Ubiquilin-1 and protein quality control in Alzheimer disease

Single nucleotide polymorphisms in the ubiquilin-1 gene may confer risk for late-onset Alzheimer disease (AD). We have shown previously that ubiquilin-1 functions as a molecular chaperone for the amyloid precursor protein (APP) and that protein levels of ubiquilin-1 are decreased in the brains of AD patients. We have recently found that ubiquilin-1 regulates APP trafficking and subsequent secretase processing by stimulating non-degradative ubiquitination of a single lysine residue in the cytosolic domain of APP. Thus, ubiquilin-1 plays a central role in regulating APP biosynthesis, trafficking and ultimately toxicity. As ubiquilin-1 and other ubiquilin family members have now been implicated in the pathogenesis of numerous neurodegenerative diseases, these findings provide mechanistic insights into the central role of ubiquilin proteins in maintaining neuronal proteostasis.     

Identification of ubiquilin, a novel presenilin interactor that increases presenilin protein accumulation

Mutations in the highly homologous presenilin genes encoding presenilin-1 and presenilin-2 (PS1 and PS2) are linked to early-onset Alzheimer's disease (AD). However, apart from a role in early development, neither the normal function of the presenilins nor the mechanisms by which mutant proteins cause AD are well understood. We describe here the properties of a novel human interactor of the presenilins named ubiquilin. Yeast two-hybrid (Y2H) interaction, glutathione S-transferase pull-down experiments, and colocalization of the proteins expressed in vivo, together with coimmunoprecipitation and cell fractionation studies, provide compelling evidence that ubiquilin interacts with both PS1 and PS2. Ubiquilin is noteworthy since it contains multiple ubiquitin-related domains typically thought to be involved in targeting proteins for degradation. However, we show that ubiquilin promotes presenilin protein accumulation. Pulse-labeling experiments indicate that ubiquilin facilitates increased presenilin synthesis without substantially changing presenilin protein half-life. Immunohistochemistry of human brain tissue with ubiquilin-specific antibodies revealed prominent staining of neurons. Moreover, the anti-ubiquilin antibodies robustly stained neurofibrillary tangles and Lewy bodies in AD and Parkinson's disease affected brains, respectively. Our results indicate that ubiquilin may be an important modulator of presenilin protein accumulation and that ubiquilin protein is associated with neuropathological neurofibrillary tangles and Lewy body inclusions in diseased brain.     

Ubiquilin 1 interacts with Orai1 to regulate calcium mobilization

Store-operated calcium entry (SOCE) channels composed of Stim and Orai proteins play a critical role in diverse biological processes. Upon endoplasmic reticulum (ER)-mediated calcium (Ca²⁺) depletion, Stim proteins oligomerize with Orai to initiate Ca²⁺ influx across the plasma membrane. The ubiquitin-like (UBL) and ubiquitin-associated (UBA) domains of ubiquilin 1 are involved in the degradation of presenilin and polyglutamine proteins. Through screening of Orai1 interaction partner(s) that might have an effect on SOCE, ubiquilin 1 was identified as a target of Orai1. However, the UBL and UBA domains of ubiquilin 1 were dispensable for this interaction. Additionally, ubiquilin 1 and Orai1 colocalized in the cytosolic compartment. Ubiquilin 1 increased the ubiquitination of Orai1, resulting in the formation of a high-molecular-weight form. MG132, a proteasome inhibitor, failed to block the degradation of Orai1, whereas bafilomycin A, a lysosome inhibitor, prevented Orai1 degradation. Confocal microscopy studies demonstrated that a fraction of Orai1 colocalized with ubiquilin 1 and the autophagosomal marker LC3. Because Orai1 is a constituent of SOCE, we determined the effect of ubiquilin 1 on Orai1-mediated Ca²⁺ influx. As we expected, intracellular Ca²⁺ mobilization, a process normally potentiated by Orai1, was downregulated by ubiquilin 1. Taken together, these findings suggest that ubiquilin 1 downregulates intracellular Ca²⁺ mobilization and its downstream signaling by promoting the ubiquitination and lysosomal degradation of Orai1.     

Ubiquilin at a crossroads in protein degradation pathways

Ubiquilin proteins are conserved across all eukaryotes and function in the regulation of protein degradation. We found that ubiquilin functions to regulate macroautophagy and that the protein is also a substrate of chaperone-mediated autophagy.Key words: autophagy, cell death, LC3, protein turnover, ubiquitinUbiquilin proteins are present in all eukaryotes and appear to function in protein degradation pathways. Humans contain four ubiquilin genes each encoding a separate protein. The proteins are approximately 600 amino acids in length and share extensive homology with one another. They are characterized by an N-terminal sequence that is very similar to ubiquitin, called the ubiquitin-like domain (UBL), followed by a longer, more variable central domain, and terminate with a conserved 50-amino-acid sequence called a ubiquitin-associated domain (UBA). This structural organization is characteristic of proteins that function to deliver ubiquitinated proteins to the proteasome for degradation. In accordance with this function, the UBL domain of ubiquilin binds subunits of the proteasome, and its UBA domain binds to polyubiquitin chains that are typically conjugated onto proteins that are marked for destruction. Indeed, we recently showed that ubiquilin is recruited to the endoplasmic reticulum where it binds and promotes the degradation of misfolded proteins to the proteasome during ER-associated degradation (ERAD).Remarkably, ubiquilin was also recently reported to be involved in macroautophagy. The finding was based on colocalization of ubiquilin with autophagosomal marker LC3 in cells, and because overexpression of ubiquilin-1 suppresses and silencing of its expression enhances, starvation-induced cell death. In our recently published paper we describe our evidence linking ubiquilin to autophagy. We demonstrate that ubiquilin is indeed present in different structures associated with macroautophagy and that it is required for a critical step in autophagosome formation. Additionally, we also demonstrate that ubiquilin is a substrate of chaperone-mediated autophagy. The findings suggest that ubiquilin might play an important, and perhaps a crucial, role in dictating the pathway of protein degradation in cells.In previous studies we found that ubiquilin proteins expressed in normal growing HeLa cells are very stable with a rate of turnover in excess of 20 h. Because most long-lived proteins are degraded by autophagy, we felt it was important to distinguish whether ubiquilin localization in autophagosomes was simply related to the expected route of degradation of the protein or whether it was related to some special function in autophagy. Accordingly, our experiments were designed to distinguish between these two possibilities.Using double immunofluorescence microscopy we found that endogenous ubiquilin and LC3 proteins are present in puncta in HeLa cells. To ensure this was not an artifact of the staining procedure, we cotransfected HeLa cells with ubiquilin-1 and LC3 expression constructs that were tagged with either mRFP or GFP proteins and again found that the two expressed proteins are colocalized in puncta, irrespective of which tag was fused to the proteins. Further evidence supporting ubiquilin localization to autophagosomes was obtained by showing strong enrichment of ubiquilin proteins upon purification of autophagosomes from mouse liver and by the strong immunogold staining of the protein in autophagosomes in mouse brains in a transgenic mouse model of Alzheimer disease.To determine if ubiquilin localization to autophagosomes is mediated by interaction with LC3 we conducted immunoprecipitation experiments to examine whether the two proteins coimmunoprecipitate with each other. Indeed, our results showed that the two proteins coimmunoprecipitate with one another, indicating that they bind together in a complex. However, we did not detect any strong binding between bacterially expressed forms of the proteins, suggesting that the interaction between the proteins in cells might be mediated by a bridging factor(s).We next used a pH-sensitive tandem-tagged mCherry-GFP-LC3 reporter that is used to monitor maturation of autophagosomes to autolysosomes to determine whether ubiquilin is present during the different steps of macroautophagy. Indeed, we found that anti-ubiquilin staining is present throughout the different structures involved in the process, and interestingly, we also noted that the structures are enriched for K48- and K63-ubiquitin linkages. Because ubiquilin contains a UBA domain that binds ubiquitin chains we examined whether proteins containing K48- and K63-ubiquitin linkages coimmunoprecipitate with ubiquilin. Indeed, our immunoblots indicated that proteins containing both of these types of linkages coprecipitate with ubiquilin, consistent with the idea that ubiquilin might target proteins with diverse ubiquitin linkages for degradation by autophagy.To determine if ubiquilin is required for autophagy, we knocked down the ubiquilin-1 and -2 proteins in HeLa cells (which mainly express these two ubiquilin isoforms) by siRNA transfection and examined if loss of the proteins altered LC3-I and LC3-II levels. Interestingly, we found that ubiquilin knockdown over a 72 h time period is associated with a progressive increase in LC3-I levels and a concomitant decrease in LC3-II levels. Furthermore, ubiquilin knockdown led to an ∼45% reduction in the number of cells containing five or more autophagosomes. Based on these results we propose that ubiquilin is required for maturation of LC3-I to LC3-II, which we speculate might be related to the requirement of the protein in macroautophagy.We next asked if ubiquilin protein is consumed during autophagy. We examined this by treating HeLa cells with puromycin to induce protein misfolding and macroautophagy. Immunoblot analysis of the protein lysates examined at 2 h intervals over a 7 h period of exposure to puromycin revealed a direct correlation between stimulation of macroautophagy and a time-dependent decrease in the ubiquilin and LC3-II protein levels. The time-dependent decline in the proteins is inhibited by treatment of cells with two different autophagy inhibitors, 3-methyladenine and bafilomycin A₁. The results suggest that ubiquilin protein is consumed during macroautophagy.The consumption of ubiquilin during macroautophagy prompted us to examine if ubiquilin might also be involved in chaperone-mediated autophagy (CMA), which involves the active transport of proteins into lysosomes. Support for this idea arose because ubiquilin proteins contain two sequences that conform to a pentapeptide motif involved in CMA. An in vitro CMA assay using recombinant GST-ubiquilin-1 fusion protein and purified lysosomes confirmed ubiquilin is an active CMA substrate. The results suggested that ubiquilin can be consumed by two different types of autophagy, macroautophagy and CMA. We speculate that this dual mode of consumption may provide a potential switch whereby changes in ubiquilin levels beyond a certain threshold might trigger execution of either macroautophagy or CMA. The idea that such a switch exists stems from previous work that showed inhibition of CMA can lead to activation of macroautophagy and vice versa.Several intriguing new questions emerge from this and previous works, including what exact function ubiquilin serves in autophagy, particularly in the execution of macroautophagy and CMA. Is there a signal that instructs ubiquilin to choose between its known functions in autophagy and ERAD or is the choice random? What role do its different domains play in these processes? The answers to these questions are likely to be important because in previous studies we showed that overexpression of ubiquilin protects cells against potentially toxic mutant huntingtin proteins containing polyglutamine expansions. In our new work we also found that ubiquilin overexpression protects cells against starvation-induced cell death caused by mutations in presenilin-2 proteins. The underlying conclusion from these studies is that ubiquilin appears to play important roles in regulating protein degradation pathways that are likely to have important implications in cell survival. Clearly, understanding ubiquilin function in different protein degradation pathways could lead to novel approaches to prevent diseases associated with protein misfolding.     

A method of mapping protein sumoylation sites by mass spectrometry using a modified small ubiquitin-like modifier 1 (SUMO-1) and a computational program

Post-translational modification by small ubiquitin-like modifier 1 (SUMO-1) is a highly conserved process from yeast to humans and plays important regulatory roles in many cellular processes. Sumoylation occurs at certain internal lysine residues of target proteins via an isopeptide bond linkage. Unlike ubiquitin whose carboxyl-terminal sequence is RGG, the tripeptide at the carboxyl terminus of SUMO is TGG. The presence of the arginine residue at the carboxyl terminus of ubiquitin allows tryptic digestion of ubiquitin conjugates to yield a signature peptide containing a diglycine remnant attached to the target lysine residue and rapid identification of the ubiquitination site by mass spectrometry. The absence of lysine or arginine residues in the carboxyl terminus of mammalian SUMO makes it difficult to apply this approach to mapping sumoylation sites. We performed Arg scanning mutagenesis by systematically substituting amino acid residues surrounding the diglycine motif and found that a SUMO variant terminated with RGG can be conjugated efficiently to its target protein under normal sumoylation conditions. We developed a Programmed Data Acquisition (PDA) mass spectrometric approach to map target sumoylation sites using this SUMO variant. A web-based computational program designed for efficient identification of the modified peptides is described.     

Ubiquitination of p21Cip1/WAF1 by SCFSkp2: substrate requirement and ubiquitination site selection

Multiple proteolytic pathways are involved in the degradation of the cyclin-dependent kinase inhibitor p21(Cip1/WAF1). Timed destruction of p21(Cip1/WAF1) plays a critical role in cell-cycle progression and cellular response to DNA damage. The SCF(Skp2) complex (consisting of Rbx1, Cul1, Skp1, and Skp2) is one of the E3 ubiquitin ligases involved in ubiquitination of p21(Cip1/WAF1). Little is known about how SCF(Skp2) recruits its substrates and selects particular acceptor lysine residues for ubiquitination. In this study, we investigated the requirements for SCF(Skp2) recognition of p21(Cip1/WAF1) and lysine residues that are ubiquitinated in vitro and inside cells. We demonstrate that ubiquitination of p21(Cip1/WAF1) requires a functional interaction between p21(Cip1/WAF1) and the cyclin E-Cdk2 complex. Mutation of both the cyclin E recruitment motif (RXL) and the Cdk2-binding motif (FNF) at the N terminus of p21(Cip1/WAF1) abolishes its ubiquitination by SCF(Skp2), while mutation of either motif alone has minimal effects, suggesting either contact is sufficient for substrate recruitment. Thus, SCF(Skp2) appears to recognize a trimeric complex consisting of cyclin E-Cdk2-p21(Cip1/WAF1). Furthermore, we show that p21(Cip1/WAF1) can be ubiquitinated at four distinct lysine residues located in the carboxyl-terminal region but not two other lysine residues in the N-terminal region. Any one of these four lysine residues can be targeted for ubiquitination in the absence of the others in vitro, and three of these four lysine residues are also ubiquitinated in vivo, suggesting that there is limited specificity in the selection of ubiquitination sites. Interestingly, mutation of the carboxyl-terminal proline to lysine enables ubiquitin conjugation at the carboxyl terminus of the substrate both in vitro and in vivo. Thus, our results highlight a unique property of the ubiquitination enzymatic reaction in that substrate ubiquitination site selection can be remarkably diverse and occur in distinct spatial areas.     

Interaction with telencephalin and the amyloid precursor protein predicts a ring structure for presenilins.

The carboxyl terminus of presenilin 1 and 2 (PS1 and PS2) binds to the neuron-specific cell adhesion molecule telencephalin (TLN) in the brain. PS1 deficiency results in the abnormal accumulation of TLN in a yet unidentified intracellular compartment. The first transmembrane domain and carboxyl terminus of PS1 form a binding pocket with the transmembrane domain of TLN. Remarkably, APP binds to the same regions via part of its transmembrane domain encompassing the critical residues mutated in familial Alzheimer's disease. Our data surprisingly indicate a spatial dissociation between the binding site and the proposed catalytic site near the critical aspartates in PSs. They provide important experimental evidence to support a ring structure model for PS.     

Ubiquilin-1 Overexpression Increases the Lifespan and Delays Accumulation of Huntingtin Aggregates in the R6/2 Mouse Model of Huntington's Disease

Huntington''s Disease (HD) is a neurodegenerative disorder that is caused by abnormal expansion of a polyglutamine tract in huntingtin (htt) protein. The expansion leads to increased htt aggregation and toxicity. Factors that aid in the clearance of mutant huntingtin proteins should relieve the toxicity. We previously demonstrated that overexpression of ubiqulin-1, which facilitates protein clearance through the proteasome and autophagy pathways, reduces huntingtin aggregates and toxicity in mammalian cell and invertebrate models of HD. Here we tested whether overexpression of ubiquilin-1 delays or prevents neurodegeneration in R6/2 mice, a well-established model of HD. We generated transgenic mice overexpressing human ubiquilin-1 driven by the neuron-specific Thy1.2 promoter. Immunoblotting and immunohistochemistry revealed robust and widespread overexpression of ubiquilin-1 in the brains of the transgenic mice. Similar analysis of R6/2 animals revealed that ubiquilin is localized in huntingtin aggregates and that ubiquilin levels decrease progressively to 30% during the end-stage of disease. We crossed our ubiquilin-1 transgenic line with R6/2 mice to assess whether restoration of ubiquilin levels would delay HD symptoms and pathology. In the double transgenic progeny, ubiquilin levels were fully restored, and this correlated with a 20% increase in lifespan and a reduction in htt inclusions in the hippocampus and cortex. Furthermore, immunoblots indicated that endoplasmic reticulum stress response that is elevated in the hippocampus of R6/2 animals was attenuated by ubiquilin-1 overexpression. However, ubiquilin-1 overexpression neither altered the load of htt aggregates in the striatum nor improved motor impairments in the mice.     

Presenilins interact with armadillo proteins including neural-specific plakophilin-related protein and beta-catenin

Abstract : Missense substitutions in the presenilin 1 (PS1) and presenilin 2 (PS2) proteins are associated with early-onset familial Alzheimer's disease. We have used yeast-two-hybrid and coimmunoprecipitation methods to show that the large cytoplasmic loop domains of PS1 and PS2 interact specifically with three members of the armadillo protein family, including β-catenin, p0071, and a novel neuronal-specific armadillo protein—neural plakophilin-related armadillo protein (NPRAP). The PS1 : NPRAP interaction occurs between the arm repeats of NPRAP and residues 372-399 at the C-terminal end of the large cytoplasmic loop of PS1. The latter residues contain a single arm -like domain and are highly conserved in the presenilins, suggesting that they form a functional armadillo protein binding site for the presenilins.     

Interaction between presenilin 1 and ubiquilin 1 as detected by fluorescence lifetime imaging microscopy and a high-throughput fluorescent plate reader

Presenilin 1 (PS1) in its active heterodimeric form is the catalytic center of the gamma-secretase complex, an enzymatic activity that cleaves amyloid precursor protein (APP) to produce amyloid beta (Abeta). Ubiquilin 1 is a recently described PS1 interacting protein, the overexpression of which increases PS1 holoprotein levels and leads to reduced levels of functionally active PS1 heterodimer. In addition, it has been suggested that splice variants of the UBQLN1 gene are associated with an increased risk of developing Alzheimer disease (AD). However, it is still unclear whether PS1 and ubiquilin 1 interact when expressed at endogenous levels under normal physiological conditions. Here, we employ three novel fluorescence resonance energy transfer-based techniques to investigate the interaction between PS1 and ubiquilin 1 in intact cells. We consistently find that the ubiquilin 1 N terminus is in close proximity to several epitopes on PS1. We show that ubiquilin 1 interacts both with PS1 holoprotein and heterodimer and that the interaction between PS1 and ubiquilin 1 takes place near the cell surface. Furthermore, we show that the PS1-ubiquilin 1 interaction can be detected between endogenous proteins in primary neurons in vitro as well as in brain tissue of healthy controls and Alzheimer disease patients, providing evidence of its physiological relevance.     

Presenilin 1 mutations activate gamma 42-secretase but reciprocally inhibit epsilon-secretase cleavage of amyloid precursor protein (APP) and S3-cleavage of notch

The presenilin 1 (PS1) and presenilin 2 (PS2) proteins are necessary for proteolytic cleavage of the amyloid precursor protein (APP) within its transmembrane domain. One of these cleavage events (termed gamma-secretase) generates the C-terminal end of the Abeta-peptide by proteolysis near residue 710 or 712 of APP(770). Another event (termed gamma-like or epsilon-secretase cleavage) cleaves near residue 721 at approximately 2-5 residues inside the cytoplasmic membrane boundary to generate a series of stable, C-terminal APP fragments. This latter cleavage is analogous to S3-cleavage of Notch. We report here that specific mutations in the N terminus, loop, or C terminus of PS1 all increase the production of Abeta(42) but cause inhibition of both epsilon-secretase cleavage of APP and S3-cleavage of Notch. These data support the hypothesis that epsilon-cleavage of APP and S3-cleavage of Notch are similar events. They also argue that, although both the gamma-site and the epsilon-site cleavage of APP are presenilin-dependent, they are likely to be independent catalytic events.     

Dimerization of ubiquilin is dependent upon the central region of the protein: evidence that the monomer, but not the dimer, is involved in binding presenilins

Ubiquilin proteins have been shown to interact with a wide variety of other cellular proteins, often regulating the stability and degradation of the interacting protein. Ubiquilin contains a UBL (ubiquitin-like) domain at the N-terminus and a UBA (ubiquitin-associated) domain at the C-terminus, separated by a central region containing Sti1-like repeats. Little is known about regulation of the interaction of ubiquilin with other proteins. In the present study, we show that ubiquilin is capable of forming dimers, and that dimerization requires the central region of ubiquilin, but not its UBL or the UBA domains. Furthermore, we provide evidence suggesting that monomeric ubiquilin is likely to be the active form that is involved in binding presenilin proteins. Our results provide new insight into the regulatory mechanism underlying the interaction of ubiquilin with presenilins.     

Agonist-promoted ubiquitination of the G protein-coupled receptor CXCR4 mediates lysosomal sorting

Ligand-induced trafficking plays an important role in the physiologic regulation of many G protein-coupled receptors (GPCRs). Although numerous GPCRs are sorted to a degradative pathway upon prolonged stimulation, the molecular events leading to degradation are poorly understood. Here we report that the human immunodeficiency virus co-receptor CXCR4 undergoes rapid agonist-promoted degradation by a process involving endocytosis via clathrin-coated pits and subsequent sorting to lysosomes. Studies analyzing the sorting of various CXCR4 mutants revealed the presence of a degradation motif (SSLKILSKGK) in the carboxyl terminus of CXCR4. The first two serines as well as the dileucine motif were critical for agonist-induced endocytosis, whereas all three serines but not the dileucine were important in mediating degradation. Mutation of the three lysine residues had no effect on CXCR4 endocytosis yet completely inhibited receptor degradation. Because lysine residues represent potential sites of ubiquitination, we also examined the ubiquitination of CXCR4. Interestingly, CXCR4 was shown to undergo rapid agonist-promoted ubiquitination that was attenuated by mutation of the lysine residues within the degradation motif. These studies implicate a specific role for ubiquitination in sorting endocytosed GPCRs to lysosomes.     

A conserved cysteine is essential for Pex4p-dependent ubiquitination of the peroxisomal import receptor Pex5p

The peroxisomal protein import receptor Pex5p is modified by ubiquitin, both in an Ubc4p-dependent and -independent manner. Here we show that the two types of ubiquitination target different residues in the NH(2)-terminal region of Pex5p and we identify Pex4p (Ubc10p) as the ubiquitin-conjugating enzyme required for Ubc4p-independent ubiquitination. Whereas Ubc4p-dependent ubiquitination occurs on two lysine residues, Pex4p-dependent ubiquitination neither requires lysine residues nor the NH(2)-terminal alpha-NH(2) group. Instead, a conserved cysteine residue appears to be essential for both the Pex4p-dependent ubiquitination and the overall function of Pex5p. In addition, we show that this form of ubiquitinated Pex5p is susceptible to the reducing agent beta-mercaptoethanol, a compound that is unable to break ubiquitin-NH(2) group linkages. Together, our results strongly suggest that Pex4p-dependent ubiquitination of Pex5p occurs on a cysteine residue.     

Identification of gamma-secretase inhibitor potency determinants on presenilin

Production of amyloid beta peptides (Abeta), followed by their deposition in the brain as amyloid plaques, contributes to the hallmark pathology of Alzheimer disease. The enzymes responsible for production of Abeta, BACE1 and gamma-secretase, are therapeutic targets for treatment of Alzheimer disease. Two presenilin (PS) homologues, referred to as PS1 and PS2, comprise the catalytic core of gamma-secretase. In comparing presenilin selectivity of several classes of gamma-secretase inhibitors, we observed that sulfonamides in general tend to be more selective for inhibition of PS1-comprising gamma-secretase, as exemplified by ELN318463 and BMS299897. We employed a combination of chimeric constructs and point mutants to identify structural determinants for PS1-selective inhibition by ELN318463. Our studies identified amino acid residues Leu(172), Thr(281), and Leu(282) in PS1 as necessary for PS1-selective inhibition by ELN318463. These residues also contributed in part to the PS1-selective inhibition by BMS299897. Alanine scanning mutagenesis of areas flanking Leu(172), Thr(281), and Leu(282) identified additional amino acids that affect inhibitor potency of not only these sulfonamides but also nonsulfonamide inhibitors, without affecting Abeta production and presenilin endoproteolysis. Interestingly, many of these same residues have been identified previously to be important for gamma-secretase function. These findings implicate TM3 and a second region near the carboxyl terminus of PS1 aminoterminal fragment in mediating the activity of gamma-secretase inhibitors. Our observations demonstrate that PS-selective inhibitors of gamma-secretase are feasible, and such inhibitors may allow differential inhibition of Abeta peptide production and Notch signaling.     

Ubiquitin carrier protein-catalyzed ubiquitin transfer to histones. Mechanism and specificity

Ubiquitinated derivatives of histones H2A and H2B, in which the carboxyl terminus of ubiquitin is joined to epsilon-amino groups of specific lysine residues of each histone, occur in vivo. Certain ubiquitin carrier proteins (E2s) catalyze ubiquitin transfer to histones (Pickart, C. M., and Rose, I. A. (1985) J. Biol. Chem. 260, 1573-1581). The catalytic activities of these purified ubiquitin carrier proteins have been quantitatively characterized with purified histones, in order to determine if one or more of them exhibits specificity for H2A over other histones (H3,H4) which are not known to be ubiquitinated in vivo. The results show the following. 1) No E2 exhibits strong specificity for H2A over the other histones. 2) For a given histone, kinetics of formation of its monoubiquitinated adduct do not differ strongly among the E2s; sigmoid kinetics (nH = 2) are generally observed, with values of K 0.5 ranging from 2-6 microM. 3) E214K catalyzes primarily monoubiquitination. 4) E220K catalyzes multiple ubiquitination (up to three ubiquitin/histone) by a processive mechanism that involves joining of ubiquitin carboxyl termini to multiple histone lysine residues. 5) E235K also catalyzes processive ubiquitination, with formation of polyubiquitinated products exhibiting a lag phase. Many of the polyubiquitinated adducts produced at low histone concentration are larger than expected for monoubiquitination of every histone-lysine residue, and polyubiquitination is selectively inhibited by substitution of reductively methylated ubiquitin for ubiquitin. These results suggest that E235K uniquely catalyzes ubiquitin transfer to lysine residues of previously conjugated ubiquitin molecule(s). The implications of these results for biological mechanisms of histone ubiquitination are discussed.     

The TREX1 C-terminal Region Controls Cellular Localization through Ubiquitination

TREX1 is an autonomous 3′-exonuclease that degrades DNA to prevent inappropriate immune activation. The TREX1 protein is composed of 314 amino acids; the N-terminal 242 amino acids contain the catalytic domain, and the C-terminal region (CTR) localizes TREX1 to the cytosolic compartment. In this study, we show that TREX1 modification by ubiquitination is controlled by a highly conserved sequence in the CTR to affect cellular localization. Transfection of TREX1 deletion constructs into human cells demonstrated that this sequence is required for ubiquitination at multiple lysine residues through a “non-canonical” ubiquitin linkage. A proteomic approach identified ubiquilin 1 as a TREX1 CTR-interacting protein, and this interaction was verified in vitro and in vivo. Cotransfection studies indicated that ubiquilin 1 localizes TREX1 to cytosolic punctate structures dependent upon the TREX1 CTR and lysines within the TREX1 catalytic core. Several TREX1 mutants linked to the autoimmune diseases Aicardi-Goutières syndrome and systemic lupus erythematosus that exhibit full catalytic function were tested for altered ubiquitin modification and cellular localization. Our data show that these catalytically competent disease-causing TREX1 mutants exhibit differential levels of ubiquitination relative to WT TREX1, suggesting a novel mechanism of dysfunction. Furthermore, these differentially ubiquitinated disease-causing mutants also exhibit altered ubiquilin 1 co-localization. Thus, TREX1 post-translational modification indicates an additional mechanism by which mutations disrupt TREX1 biology, leading to human autoimmune disease.