RAD51B protein. The expression of the EVL protein is not ubiquitous, but it is significantly expressed in breast cancer-derived MCF7 cells. These results suggest that the EVL protein is a novel recombination factor that may be required for repairing specific DNA lesions, and that may cause tumor malignancy by its inappropriate expression.Chromosomal DNA double strand breaks (DSBs)² are potential inducers of chromosomal aberrations and tumorigenesis, and they are accurately repaired by the homologous recombinational repair (HRR) pathway, without base substitutions, deletions, and insertions (1–3). In the HRR pathway (4, 5), single-stranded DNA (ssDNA) tails are produced at the DSB sites. The RAD51 protein, a eukaryotic homologue of the bacterial RecA protein, binds to the ssDNA tail and forms a helical nucleoprotein filament. The RAD51-ssDNA filament then binds to the intact double-stranded DNA (dsDNA) to form a three-component complex, containing ssDNA, dsDNA, and the RAD51 protein. In this three-component complex, the RAD51 protein promotes recombination reactions, such as homologous pairing and strand exchange (6–9).The RAD51 protein requires auxiliary proteins to promote the homologous pairing and strand exchange reactions efficiently in cells (10–12). In humans, the RAD52, RAD54, and RAD54B proteins directly interact with the RAD51 protein (13–17) and stimulate the RAD51-mediated homologous pairing and/or strand exchange reactions in vitro (18–21). The human RAD51AP1 protein, which directly binds to the RAD51 protein (22), was also found to stimulate RAD51-mediated homologous pairing in vitro (23, 24). The BRCA2 protein contains ssDNA-binding, dsDNA-binding, and RAD51-binding motifs (25–33), and the Ustilago maydis BRCA2 ortholog, Brh2, reportedly stimulated RAD51-mediated strand exchange (34, 35). Most of these RAD51-interacting factors are known to be required for efficient RAD51 assembly onto DSB sites in cells treated with ionizing radiation (10–12).The RAD51B (RAD51L1, Rec2) protein is a member of the RAD51 paralogs, which share about 20–30% amino acid sequence similarity with the RAD51 protein (36–38). RAD51B-deficient cells are hypersensitive to DSB-inducing agents, such as cisplatin, mitomycin C (MMC), and γ-rays, indicating that the RAD51B protein is involved in the HRR pathway (39–44). Genetic experiments revealed that RAD51B-deficient cells exhibited impaired RAD51 assembly onto DSB sites (39, 44), suggesting that the RAD51B protein functions in the early stage of the HRR pathway. Biochemical experiments also suggested that the RAD51B protein participates in the early to late stages of the HRR pathway (45–47).In the present study, we found that the human EVL (Ena/Vasp-like) protein binds to the RAD51 and RAD51B proteins in a HeLa cell extract. The EVL protein is known to be involved in cytoplasmic actin remodeling (48) and is also overexpressed in breast cancer (49). Like the RAD51B knockdown cells, the EVL knockdown cells partially impaired RAD51 foci formation after DSB induction, suggesting that the EVL protein enhances RAD51 assembly onto DSB sites. The purified EVL protein preferentially bound to ssDNA and stimulated RAD51-mediated homologous pairing and strand exchange. The EVL protein also promoted the annealing of complementary strands. These recombination reactions that were stimulated or promoted by the EVL protein were further enhanced by the RAD51B protein. These results strongly suggested that the EVL protein is a novel factor that activates RAD51-mediated recombination reactions, probably with the RAD51B protein. We anticipate that, in addition to its involvement in cytoplasmic actin dynamics, the EVL protein may be required in homologous recombination for repairing specific DNA lesions, and it may cause tumor malignancy by inappropriate recombination enhanced by EVL overexpression in certain types of tumor cells.     

Cleavage at Arg-1689 Influences Heavy Chain Cleavages during Thrombin-catalyzed Activation of Factor VIII

The procofactor, factor VIII, is activated by thrombin or factor Xa-catalyzed cleavage at three P1 residues: Arg-372, Arg-740, and Arg-1689. The catalytic efficiency for thrombin cleavage at Arg-740 is greater than at either Arg-1689 or Arg-372 and influences reaction rates at these sites. Because cleavage at Arg-372 appears rate-limiting and dependent upon initial cleavage at Arg-740, we investigated whether cleavage at Arg-1689 influences catalysis at this step. Recombinant B-domainless factor VIII mutants, R1689H and R1689Q were prepared and stably expressed to slow and eliminate cleavage, respectively. Specific activity values for the His and Gln mutations were ∼50 and ∼10%, respectively, that of wild type. Thrombin activation of the R1689H variant showed an ∼340-fold reduction in the rate of Arg-1689 cleavage, whereas the R1689Q variant was resistant to thrombin cleavage at this site. Examination of heavy chain cleavages showed ∼4- and 11-fold reductions in A2 subunit generation and ∼3- and 7-fold reductions in A1 subunit generation for the R1689H and R1689Q mutants, respectively. These results suggest a linkage between light chain cleavage and cleavages in heavy chain. Results obtained evaluating proteolysis of the factor VIII mutants by factor Xa revealed modest rate reductions (<5-fold) in generating A2 and A1 subunits and in cleaving light chain at Arg-1721 from either variant, suggesting little dependence upon prior cleavage at residue 1689 as compared with thrombin. Overall, these results are consistent with a competition between heavy and light chains for thrombin exosite binding and subsequent proteolysis with binding of the former chain preferred.Factor VIII, a plasma protein missing or defective in individuals with hemophilia A, is synthesized as an ∼300-kDa single chain polypeptide corresponding to 2332 amino acids. Within the protein are six domains based on internal homologies and ordered as NH₂-A1-A2-B-A3-C1-C2-COOH (1, 2). Bordering the A domains are short segments containing high concentrations of acidic residues that follow the A1 and A2 domains and precede the A3 domain and are designated a1 (residues 337–372), a2 (residues 711–740), and a3 (1649–1689). Factor VIII is processed by cleavage at the B-A3 junction to generate a divalent metal ion-dependent heterodimeric protein composed of a heavy chain (A1-a1-A2-a2-B domains) and a light chain (a3-A3-C1-C2 domains) (3).The activated form of factor VIII, factor VIIIa, functions as a cofactor for factor IXa, increasing its catalytic efficiency by several orders of magnitude in the phospholipid- and Ca²⁺-dependent conversion of factor X to factor Xa (4). The factor VIII procofactor is converted to factor VIIIa through limited proteolysis catalyzed by thrombin or factor Xa (5, 6). Thrombin is believed to act as the physiological activator of factor VIII, as association of factor VIII with von Willebrand factor impairs the capacity for the membrane-dependent factor Xa to efficiently activate the procofactor (5, 7). Activation of factor VIII occurs through proteolysis by either protease via cleavage of three P1 residues at Arg-740 (A2-B domain junction), Arg-372 (A1-A2 domain junction), and Arg-1689 (a3-A3 junction) (5). After factor VIII activation, there is a weak electrostatic interaction between the A1 and A2 domains of factor VIIIa (8, 9) and spontaneous inactivation of the cofactor occurs through A2 subunit dissociation from the A1/A3-C1-C2 dimer, consequently dampening factor Xase (3).Thrombin cleavage of factor VIII appears to be an ordered pathway, with relative rates at Arg-740 > Arg-1689 > Arg-372 and the initial proteolysis at Arg-740 facilitating proteolysis at Arg-372 as well as Arg-1689 (10). This latter observation was based upon results showing that mutations at Arg-740, impairing this cleavage, significantly reduced cleavage rates at the two other P1 sites. Thrombin-catalyzed activation of factor VIII is dependent upon interactions involving the anion binding exosites of the proteinase (11, 12). Exosite binding is believed to determine substrate affinity, whereas subsequent active site docking primarily affects V_max (13). Furthermore, the complex interactions involving multiple cleavages within a single substrate may utilize a ratcheting mechanism (14) where presentation of the scissile bond is facilitated by a prior cleavage event.Cleavage at Arg-372 is a critical step in thrombin activation of factor VIII as it exposes a cryptic functional factor IXa-interactive site in the A2 domain (15), whereas cleavage at Arg-1689 liberates factor VIII from von Willebrand factor (16) and contributes to factor VIIIa specific activity (17, 18). Although cleavage at Arg-740 represents a fast step relative to cleavages at other P1 residues in the activation of factor VIII (19), the influence of Arg-1689 cleavage on cleavages in the heavy chain remains unknown. In the present study cleavage at Arg-1689 is examined using recombinant factor VIII variants possessing single point mutations of R1689Q and R1689H. Results indicating reduced rates of A1 and A2 subunit generation, which are dependent upon the residue at position 1689, suggest that cleavage at Arg-1689 affects rates of proteolysis at Arg-740 and Arg-372. These observations are consistent with a mechanism whereby heavy chain and light chain compete for a binding thrombin exosite(s), with heavy chain preferred over light chain. In this competition mechanism, cleavage at Arg-740 is favored over Arg-1689. Subsequent cleavage at Arg-372 in heavy chain may involve a ratcheting mechanism after initial cleavage at Arg-740. On the other hand, the mechanism for factor Xa-catalyzed activation of factor VIII appears to be less dependent on cleavage at the Arg-1689 site as compared with thrombin.     

Sequential Loading of Saccharomyces cerevisiae Ku and Cdc13p to Telomeres

Ku is a heterodimeric protein involved in nonhomologous end-joining of the DNA double-stranded break repair pathway. It binds to the double-stranded DNA ends and then activates a series of repair enzymes that join the broken DNA. In addition to its function in DNA repair, the yeast Saccharomyces cerevisiae Ku (Yku) is also a component of telomere protein-DNA complexes that affect telomere function. The yeast telomeres are composed of duplex C_1–3(A/T)G_1–3 telomeric DNA repeats plus single-stranded TG_1–3 telomeric DNA tails. Here we show that Yku is capable of binding to a tailed-duplex DNA formed by telomeric DNA that mimics the structure of telomeres. Addition of Cdc13p, a single-stranded telomeric DNA-binding protein, to the Yku-DNA complex enables the formation of a ternary complex with Cdc13p binding to the single-stranded tail of the DNA substrate. Because pre-loading of Cdc13p to the single-stranded telomeric tail inhibits the binding of Yku, the results suggested that loading of Yku and Cdc13p to telomeres is sequential. Through generating a double-stranded break near telomeric DNA sequences, we found that Ku protein appears to bind to the de novo synthesized telomeres earlier than that of Cdc13p in vivo. Thus, our results indicated that Yku interacts directly with telomeres and that sequential loading of Yku followed by Cdc13p to telomeres is required for both proteins to form a ternary complex on telomeres. Our results also offer a mechanism that the binding of Cdc13p to telomeres might prevent Yku from initiating DNA double-stranded break repair pathway on telomeres.DNA damages in the form of double-stranded breaks (DSBs)⁴ compromise the integrity of genomes. Failure in repairing or mis-repairing double-stranded breaks can lead to chromosome instability and eventually cell death or cancer (1). Double-stranded breaks are repaired by two main pathways, the homologous recombination and nonhomologous DNA end-joining. In nonhomologous DNA end-joining, Ku is the first protein to bind to the DNA ends to initiate the repair pathway (2). Upon binding, Ku then recruits a series of repair enzymes to join the broken ends (2). Ku is a heterodimeric protein composed of 70- and ∼80-kDa subunits. In Saccharomyces cerevisiae, Ku includes Yku70 and Yku80 subunits. Because the biochemical configuration of the broken ends could be very diverse on DSBs, Ku binds to double-stranded ends in a sequence- and energy-independent manner. It is capable of binding to DNA ends with blunt 3′-overhangs or 5′-overhangs as well as double-stranded DNA with nicks, gaps, or internal loops (3–7). However, Ku does not have high affinity to single-stranded DNA. The crystal structure of human Ku heterodimer indicates that it forms a ring structure that encircles duplex DNA (7). This unique structure feature enables Ku to recognize DNA ends and achieves its high affinity binding.In additional to the role in double-stranded break repair, Ku was shown to be a component of telomeric protein-DNA complex in yeast and mammals (8–10). Telomeres are terminal structures of chromosomes composed of short tandem repeated sequences (11, 12). Mutation of YKU70 or YKU80 causes defects in telomere structure (13–15), telomere silencing (16–19), and replication timing of telomeres (20). The function of yeast Ku (Yku) on telomeres could mediate through protein-protein interaction with Sir4p or protein-RNA interaction with Tlc1 RNA (21, 22). For example, through the interaction with Sir4p, Yku selectively affects telomeres silencing but not the silent mating type loci (17). Yku could also bind to telomerase Tlc1 RNA for telomere length maintenance (22). Judged by the DNA binding activity of Yku, it is reasonable to suggest that it may bind directly to telomeric DNA. Indeed, it was shown that human Ku is capable of binding directly to telomeric DNA in vitro (15). Moreover, because the deletion of SIR4 in budding yeast (23) or Taz1 in fission yeast (24) does not abolish the association of Ku with chromosomal ends, this suggests that Ku might bind directly to telomeric DNA in cells. However, because yeast telomeres have a short 12–14-mer single-stranded tail (25), it is uncertain whether Yku could pass the single-stranded region to reach its binding site. The direct binding of Yku to telomeric DNA has not been experimentally determined.In contrast to double-stranded breaks, the ends of linear chromosomes are not recognized by repair enzymes as DNA damage. In S. cerevisiae, Cdc13p is the single-stranded TG_1–3 DNA-binding protein that enables cells to differentiate whether the ends of a linear DNA are telomeres or broken ends (26–29). Thus, although the mechanism of how cells prevent the activation of DSB repair pathway in telomere is unclear, it is likely that binding of Cdc13p to telomeres might inhibit the initiation of DNA damage response by the Ku protein. Here, using a tailed-duplex DNA synthesized by telomeric DNA sequences to mimic telomere structure, we showed that Yku binds directly to this tailed-duplex DNA substrate and forms a ternary complex with Cdc13p. Our results also showed that Yku loaded to a de novo synthesized telomere earlier than Cdc13p in vivo. These results support the direct binding of Yku to telomeric DNA and that the spatial orientation of Cdc13p might block the activation of DSB repair pathway on telomeres.     

VCP Mutations Causing Frontotemporal Lobar Degeneration Disrupt Localization of TDP-43 and Induce Cell Death

Frontotemporal lobar degeneration (FTLD) with inclusion body myopathy and Paget disease of bone is a rare, autosomal dominant disorder caused by mutations in the VCP (valosin-containing protein) gene. The disease is characterized neuropathologically by frontal and temporal lobar atrophy, neuron loss and gliosis, and ubiquitin-positive inclusions (FTLD-U), which are distinct from those seen in other sporadic and familial FTLD-U entities. The major component of the ubiquitinated inclusions of FTLD with VCP mutation is TDP-43 (TAR DNA-binding protein of 43 kDa). TDP-43 proteinopathy links sporadic amyotrophic lateral sclerosis, sporadic FTLD-U, and most familial forms of FTLD-U. Understanding the relationship between individual gene defects and pathologic TDP-43 will facilitate the characterization of the mechanisms leading to neurodegeneration. Using cell culture models, we have investigated the role of mutant VCP in intracellular trafficking, proteasomal function, and cell death and demonstrate that mutations in the VCP gene 1) alter localization of TDP-43 between the nucleus and cytosol, 2) decrease proteasome activity, 3) induce endoplasmic reticulum stress, 4) increase markers of apoptosis, and 5) impair cell viability. These results suggest that VCP mutation-induced neurodegeneration is mediated by several mechanisms.Frontotemporal lobar degeneration (FTLD)² accounts for 10% of all late onset dementias and is the third most frequent neurodegenerative disease after Alzheimer disease and dementia with Lewy bodies (1). FTLD with ubiquitin-immunoreactive inclusions is genetically, clinically, and neuropathologically heterogeneous (2, 3). FTLD-U comprises several distinct entities, including sporadic forms and familial cases caused by mutations in the genes encoding VCP (valosin-containing protein), GRN (progranulin), CHMP2B (charged multivesicular body protein 2B), TDP-43 (TAR DNA-binding protein of 43 kDa) and an unknown gene linked to chromosome 9 (2, 3). Frontotemporal dementia with inclusion body myopathy and Paget disease of bone is a rare, autosomal dominant disorder caused by mutations in the VCP gene located on chromosome 9p13-p12 (4-10) (Fig. 1). This multisystem disease is characterized by progressive muscle weakness and atrophy, increased osteoclastic bone resorption, and early onset frontotemporal dementia, also called FTLD (9, 11). Mutations in VCP are also associated with dilatative cardiomyopathy with ubiquitin-positive inclusions (12). Neuropathologic features of FTLD with VCP mutation include frontal and temporal lobar atrophy, neuron loss and gliosis, and ubiquitin-positive inclusions (FTLD-U). The majority of aggregates are ubiquitin- and TDP-43-positive neuronal intranuclear inclusions (NIIs); a smaller proportion is made up of TDP-43-immunoreactive dystrophic neurites (DNs) and neuronal cytoplasmic inclusions (NCIs). A small number of inclusions are VCP-immunoreactive (5, 13). Pathologic TDP-43 in inclusions links a spectrum of diseases in which TDP-43 pathology is a primary feature, including FTLD-U, motor neuron disease, including amyotrophic lateral sclerosis, FTLD with motor neuron disease, and inclusion body myopathy and Paget disease of bone, as well as an expanding spectrum of other disorders in which TDP-43 pathology is secondary (14, 15).Open in a separate windowFIGURE 1.Model of pathogenic mutations and domains in valosin-containing protein. CDC48 (magenta), located within the N terminus (residues 22-108), binds the following cofactors: p47, gp78, and Npl4-Ufd1 (23-25, 28). There are two AAA-ATPase domains (AAA; blue) at residues 240-283 and 516-569, which are joined by two linker regions (L1 and L2; red).TDP-43 proteinopathy in FTLD with VCP mutation has a biochemical signature similar to that seen in other sporadic and familial cases of FTLD-U, including sporadic amyotrophic lateral sclerosis, FTLD-motor neuron disease, FTLD with progranulin (GRN) mutation, and FTLD linked to chromosome 9p (3, 16). TDP-43 proteinopathy in these disorders is characterized by hyperphosphorylation of TDP-43, ubiquitination, and cleavage to form C-terminal fragments detected only in insoluble brain extracts from affected brain regions (16). Identification of TDP-43 as the major component of the ubiquitin-immunoreactive inclusions of FTLD with VCP mutation supports the hypothesis that VCP gene mutations cause an alteration of VCP function, leading to TDP-43 proteinopathy.VCP/p97 (valosin-containing protein) is a member of the AAA (ATPase associated with diverse cellular activities) superfamily. The N-terminal domain of VCP has been shown to be involved in cofactor binding (CDC48 (cell division cycle protein 48)) and two AAA-ATPase domains that form a hexameric complex (Fig. 1) (17). Recently, it has been shown that the N-terminal domain of VCP binds phosphoinositides (18, 19). AKT (activated serine-threonine protein kinase) phosphorylates VCP and is required for constitutive VCP function (20, 21). AKT is activated through phospholipid binding and phosphorylation via the phosphoinositide 3-kinase signaling pathway, which is involved in cell survival (22). The lipid binding domain may recruit VCP to the cell membrane where it is phosphorylated by AKT (19).The diversity of VCP functions is modulated, in part, by a variety of intracellular cofactors, including p47, gp78, and Npl4-Ufd1 (23). Cofactor p47 has been shown to play a role in the maintenance and biogenesis of both the endoplasmic reticulum (ER) and Golgi apparatus (24). The structure of p47 contains a ubiquitin regulatory X domain that binds the N-terminus of VCP, and together they act as a chaperone to deliver membrane fusion machinery to the site of adjacent membranes (25). The function of the p47-VCP complex is dependent upon cell division cycle 2 (CDC2) serine-threonine kinase phosphorylation of p47 (26, 27). Also, VCP has been found to interact with the cytosolic tail of gp78, an ER membrane-spanning E3 ubiquitin ligase that exclusively binds VCP and enhances ER-associated degradation (ERAD) (28). The Npl4-Ufd1-VCP complex is involved in nuclear envelope assembly and targeting of proteins through the ubiquitin-proteasome system (29, 30). The cell survival response of this complex has been found to be important in DNA damage repair though activation by phosphorylation and its recruitment to double-stranded breaks (20, 31). The Npl4-Ufd1-VCP cytosolic complex is also recruited to the ER membrane, interacting with Derlin 1, VCP-interacting membrane proteins (VIMP), and other complexes. At the ER membrane, these misfolded proteins are targeted to the proteasome via ERAD (32-34). VCP also targets IKKβ for ubiquitination to the ubiquitin-proteasome system, implicating VCP in the cell survival pathway and neuroprotection (21, 35-37).To investigate the mechanism of neurodegeneration caused by VCP mutations, we first tested the hypothesis that VCP mutations decrease cell viability in vitro using a neuroblastoma SHSY-5Y cell line and then investigated cellular pathways that are known to lead to neurodegeneration, including decrease in proteasome activity, caspase-mediated degeneration, and a change in cellular localization of TDP-43.