Biochemical Journal

Research article

T-cell regulator RNF125/TRAC-1 belongs to a novel family of ubiquitin ligases with zinc fingers and a ubiquitin-binding domain

Ana Lucia Giannini, Yifang Gao, Marie-José Bijlmakers

Abstract

The recently identified RNF125 [RING (really interesting new gene) finger protein 125], or TRAC-1 (T-cell RING protein in activation 1), is unique among ubiquitin ligases in being a positive regulator of T-cell activation. In addition, TRAC-1 has been shown to down-modulate HIV replication and to inhibit pathogen-induced cytokine production. However, apart from the presence of an N-terminal C3HC4 (Cys3-His-Cys4) RING domain, the TRAC-1 protein remains uncharacterized. In the present paper, we report novel interactions and modifications for TRAC-1, and elucidate its domain organization. Specifically, we determine that TRAC-1 associates with membranes and is excluded from the nucleus through myristoylation. Our data are further consistent with a crucial role for the C-terminus in TRAC-1 function. In this region, novel domains were recognized through the identification of three closely related proteins: RNF114, RNF138 and RNF166. TRAC-1 and its relatives were found to contain, apart from the RING domain, a C2HC (Cys2-His-Cys)- and two C2H2 (Cys2-His2)-type zinc fingers, as well as a UIM (ubiquitin-interacting motif). The UIM of TRAC-1 binds Lys48-linked polyubiquitin chains and is, together with the RING domain, required for auto-ubiquitination. As a consequence of auto-ubiquitination, the half-life of TRAC-1 is shorter than 30 min. The identification of these novel modifications, interactions, domains and relatives significantly widens the contexts for investigating TRAC-1 activity and regulation.

  • myristoylation
  • RING (really interesting new gene) finger protein 125/T-cell RING protein in activation 1 (RNF125/TRAC-1)
  • T-cell activation
  • ubiquitin-interacting motif (UIM)
  • ubiquitin ligase
  • zinc finger

INTRODUCTION

The activation of T-cells by their ligands, MHC/peptide complexes, is essential for the initiation of an adaptive immune response. The multitude of signalling pathways that are initiated from the TCR (T-cell receptor) need careful regulation to ensure that an appropriate response, which can vary from T-cell activation through anergy induction to apoptosis, is induced. Recently, it has become clear that ubiquitination, the attachment of the 76-amino-acid ubiquitin to target proteins, is crucially involved in the regulation of T-cell functions.

Ubiquitination has long been known to target damaged proteins for degradation, but is now also recognized to modulate the function, localization and interactions of target proteins [14]. Like phosphorylation, ubiquitination is a common regulatory modification that is rapidly inducible and reversible. The modification of proteins by ubiquitination requires the sequential activity of three classes of proteins [5]. An ubiquitin-activating enzyme, or E1, binds ubiquitin and transfers it to the active site of an ubiquitin-conjugating enzyme, or E2. E2 proteins interact with the ubiquitin ligases, or E3s, and promote the attachment of ubiquitin to substrates of these proteins. Ubiquitin is attached primarily to lysine residues on target proteins and, subsequently, polyubiquitin chains can be formed. The presence of four or more ubiquitin proteins linked to each other via Lys48 serves as a signal for degradation by the proteasome. However, a polyubiquitin chain linked via alternative lysine residues, as well as mono-ubiquitination, modulate the activity of substrates in a degradation-independent manner [68].

The ubiquitin ligases are central to ubiquitination by selecting substrates and interacting with E2 proteins. These E3s can be recognized by the presence of an E2-interacting domain, of which the RING (really interesting new gene), HECT (homologous with E6-associated protein C-terminus) and U-box domains are the best characterized [9,10]. In agreement with their role in recruiting selected sets of substrates, the ubiquitin ligases comprise a large and heterogeneous group. It is estimated that >400 are encoded in mammalian genomes [11], the majority of which remain to be characterized.

Given its versatility, ubiquitination can be predicted to impinge on many aspects of T-cell function. So far, a role for this modification has been demonstrated in the internalization and degradation of the TCR [12], the activation of NF-κB (nuclear factor κB) [13] and the down-modulation of critical enzymes such as ZAP-70 (ζ-chain-associated protein kinase of 70 kDa), PKCθ (protein kinase Cθ), PLCγ (phospholipase Cγ) and ERK (extracellular-signal-regulated kinase) 1/2 [1416]. Furthermore, we and others have shown the selective ubiquitination of active forms of Lck, a Src-related tyrosine kinase that is essential for T-cell activation [17,18]. The importance of ubiquitination in T-cell function is also convincingly illustrated by the critical roles that have emerged for several ubiquitin ligases, such as c-Cbl, Cbl-b, Itch, GRAIL (gene related to anergy in lymphocytes) and Roquin (reviewed in [1922]). For instance, disruption of the genes for Cbl-b [23,24] and Roquin [25] in mice leads to an enhanced susceptibility to autoimmune diseases, whereas the absence of c-Cbl results in defects in T-cell development [26,27]. In itchy mice, the gene for Itch is disrupted as the result of a naturally occurring mutation, which causes a wide spectrum of immune and inflammatory disorders [28]. GRAIL is essential for the induction of T-cell anergy [29,30], or unresponsiveness, which is crucial for peripheral tolerance. Although these proteins act via widely differing mechanisms, they share a negative regulatory effect on T-cell activation.

The RING domain protein TRAC-1 (T-cell RING protein in activation 1) was identified in a functional screen for T-cell regulators [31]. This protein stands out in two major respects from the ubiquitin ligases with functions in T-cells described above. First, TRAC-1 is predominantly expressed in lymphoid cells [31], in contrast with the ubiquitous expression of the other proteins. Secondly, interfering with TRAC-1 expression by antisense DNA inhibited T-cell activation [32], indicating that, unlike the other ligases, TRAC-1 is a positive T-cell regulator.

However, recent reports have demonstrated inhibitory activities for TRAC-1 in other processes. TRAC-1 was found to ubiquitinate and down-modulate RIG-I (retinoic acid-inducible gene I) [33], a protein that detects viral double-stranded DNA and induces the production of cytokines, including type I IFNs (interferons). TRAC-1 was shown to be up-regulated in response to IFN and was postulated to provide a negative-feedback loop for cytokine production. In another study, TRAC-1 was reported to reduce HIV replication [34]. TRAC-1 was found to be up-regulated in IL (interleukin)-4-stimulated CD4+CD38 cells in which HIV replicates with low efficiency relative to CD4+CD38+ cells, and a negative effect of TRAC-1 on HIV transcription was demonstrated [34].

Despite these various important roles, little is known about the TRAC-1 protein and its regulation. Although it is clear that the N-terminal C3HC4 (Cys3-His-Cys4) RING domain is important for ubiquitin ligase activity, as it is for other ubiquitin ligases, dominant-negative effects of truncated TRAC-1 suggested additional as yet undefined roles for the C-terminal region [32]. The present study characterizes the TRAC-1 protein in some detail. Two novel modifications for TRAC-1 are demonstrated, myristoylation and auto-ubiquitination, which are important for membrane association and stability of TRAC-1 respectively. Furthermore, in the C-terminal region of TRAC-1, the presence of three zinc-binding and one ubiquitin-interacting motifs are identified. These features permit TRAC-1 to be recognized as belonging to a new subfamily of RING ubiquitin ligases, together with RNF (RING finger protein) 114, RNF138 and RNF166. These findings considerably widen the scope for studying the various functions of TRAC-1 and that of its relatives.

EXPERIMENTAL

Reagents

Chemicals were from Sigma–Aldrich unless indicated otherwise.

cDNA

TRAC-1 cDNA was amplified from cDNA of human primary T-cells using primers based on the RNF125 mRNA sequence (GenBank® accession number NM_017831). TRAC-1 cDNA was subcloned into pcDNA3.1A(−) (Invitrogen), pEGFP-N3 (Invitrogen) and PGEX-5X2 (GE Healthcare) to express proteins with C-terminal Myc/His6, GFP (green fluorescent protein) and GST (glutathione transferase) tags respectively. For yeast two-hybrid experiments, constructs were cloned into pGBKT7 (Clontech) to express GAL4-binding domain fusion proteins, and into a pVP16-derived plasmid [35] to express GAL4-activation domain fusion proteins. The mutants C37A/C40A-TRAC-1, G2A-TRAC-1 and V217P/S221Q-TRAC-1 were generated by site-directed mutagenesis. The truncated proteins TRAC-1ΔC and TRAC-1Δ205 were created by PCR using primers that introduce stop codons at positions 171 and 206 respectively. GST–TRAC-UIM (ubiquitin-interacting motif) was generated by subcloning a cDNA fragment encoding amino acids 181–232, generated by PCR, in-frame with GST in PGEX-5X2. GST–V/S-UIM (V217P/S221Q-TRAC-1-UIM) was made following amplification of a similar fragment from V217P/S221Q-TRAC-1 cDNA. All TRAC-1 constructs were verified by sequencing. The generation of UD (unique domain)–GFP cDNA has been described previously [36]. HA (haemagglutinin)–ubiquitin cDNA was a gift from M. Treier (EMBL, Heidelberg, Germany), and UbcH5a cDNA was a gift from M. Malim (King's College London).

Cells and transfections

Jurkat T-cells were maintained at 37 °C under 5% CO2 in RPMI 1640 medium (Cambrex) supplemented with 10% (v/v) FCS (fetal calf serum) (Helena Biosciences), 100 units/ml penicillin and 0.1 mg/ml streptomycin (Gibco). Primary human T-cells were enriched from buffy coats using Lymphoprep (Axis-Shield) gradients and subsequent purification through a nylon wool (Kisker) column. Typically, 90% pure T-cell populations were obtained, measured by anti-CD3ε staining and FACS analysis. Isolated T-cells were maintained in RPMI 1640 medium, 10% (v/v) FCS, 100 units/ml penicillin and 0.1 mg/ml streptomycin and were used for experiments within 24 h of isolation. COS-7, HeLa and HEK-293T (human embryonic kidney) cells were grown in DMEM (Dulbecco's modified Eagle's medium) (Cambrex), 10% (v/v) FCS, 100 units/ml penicillin and 0.1 mg/ml streptomycin. For transfection, 107 Jurkat T-cells were electroporated in 250 μl of RPMI 1640 medium containing 10% (v/v) FCS, using a Bio-Rad gene pulser at 250 V and 975 μF in the presence of 20 μg of DNA. Primary T-cells were transfected at 2×106 cells in 100 μl of human T-cell Nucleofector™ solution (Amaxa Biosystems) with 5 μg of DNA, using program U-14 of the Amaxa Nucleofector. HEK-293T cells were transfected using the calcium phosphate method with 15 μg of DNA per 10-cm-diameter tissue-culture dish. COS-7 cells were transfected using Nucleofector™, and HeLa cells were transfected using FuGENE™ (Roche Applied Science). For inhibition of proteasomal degradation, cells were cultured in the presence of 50 μM MG-132 (Calbiochem), added from a 50 mM stock in DMSO. The half-life of TRAC-1 proteins was determined by exposing equal numbers of cells to 100 μg/ml cycloheximide for various times.

Antibodies

To detect tagged TRAC-1 proteins, anti-Myc 9E10, anti-GFP (Roche Applied Science) and anti-GST (GE Healthcare) mAbs (monoclonal antibodies) were used. Ubiquitination was detected with Covance P4G7 mAbs against ubiquitin or HA.11 mAb against the HA tag. The anti-(transferrin receptor) mAb H68.4 was from Zymed, anti-His6 rabbit polyclonal was from Qiagen, rabbit anti-GM130 (cis-Golgi matrix protein of 130 kDa) (ab40881) was from Abcam, rabbit polyclonal antibodies C-15 against c-Cbl and H-114 against Hsp90α/β (heat-shock protein 90α/β) were from Santa Cruz Biotechnology. To stimulate T-cells, anti-CD3 mAb UCHT1 and anti-CD28 mAb ANC28.1 (Ancell) were used. APC (allophycocyanin)-conjugated anti-CD69 was from BD Pharmingen. The horseradish-peroxidase-conjugated goat anti-rabbit and rabbit anti-mouse antibodies were from Perbio Science, as was the rhodamine-conjugated goat anti-mouse antibody.

T-cell activation and FACS analysis

At 8–16 h post-transfection, primary human T-cells, or Jurkat T-cells, were stimulated with plate-bound anti-CD3 and anti-CD28 antibodies (10 μg/ml each). Cells were activated for 18 h and subsequently stained with APC-conjugated anti-CD69 in 2% (v/v) FCS in PBS on ice for 30 min. Following fixation in 3% (w/v) paraformaldehyde, a minimum of 105 cells were acquired by FACS using a FACScalibur (Becton Dickinson), and gated on healthy cells based on forward and side scatter properties (typically 50% cell death after transfection). Instrument settings for acquisition were optimized using unstained, GFP+ and APC–CD69-stained GFP cells. Analysis was performed using CellQuest (Becton Dickinson) software. Dot-blot quadrants were set so that <1% of untransfected controls were present in the GFP+ quadrants and <1% of inactivated controls in the CD69+ quadrants. For each transfection, the percentage of CD69+ cells was calculated for the GFP and GFP+ cell populations. Thus UL/(UL+LL) gave the percentage of CD69+ cells for the GFP cells, and UR/(UR+LR) gave the percentage of CD69+ for the GFP+ cells, where UL is upper left quadrant, LL is lower left quadrant, UR is upper right quadrant, and LR is lower right quadrant.

IL-2 ELISA

The concentration of IL-2 in the culture supernatants of stimulated and sorted GFP+ Jurkat T-cells was determined using an IL-2 ELISA kit (eBioscience) according to the manufacturer's instructions. Culture medium was used as blank and all samples were analysed in duplicate. A standard curve was made using purified IL-2.

Immunoprecipitation and Western blotting

Cells were lysed in NP-40 buffer (1% Nonidet P-40, 20 mM Tris/HCl, pH 7.8, 150 mM NaCl and 2 mM MgCl2), supplemented with the protease inhibitors PMSF (1 mM) and CLAP (5 μg/ml each of chymostatin, pepstatin A and antipain hydrochloride, and 10 μg/ml leupeptin hemisulfate), and left on ice for 30 min. For the detection of ubiquitinated proteins, the lysis buffer was supplemented with 0.1% SDS and 5 mM NEM (N-ethylmaleimide). Nuclei and cell debris were removed by centrifugation at 13000 g for 5 min at 4 °C. For direct analysis, lysates were denatured in reducing SDS sample buffer (5% 2-mercaptoethanol) for 5 min at 95 °C, and loaded on SDS/10%polyacrylamide gels. Immunoprecipitations, SDS/PAGE and Western blotting were performed as described previously [17]. Densitometry of blots was performed using Bio-Rad Quantity One software. The density of TRAC-1 bands was determined following subtraction of background in an equal surface area.

In vitro ubiquitination assays

Escherichia coli strain BL21DE3(pLysS) cells (Novagen) were transformed with TRAC-1 constructs cloned into PGEX-5X2 to allow production of TRAC-1–GST fusion proteins. Fusion proteins were purified on glutathione–Sepharose beads (GE Healthcare) after lysis of bacteria in the presence of 1% sarkosyl, according to the manufacturer's instructions. For the ubiquitination assays, 10 μl of GST–beads (∼2 μg of protein) was added to 50 μl of ubiquitination buffer (50 mM Tris/HCl, pH 7.4, 2.5 mM MgCl2, 0.5 mM dithiothreitol and 10 mM ATP) together with 50 ng of E1, 2 μg of ubiquitin and 1 μg of E2, before incubation for 90 min at 30 °C. Ubiquitin, E1 and an E2 sampler pack containing Ubc (ubiquitin-conjugating enzyme) H1, 2, 3, 5a, 5b, 5c, 6, 7, 9 and 10 (UW8975) were purchased from Biomol.

Yeast two-hybrid experiments

To measure interactions between TRAC-1 proteins and UbcH5a, Y190 cells were co-transformed with combinations of constructs cloned into pGBKT7- and pVP16-derived plasmids. Transformants were selected by growth on medium lacking tryptophan and leucine, and β-galactosidase activity was measured in three pools of transformants using CPRG (Chlorophenol Red-β-D-galactopyranoside) (Roche Applied Science) as substrate.

[3H]Myristic acid labelling

HEK-293T cells were labelled 24 h after transfection with [9,10-3H]myristic acid as described previously [37]. Briefly, cells were pre-incubated in labelling medium [DMEM, 2% (v/v) FCS, 5 mM sodium pyruvate (Gibco) and 4× non-essential amino acids (Gibco)] for 60 min at 37 °C under 5% CO2. [9,10-3H]Myristic acid in ethanol (10–60 Ci/mmol) (DuPont) was dried under nitrogen and taken up in labelling medium at 125 μCi/ml. Cells were labelled with 250 μCi per 10-cm-diameter plate for 4 h at 37 °C under 5% CO2. After labelling, cells were processed for immunoprecipitation and SDS/PAGE. Proteins were then transferred on to nitrocellulose membranes and visualized by autoradiography using Kodak Biomax MS film and a Biomax Transcreen-LE (Kodak) intensifying screen, or by Western blotting.

Membrane flotation assays

HEK-293T or Jurkat T-cells were harvested 24 h post-transfection, and PNSs (postnuclear supernatants) were generated by sonicating the cells in hypotonic buffer (20 mM Tris/HCl, pH 7.8, PMSF and CLAP) and pelleting nuclei at 1000 g for 5 min. PNSs were adjusted to 70% (w/v) sucrose in 2.5 ml, and overlaid with 6 ml of 65% (w/v) and 2.5 ml of 10% (w/v) sucrose following the method of [38]. Gradients were centrifuged at 120000 g for 18 h, after which 11 fractions each of 1 ml were collected. Aliquots of each fraction were analysed by SDS/PAGE and immunoblotting.

Immunofluorescence

Cells on 13 mm glass coverslips were fixed with 3% (w/v) paraformaldehyde 24 h after transfection, permeabilized in 0.1% Triton X-100 in PBS and stained as described previously [36]. Coverslips were mounted in Mowiol (Calbiochem-Novachem) and observed using a Leica TCP SP2 AOBSTM confocal microscope. Cross-correlation values were determined on an overall pixel scale by thresholding out the area of low intensities (<15%) [39] using TRI2 software version 2.2.2.1 (Gray Cancer Institute).

Ubiquitin pull-down with recombinant GST-fusion proteins

GST, GST–TRAC-UIM or GST–V/S-UIM was purified from 10 ml cultures of transformed E. coli BL21DE3(pLysS) cells with 50 μl of glutathione–Sepharose beads. A 20 μl aliquot of beads was incubated overnight at 4 °C with NP-40 lysates of HEK-293T cells transfected with HA–ubiquitin (one-third of a 10-cm-diameter dish per recombinant protein). Beads were washed three times with NP-40 lysis buffer, heated to 65 °C in SDS sample buffer and analysed by SDS/PAGE and Western blotting. To detect binding of purified polyubiquitin, 20 μl aliquots of beads were each incubated with 1 μg of Lys48-linked polyubiquitin2-7 (Biomol) in PBS containing 0.1% BSA and analysed as above.

RESULTS

The C-terminal region of TRAC-1 is important for its function in T-cells

To study the activity of TRAC-1, a construct for a C-terminally GFP-tagged TRAC-1 fusion protein (TRAC-1–GFP) was generated and expressed in primary T-cells by nucleofection. The cells were stimulated with anti-CD3 and anti-CD28 and stained for the activation marker CD69. Analysis of FACS plots showed that TRAC-1–GFP+ cells to a large extent failed to up-regulate CD69, compared with TRAC-1–GFP cells within the same transfection (Figure 1A, panel 3). Separate analysis of GFP, GFP-low and GFP-high cells from this transfection showed a dose-dependent effect of TRAC-1–GFP levels on CD69 expression (Figure 1B), with a 70% decrease observed for GFP-high cells (16% CD69+ cells in the GFP-high compared with 53% in the GFP population). On average, the expression of TRAC-1–GFP resulted in a ∼50% decrease in the induction of CD69 after activation, compared with GFP-expressing cells (Figure 1C). This negative effect was observed in primary T-cells as well as in Jurkat T-cells (Figure 1D). TRAC-1–GFP also drastically decreased the induction of another T-cell activation marker, the secretion of IL-2 (Figure 1E). Thus, similarly to results reported previously for TRAC-1ΔC, a protein truncated at residue 170, TRAC-1–GFP has a dominant inhibitory effect on T-cell activation. This suggests an important role for the C-terminal region of TRAC-1, which is missing in TRAC-1ΔC and may be inaccessible in TRAC-1–GFP owing to the presence of a GFP protein that is similar in size to TRAC-1 itself.

Figure 1 TRAC-1–GFP fusion protein inhibits T-cell activation

(A) Human primary T-cells were nucleofected with peGFP-N3 (GFP, panel 2), or with peGFP-N3 containing TRAC-1 (panel 3) or C37A/C40A-TRAC-1 (panel 4) cDNA to express C-terminally tagged GFP-fusion proteins. At 16 h after transfection, cells were stimulated with plate-bound anti-CD3/28 for 18 h. Untransfected unstimulated cells were included as controls (panel 1). Cells were stained with anti-CD69–APC, acquired by FACS and gated on live cells. The percentage of cells in each quadrant is indicated. (B) The percentage of CD69+ cells was calculated separately for GFP (fluorescence intensity 0–10), GFP-low (fluorescence intensity 10–100) and GFP-high (fluorescence intensity >100) populations of the experiment in (A). (C) Six experiments were performed as in (A). For each transfection, the percentage of CD69+ cells in the GFP+ population was divided by that in the GFP population (see the Experimental section). The averages of these ratios are represented for each of the transfected constructs. (D) Jurkat T-cells were transfected with GFP-, TRAC-1–GFP- or C37A/C40A-TRAC-1–GFP-expressing constructs. At 24 h after transfection, GFP+ cells were sorted by MoFlo® and stimulated with plate-bound anti-CD3/CD28 for 48 h. FACS plots of cells stained with anti-CD69–APC are shown. (E) The culture supernatants of sorted Jurkat T-cells in (D) were analysed for the presence of IL-2 by ELISA. A representative of two experiments is shown. (F) Bacterially expressed GST-fusion proteins of TRAC-1 and C37A/C40A-TRAC-1 were captured on glutathione–Sepharose beads and incubated for 90 min at 30 °C with purified E1, His6-tagged E2 UbcH5c, ubiquitin (Ub) and ATP. After the reaction, beads were analysed by Western blotting with antibodies against ubiquitin to detect ubiquitin ligase activity (top). The reaction mixture was blotted with anti-GST (middle) and anti-His6 (bottom) to detect the presence of TRAC-1 proteins and UbcH5c respectively. Molecular masses are indicated (kDa). (G) Yeast was transformed with GAL4-binding domain (BD)- and -activation domain (AD)-containing vectors, either without insert (−) or with TRAC-1 (wild-type or the C37A/C40A mutant) or UbcH5a as inserts, as indicated. An interaction between proteins results in β-galactosidase activity and was measured with CPRG as substrate.

For TRAC-1ΔC, mutations in the RING domain were shown to abolish its inhibitory activity [32]. To determine whether this is also the case for TRAC-1–GFP, two of the structurally important Zn2+-chelating cysteine residues, Cys37 and Cys40, were replaced by alanine (see Figure 4A for the amino acid sequence of TRAC-1). Expression of C37A/C40A-TRAC-1–GFP in T-cells showed that, in contrast with TRAC-1–GFP, this protein did not to any considerable extent inhibit T-cell activation, as measured by the up-regulation of CD69 (Figures 1A, panel 4, and 1B–1D). Similarly, C37A/C40A-TRAC-1–GFP did not inhibit the production of IL-2 (Figure 1E). Rather, an increase in IL-2 levels was observed, which may suggest that, following T-cell activation, TRAC-1 has a dampening effect on IL-2 synthesis. The lack of ubiquitin ligase activity for the RING domain mutant C37A/C40A-TRAC-1 was verified by in vitro auto-ubiquitination experiments (Figure 1F). Initial screening of ten different E2 proteins showed that TRAC-1 co-operates with members of the UbcH5 family, similarly to the preference reported previously [32]. An inability of the C37A/C40A-TRAC-1 mutant to associate with UbcH5a was demonstrated further in yeast two-hybrid experiments (Figure 1G). Together, these experiments demonstrate that altering the C-terminus of TRAC-1 provokes a RING domain-dependent dominant inhibitory activity. To better understand the normal activity of TRAC-1, we next investigated its modifications, subcellular localization and the presence of domains other than the RING domain.

Myristoylation and localization of TRAC-1

A myristoylation consensus sequence, (M)GXXT/S, is present at the extreme N-terminus (see Figure 4A), which predicts that TRAC-1 is modified by the attachment of myristic acid to Gly2, following the proteolytic removal of the methionine residue [40,41]. Myristoylation is a co-translational irreversible acylation that has profound effects on the localization and activity of proteins by enhancing the affinity for membranes and influencing protein–protein interactions.

To investigate whether TRAC-1 is myristoylated, HEK-293T cells were transfected with TRAC-1–Myc constructs and labelled with [3H]myristic acid. Following immunoprecipitation, incorporation of [3H]myristic acid could be detected for both wild-type TRAC-1 and the RING-deficient C37A/C40A-TRAC-1 (Figure 2A). Substitution of alanine for Gly2 in the G2A-TRAC-1 mutant prevented this labelling, demonstrating that Gly2 is used as a myristoylation site (Figure 2A). The higher intensity of [3H]myristic acid labelling for C37A/C40A-TRAC-1 compared with wild-type TRAC-1 most likely reflects the considerably longer half-life of the mutant (see below), which leads to greater accumulation of protein during the 4 h labelling.

Figure 2 TRAC-1 is myristoylated and partially membrane-associated

(A) HEK-293T cells were transiently transfected with TRAC-1–Myc constructs and grown in the presence of [3H]myristic acid for 4 h. TRAC-1–Myc proteins were immunoprecipitated with anti-Myc antibodies. One-half of the sample was analysed by SDS/PAGE and autoradiography (upper panel), the other half by immunoblotting with anti-Myc antibody (lower panel). (B) HEK-293T cells transfected with TRAC-1–Myc constructs were homogenized in hypotonic buffer and fractionated on discontinuous 70%/65%/10% sucrose gradients. Fractions were collected from the top (fraction 1), and aliquots were analysed by immunoblotting with anti-Myc antibodies to detect TRAC-1 proteins, as well as with antibodies against Hsp90, a soluble protein, and transferrin receptor (TFR), a transmembrane protein. (C) COS-7 cells transfected with GFP and either TRAC-1–Myc or G2A-TRAC-1–Myc cDNAs were grown on 13 mm glass coverslips. At 24 h after transfection, cells were permeabilized, fixed and stained with anti-Myc as primary and rhodamine-conjugated goat-anti-mouse as secondary antibodies. Confocal images of single channels as well as overlap images are shown. Scale bar, 10 μm. A cytofluorogram (right-hand panels) is given to show the intensities of red and green fluorophores per pixel. The relative amount of co-localization was determined using cross-correlation analysis, and the values (with 0 representing no co-localization, and 1 indicating complete co-localization) are shown in the cytofluorogram. (D) COS-7 cells were transfected with TRAC-1–Myc and a plasmid for UD–GFP, a myristoylated and palmitoylated protein that contains the unique domain of Lck fused to the N-terminus of GFP. Cells were stained, observed and analysed as in (C). Scale bar, 10 μm. (E) HeLa cells were transfected with TRAC-1–Myc and stained with anti-Myc and anti-GM130, a cis-Golgi marker. Scale bar, 10 μm.

To examine whether TRAC-1 is membrane-associated as a result of myristoylation, membrane flotation experiments were used. HEK-293T cells were transfected with TRAC-1–Myc constructs and homogenized in isotonic buffer in the absence of detergent. The homogenate was loaded at the bottom of discontinuous 70%/65%/10% sucrose gradients, from which fractions were collected after centrifugation. Membranes and associated proteins are expected to float to the 65%/10% interface at the top of these gradients, which was confirmed by Western blotting for the transferrin receptor (Figure 2B). Soluble proteins were excluded from these fractions, as demonstrated with the cytosolic protein Hsp90. For TRAC-1, the majority of the protein was detected in the membrane fractions (Figure 2B). This membrane association was dependent on myristoylation, since the myristoylation-deficient G2A-TRAC-1 did not accumulate here (Figure 2B). Like wild-type TRAC-1, the RING domain mutant C37A/C40A-TRAC-1 was primarily membrane-associated (Figure 2B). Small amounts of soluble protein, consistently higher for TRAC-1 than for C37A/C40A-TRAC-1, were also observed, suggesting that the RING domain influences to some extent myristoylation and/or membrane association.

To study the subcellular localization of TRAC-1 in more detail, confocal microscopy was used. Staining for TRAC-1–Myc constructs after permeabilization showed that, consistent with the presence of myristic acid, TRAC-1 was excluded from the nucleus (Figures 2C–2E). TRAC-1 showed a reticular staining with some concentration in a perinuclear region. This is reminiscent of the localization of other myristoylated proteins [42], and probably represents the distribution of TRAC-1 at various membrane compartments. In contrast, G2A-TRAC-1 was more homogeneously distributed and able to enter the nucleus. This mutant, but not wild-type TRAC-1, overlapped to a considerable extent with the soluble GFP (Figure 2C).

Localization of TRAC-1 at the plasma membrane was studied by the co-expression with UD–GFP (Figure 2D), a myristoylated and palmitoylated protein composed of the unique domain of Lck fused to GFP that localizes to a large extent to the plasma membrane [36]. Very little, if any, TRAC-1 co-localized with UD–GFP at the periphery of the cell, showing that TRAC-1 is not present at appreciable levels at the plasma membrane. However, some TRAC-1 co-localized with perinuclear UD–GFP, which was shown previously to associate with the Golgi complex [36]. Co-staining with the cis-Golgi marker GM130 confirmed the presence of TRAC-1 in the Golgi region (Figure 2E). In conclusion, TRAC-1 associates with membranes as a result of myristoylation, and is primarily located at intracellular membrane systems.

TRAC-1 has a short half-life as a result of auto-ubiquitination

The levels of TRAC-1–GFP in T-cells were found to be consistently lower than those of C37A/C40A-TRAC-1–GFP (see fluorescent intensities in Figures 1A and 1D). This suggested that TRAC-1 with an intact RING domain might be targeted for proteasomal degradation. To test whether this is the case, transfected Jurkat T-cells were incubated with the proteasome inhibitor MG-132. This treatment had no detectable effect on levels of C37A/C40A-TRAC-1–GFP, but those of TRAC-1–GFP and G2A-TRAC-1–GFP were increased after an incubation as short as 30 min (Figure 3A). This effect was not generally observed for ubiquitin ligases with intact RING domains, since levels of c-Cbl were not affected by MG-132. Neither was it specific for TRAC-1–GFP constructs, as levels of TRAC-1–Myc were increased in the presence of MG-132 as well. Moreover, higher-molecular-mass forms of TRAC-1 were detected in the presence of MG-132, indicative of its polyubiquitination (Figure 3B). To investigate TRAC-1 ubiquitination, constructs were co-transfected with HA–ubiquitin, immunoprecipitated and blotted with anti-ubiquitin antibodies. Polyubiquitinated forms were detected for TRAC-1 and G2A-TRAC-1, but not for C37A/C40A-TRAC-1 (Figure 3C). Therefore it can be concluded that TRAC-1 is subject to auto-ubiquitination.

Figure 3 TRAC-1 is unstable as a result of auto-ubiquitination

(A) Jurkat T-cells were transfected with the indicated TRAC-1–GFP constructs. The cells were either left untreated or incubated with the proteasome inhibitor MG-132 (50 μM) for 30, 60 or 120 min. Equivalent amounts of cell lysates were analysed by Western blotting with anti-GFP to detect TRAC-1–GFP proteins, or with anti-c-Cbl. (B) HEK-293T cells transfected with TRAC-1–Myc cDNA were either left untreated or incubated with MG-132 (50 μM) for 2 h. The cell lysates were blotted with anti-Myc antibodies. (C) Plasmids for Myc-tagged TRAC-1, C37A/C40A-TRAC-1 or G2A-TRAC-1 were co-transfected with HA–ubiquitin into HEK-293T cells. TRAC-1 proteins were immunoprecipitated with anti-Myc and blotted with anti-ubiquitin antibodies to detect ubiquitination (upper panel). Lysates were blotted with anti-Myc to detect the transfected TRAC-1 proteins (lower panel). Molecular masses are indicated (kDa). (D) COS-7 cells were transfected in suspension with Myc-tagged TRAC-1 or C37A/C40A-TRAC-1, and equal cell numbers were divided into five dishes. Cells were incubated the next day with medium alone (0) or with medium containing cycloheximide (CHX) (100 μg/ml) for the indicated times. Equal amounts of cell lysates were analysed by Western blotting with anti-Myc antibody. (E) Densitometry of the blots shown in (D). For each time point, the density of the TRAC-1 band following subtraction of background levels and equalized for a loading control were determined. TRAC-1 levels are expressed as a percentage of levels in untreated cells. Ub, ubiquitinated TRAC-1; Ig HC and Ig LC, heavy and light chains of the immunoprecipitating anti-Myc antibody respectively.

To examine the effect of auto-ubiquitination on the half-life of TRAC-1, cells transfected with TRAC-1 or C37A/C40A-TRAC-1 were incubated for various times with the protein synthesis inhibitor cycloheximide. These experiments revealed that TRAC-1 has a very short half-life of less than 30 min (Figures 3D and 3E). In contrast, C37A/C40A-TRAC-1 levels were reduced by only 25% after 2 h of incubation with cycloheximide. Thus TRAC-1 is an unstable protein and its rapid turnover rate is the result of auto-ubiquitination.

TRAC-1 is related to three other RING ubiquitin ligases

Protein domain searches did not recognize any domains C-terminal to the RING domain. However, amino acid alignments of TRAC-1 proteins from different species showed the presence of conserved cysteine and histidine residues in this region, particularly between residues 141 and 196. Protein BLAST searches with this part of TRAC-1 revealed that homologous sequences are present in four other human proteins: RNF114 (also known as Zfp313), RNF138 (or NARF {NLK [NEMO (NF-κB essential modifier)-like kinase]-associated RING finger protein}), RNF166 and potassium channel modulatory factor 1 (Kcmf1). In three of these proteins, RNF114, RNF138 and RNF166, the conserved sequence is similarly located close to the C-terminus. Moreover, these three proteins have sizes comparable with the 232-amino-acid TRAC-1, ranging from 228 amino acids for RNF114 to 245 amino acids for RNF138. Furthermore, like TRAC-1, these proteins contain a C3HC4 RING domain close to the N-terminus (Figure 4A). In contrast, Kcmf1 is larger, the homologous sequence is located in the middle of the protein and a C3HC4 RING domain is not present [43,44]. We therefore conclude that TRAC-1 is closely related to RNF138, RNF114 and RNF166, and that these proteins form a novel subfamily of small C3HC4 RING ubiquitin ligases.

Figure 4 TRAC-1 is homologous with three other small C3HC4 RING proteins

(A) Amino acid alignments of the human proteins TRAC-1 (GenBank® accession number Q96EQ8), RNF114 (GenBank® accession number Q9Y508), RNF138 (GenBank® accession number Q8WVD3) and RNF166 (GenBank® accession number Q96A37). Alignments were performed using vector NTI software (Invitrogen). Identical residues are highlighted in black, conserved hydrophobic resides are in light grey, other conservative changes are in darker grey. Star symbols indicate the conserved cysteine and histidine residues in the various domains. The arrows indicate amino acids in TRAC-1 that have been mutated in the present study, and the triangles show the positions where truncations have been made. (B) Schematic diagram of the domain composition of TRAC-1 and its family members. Indicated are the myristoylation site (m, present in TRAC-1 only) the RING domain, the newly identified C2HC and C2H2 zinc-binding motifs and the UIM domain. The numbers refer to amino acid positions in TRAC-1. The gene composition with the exon boundaries relative to the protein domains is depicted below. RNF138 contains one extra exon compared with the other three proteins.

The homologous C-terminal region contains two motifs that each correspond to the basic C2H2 (Cys2-His2) zinc-finger consensus sequence CX2-4C…HX2-4H [45]. The first ‘zinc-finger-like’ motif has the conventional 12-amino-acid spacing between cysteine and histidine pairs, except in TRAC-1, where only 11 residues are present (Figure 4A). The consensus sequence for this motif is CPXCX2-3ΦX4ΦΦXHCX3C (where Φ is a hydrophobic residue). The second motif contains 17 amino acids between the cysteine and histidine pairs and has the consensus sequence CPΦCX2ΦPX3PX3T/SX2ΦX2HΦX3H. These zinc-binding motifs diverge from the classical DNA-binding zinc fingers by the spacing of the hydrophobic residues and the absence of conserved DNA-binding arginine and aspartic acid residues [45]. Thus the TRAC-1 family motifs should be regarded as novel atypical zinc fingers. The overall similarity between TRAC-1 and its relatives in the region between residues 141 and 196 is 57% for RNF114 and RNF166 (with 29 and 38% identity respectively) and 54% for RNF138 (36% identity). For comparison, the sequence similarity between C3HC4 RING domains is ∼60%.

Further scrutiny of amino acid alignments has identified another homologous region with conserved cysteine and histidine residues. This motif, located between amino acids 100 and 119 in TRAC-1, resembles a C2HC (Cys2-His-Cys) zinc finger and has the consensus sequence CX2CX3ΦXΦX2ΦRXHX2T/SC (Figure 4A). Additionally, a UIM was detected by protein domain searches at the extreme C-terminus of RNF166, and some of the residues important for this domain are conserved in the other TRAC-1 family members (Figure 4A).

The relationship between the TRAC-1 family members is also evident from the similarities in their gene structure. The genes for TRAC-1, RNF114 and RNF166 contain six exons, with exons 1 and 2 together encoding the RING domain, exons 2 and 3 the C2HC-like zinc finger, exon 4 the first C2H2-like zinc finger, exon 5 the second C2H2-like zinc finger, and exon 6 a UIM-type domain. The organization of the RNF138 gene is the same, except for the presence of an extra exon, encoding 20 amino acids, between exons 3 and 4 (Figure 4B). The exon boundaries correspond to similar amino acid positions in all four proteins. In summary, TRAC-1 belongs to a new subfamily of small C3HC4 RING ubiquitin ligases. The conservation of three zinc-finger-like domains and a UIM is consistent with important interactions occurring outside the RING domain.

TRAC-1 binds ubiquitin via a C-terminal UIM

While studying the ubiquitination of TRAC-1, it was observed that the C-terminally truncated TRAC-1ΔC with a deletion of amino acids 171–232 was not subject to auto-ubiquitination (Figure 5A). This was unexpected since the absent region does not contain any lysine residues for the attachment of ubiquitin (see Figure 4A for the amino acid sequence of TRAC-1). Since RNF166 is predicted to have a UIM-type ubiquitin-binding domain, it was hypothesized that a similar domain is present in TRAC-1 and co-operates with the RING domain in auto-ubiquitination. The corresponding region of TRAC-1, amino acids 210–224, diverges from a consensus UIM motif in two places (Figure 5B): a valine residue is present instead of alanine (position 217), and a positively charged arginine residue instead of a hydrophobic or acidic amino acid (position 220).

Figure 5 TRAC-1 contains a UIM-type ubiquitin-binding domain that is required for auto-ubiquitination

(A) HEK-293T cells were transfected with plasmids expressing HA–ubiquitin and Myc-tagged wild-type TRAC-1, empty vector (−), TRAC-1ΔC, TRAC-1Δ205 or V217P/S221Q-TRAC-1. TRAC-1 proteins were immunoprecipitated with anti-Myc and blotted with anti-HA antibodies to detect ubiquitination (upper panel). Ub, ubiquitinated TRAC-1; Ig HC and Ig LC, heavy and light chains of the immunoprecipitating anti-Myc antibody respectively. The same blot was re-probed with anti-Myc antibody to detect expression of TRAC-1 proteins (lower panel). (B) Comparison of the consensus sequence for the UIM domain (according to [48]) with the TRAC-1 sequence of amino acids 210–224. The notation is as follows: e, negatively charged; X, helix favouring; Φ, hydrophobic; z, bulky hydrophobic or polar amino acid. TRAC-1 residues shaded grey agree with the UIM consensus sequences, those shaded black diverge from it. (C) HEK-293T cells were transfected with plasmids expressing HA–ubiquitin together with TRAC-1–Myc, TRAC-1–GFP or GFP. Proteins were immunoprecipitated with anti-Myc (lane 1) or anti-GFP (lanes 2 and 3) and blotted with anti-HA to detect ubiquitination (upper panel). The lysates were blotted for GFP (lower panel). (D) GST-fusion proteins were isolated on glutathione–Sepharose beads and incubated with lysates from HA–ubiquitin-transfected HEK-293T cells. Beads were analysed by Western blotting with anti-HA antibodies to detect the binding of ubiquitinated proteins to the recombinant proteins (top). TRAC-UIM, amino acids 181–232 of TRAC-1 fused to the C-terminus of GST; V/S-UIM, amino acids 181–232 with point mutations V217P and S221Q fused to the C-terminus of GST. GST itself was similarly purified and used as a control. To detect levels of expression for TRAC-UIM and V/S-UIM, the blot was probed with anti-GST antibodies (middle). This is not shown for GST because of the high expression levels of this protein. The expression of GST, relative to the other constructs, is shown on a Coomassie Blue-stained gel (bottom). (E) GST and GST-fusion proteins as in (D) were isolated on glutathione–Sepharose beads and incubated with purified Lys48-linked polyubiquitin2-7 chains. Beads alone (−) were included as a control for specific binding. Beads were analysed for binding of ubiquitin with anti-ubiquitin antibodies (top). Input Lys48 polyubiquitin2-7 (K48-Ub2-7) was analysed on the same polyacrylamide gel, but a shorter exposure of the blot is shown. Beads were blotted with anti-GST antibodies to reveal relative levels of the proteins (bottom). (F) HeLa cells were transfected with constructs expressing Myc-tagged wild-type TRAC-1, TRAC-1ΔC, TRAC-1Δ205 or V217P/S221Q-TRAC-1. At 24 h after transfection, cells were stained with anti-Myc antibodies and observed by confocal microscopy. Scale bar, 10 μm. (G) HEK-293T cells transfected with TRAC-1Δ205–Myc were homogenized in hypotonic buffer and fractionated on discontinuous 70%/65%/10% sucrose gradients as in Figure 2(B). Fractions were collected from the top, and aliquots were analysed by immunoblotting with anti-Myc antibodies. Membranes float up to the 65%/10% sucrose interface (fraction 3), whereas soluble proteins remain at the bottom (fractions 10 and 11).

To test whether this region is involved in TRAC-1 auto-ubiquitination, a protein truncated at position 205 was generated (Figure 4A). Like TRAC-1ΔC, TRAC-1Δ205 was not ubiquitinated (Figure 5A). To address further the UIM nature of this region, point mutations were introduced at Val217 and Ser221. These residues correspond to important conserved positions in the UIM consensus sequence [46,47], with the difference that, as stated above, an alanine residue is normally present instead of valine. The resulting mutant, V217P/S221Q-TRAC-1, showed a considerable reduction in ubiquitination (Figure 5A), strengthening the premise that these residues are part of a ubiquitin-binding domain that is important for auto-ubiquitination.

Since both TRAC-1ΔC and TRAC-1–GFP have a dominant inhibitory effect on T-cell activation, the auto-ubiquitination of TRAC-1–GFP was determined as well. TRAC-1–GFP ubiquitination was found to occur normally (Figure 5C) and the UIM of this protein is therefore unlikely to be impaired.

To investigate the ubiquitin-binding properties of the UIM region more directly, amino acids 181–232 of TRAC-1 were fused to the C-terminus of GST. The recombinant protein, GST–TRACUIM, was purified from bacteria on glutathione–Sepharose beads and was incubated with lysates from HA–ubiquitin-transfected HEK-293T cells. Indeed, GST–TRAC-UIM, but not GST, was able to pull-down polyubiquitinated proteins (Figure 5D). Moreover, the recognition of ubiquitinated proteins was reduced by the presence of point mutations V217P and S221Q in GST–V/S-UIM (Figure 5D). GST–TRAC-UIM was also found to bind purified Lys48-linked polyubiquitin (Figure 5E), a capacity that was again diminished for GST–V/S-UIM. Thus TRAC-1 contains a C-terminal UIM-type ubiquitin-binding domain that recognizes Lys48-linked polyubiquitin.

Finally, the effect of C-terminal mutations on the subcellular localization of TRAC-1 was investigated by immunofluorescence. TRAC-1ΔC, TRAC-1Δ205 and V217P/S221Q-TRAC-1 all showed brighter staining and a more homogeneous distribution than wild-type TRAC-1 (Figure 5F). Membrane association was not compromised by the absence of a UIM, as demonstrated for TRAC-1Δ205 in membrane fractionation experiments (Figure 5G). The more peripheral staining of these mutants, in contrast with the perinuclear staining of wild-type TRAC-1, suggests that a higher degree of plasma membrane association takes place. Thus the UIM of TRAC-1 influences its subcellular distribution, which is indicative of important intra- and/or inter-molecular interactions taking place via this domain.

DISCUSSION

To provide insights into the function of the ubiquitin ligase TRAC-1, we characterized the protein by determining modifications and identifying novel domains. As a result, a detailed map of TRAC-1 is presented (Figure 4B). At the N-terminus, TRAC-1 contains a myristoylation site that is modified by the attachment of myristic acid, leading to membrane association. Next, a C3HC4 RING domain is present, essential for ubiquitin ligase activity through the interaction with E2 proteins. C-terminal to this domain follow three atypical zinc fingers, the interactions of which remain to be determined. Finally, at the very C-terminus, a UIM-type domain that binds Lys48-linked polyubiquitin is present. Together with the RING domain, this UIM is required for auto-ubiquitination, which results in a high turnover rate of TRAC-1. Thus a large potential for substrate and regulatory interactions is present in this small ubiquitin ligase. Moreover, identical domain organizations are shown to be present in three other proteins, RNF114, RNF138 and RNF166, which are therefore identified as TRAC-1 relatives.

The results of the present study are consistent with a positive regulatory role for TRAC-1 in T-cell activation. A potent negative effect was detected for a TRAC-1–GFP fusion protein (Figures 1A–1D), similar to the effect of a C-terminally truncated TRAC-1ΔC [32]. The dominant inhibitory effects of TRAC-1–GFP and TRAC-1ΔC are both dependent on an intact RING domain, and these proteins are likely to act in similar ways. Their dominant-negative activities can be envisioned to result from an ability to compete with endogenous TRAC-1 for protein interactions, but an inability to perform normal TRAC-1 function because of the missing (in TRAC-1ΔC), or obstructed (in TRAC-1/GFP) C-terminal region. The C-terminal region could, for instance, influence the ubiquitin ligase activity or the substrate selection of TRAC-1. This hypothesis predicts that important interactions take place on both sides of amino acid 170, the residue where TRAC-1ΔC is truncated. In addition to substrates, TRAC-1 could, for instance, bind protein partners that influence its activity.

The RING domain is essential for ubiquitin ligase activity, but its role in TRAC-1 function is still unresolved. Clearly, mutations in the RING domain of dominant-negative forms negate inhibitory activities (Figures 1A–1D, [32]). On the other hand, mutations in the RING domain of the full-length protein were reported not to inhibit TRAC-1 function in T-cell activation [32]. Moreover, we observed an increase in IL-2 production in the presence of RING-deficient TRAC-1. This suggests that, whereas TRAC-1 is required for T-cell activation, it may also have a RING domain-dependent inhibitory effect on IL-2 synthesis in activated T-cells. RING domain-dependent inhibitory activities have also been reported for TRAC-1 in other processes, such as RIG-I-induced cytokine production [33] and HIV transcription [34]. Further insight into the regulation of TRAC-1 and the role of its various domains is needed to clarify these functions.

We have demonstrated that TRAC-1 is subject to myristoylation (Figure 2A), which suggests that, additionally to protein–protein interactions, protein–membrane interactions may regulate its activity. Myristoylation anchors proteins to membranes, but the weak binding of the 14-carbon myristic acid to membranes can be reversed by, for instance, phosphorylation or protein–protein interactions. The occurrence of small amounts of TRAC-1 in a soluble form (Figure 2B) may indicate that TRAC-1 can shuttle between a membrane-bound and a soluble form. The virtual absence of soluble protein for the mutant C37A/C40A-TRAC-1 suggests that interactions via the RING domain may be involved in this. However, the soluble pool of TRAC-1 may also represent proteins that are associated with the proteasomes, but not yet degraded. In addition, a direct influence of the RING domain on the efficiency of myristoylation during translation can not be fully excluded.

The identification of novel domains, zinc-finger-like motifs and a UIM offers new possibilities for TRAC-1 interactions (Figure 4). The three zinc-binding motifs of the TRAC-1 family diverge in various ways from the classical zinc finger, and the exclusion of TRAC-1 from the nucleus (Figures 2C–2E) argues against a role in DNA binding. Nevertheless, these motifs represent, with high probability, structural domains that are involved in interactions with substrates, obligatory binding partners, TRAC-1 itself or perhaps RNA. Zinc fingers often occur in tandem or in triplets. Similarly, the three zinc-binding motifs of the TRAC-1-related proteins might act together as one or two domains. In particular, the two juxtaposed C2H2 zinc fingers may represent one functional unit. Such a motif is also found outside the TRAC-1 family in Kcmf1, where it is located C-terminally to a variant [C6H2 (Cys6-His2)] RING domain. Moreover, this motif is conserved in the Drosophila orthologue of Kcmf1. The dominant inhibitory TRAC-1ΔC lacks both a C2H2 zinc finger and the UIM. Since the inhibitory TRAC-1–GFP has intact UIM function, based on its auto-ubiquitination (Figure 5C), it is more likely that the absence or obstruction of the C2H2 motif explains the inhibitory activity. However, the exact contribution of these domains to TRAC-1 function remains to be established.

The UIM domain is one of over 15 different motifs capable of binding to ubiquitin. UIM domains are mostly found in proteasome subunits, de-ubiquitinating enzymes and in proteins involved in receptor internalization, such as components of the ESCRTs (endosomal sorting complexes required for transport) [46]. To our knowledge, TRAC-1 is the first C3HC4 RING protein described to contain a UIM domain. The UIM of TRAC-1 was found to be essential for auto-ubiquitination (Figure 5A), which appears to control the stability of this protein (Figures 3D and 3E). The very short half-life of TRAC-1 (<30 min, Figures 3D and 3E) suggests that the levels of this protein can be very rapidly modulated. Shutting down its transcription would lead to a rapid decrease, and shutting down its ubiquitination to a rapid increase, in TRAC-1 levels. Down-modulation may, for instance, be required after T-cell activation, to prevent a negative impact on IL-2 synthesis. The levels of TRAC-1 were shown to be increased upon IFNα or polyI/polyC exposure [33]. It will be interesting to determine whether the auto-ubiquitination of TRAC-1 is diminished under these conditions. In addition to a role in auto-ubiquitination, the UIM could be involved in intermolecular interactions through binding to Lys48-linked ubiquitinated proteins (Figure 5E). Additionally, it may bind to Lys48-linked polyubiquitin on TRAC-1 itself and thereby influence the conformation of this protein. An involvement in important interactions is suggested by the drastic change in subcellular distribution for proteins with a deletion of, or mutations in, this domain (Figure 5F).

On the basis of amino acid sequence similarities, protein domain organization and gene organization, RNF114, RNF138 and RNF166 were identified as TRAC-1 relatives (Figure 4). Extensive protein database searches did not identify any other proteins with close similarity. Whereas the TRAC-1 gene is found in mammals only, the genes for the other three proteins are restricted to vertebrates. The restricted expression pattern of TRAC-1 compared with its relatives may point towards a more specialized role. However, tissue-expression profiles of RNF114, RNF138 and RNF166 have not yet been determined, and redundancy between the TRAC-1 family members proteins cannot at present be excluded. The similarities between TRAC-1 and its family members suggest that these proteins may be involved in similar activities. Nothing is yet known about the functions of RNF114 and RNF166, but RNF138 was identified in a yeast two-hybrid screen for proteins that interact with Xenopus NLK [48]. The protein was named NARF (for NLK-associated RING finger protein), and was shown to ubiquitinate TCF (T-cell factor)/LEF (lymphoid enhancer factor) proteins, leading to their degradation, thereby inhibiting Wnt signalling. Whether TRAC-1 performs a similar role in T-cells is currently being addressed in our laboratory.

Thus the identification of TRAC-1 relatives has considerably widened the field of TRAC-1 investigations. At the same time, the identification of modifications and domains has brought the TRAC-1 protein further into focus and opened new avenues for studies into its regulation.

Acknowledgments

We thank our colleagues at the Programme in Infection and Immunity, King's College London, for sharing ideas and reagents. In particular, we are grateful to Wayne Turnbull for cell sorting, Daniel Pennington and John Pang for help with FACS analysis, Monica Agromayor for advice on yeast two-hybrid experiments, and Adrian Hayday, Susan John and Matt Lovatt for critically reading the manuscript. We also thank Tony Ng (Randall Institute, King's College London) for help with cross-correlation analysis. This work was supported by a Career Development Award from the Medical Research Council and a project grant from The Wellcome Trust.

Abbreviations: APC, allophycocyanin; CLAP, chymostatin, leupeptin hemisulfate, antipain hydrochloride and pepstatin A; CPRG, Chlorophenol Red-β-D-galactopyranoside; DMEM, Dulbecco's modified Eagle's medium; FCS, fetal calf serum; GFP, green fluorescent protein; GM130, cis-Golgi matrix protein of 130 kDa; GST, glutathione transferase; HA, haemagglutinin; HEK-293T, human embryonic kidney; Hsp, heat-shock protein; IFN, interferon; IL, interleukin; Kcmf1, potassium channel modulatory factor 1; mAb, monoclonal antibody; NF-κB, nuclear factor κB; NLK, NEMO (NF-κB essential modifier)-like kinase; NARF, NLK-associated RING finger protein; NP-40, Nonidet P-40; PNS, postnuclear supernatant; RIG-I, retinoic acid-inducible gene I; RING, really interesting new gene; RNF, RING finger protein; TCR, T-cell receptor; TRAC-1, T-cell RING protein in activation 1; Ubc, ubiquitin-conjugating enzyme; UD, unique domain; UIM, ubiquitin-interacting motif

References

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