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Ubiquitination controls a broad range of cellular functions.The last step of the ubiquitination pathway is regulated byenzyme type 3 (E3) ubiquitin ligases. E3 enzymes are responsiblefor substrate specificity and catalyze the formation of an isopeptidebond between a lysine residue of the substrate (or the N terminusof the substrate) and ubiquitin. MIR1 and MIR2 are two E3 ubiquitinligases encoded by Kaposi's sarcomaassociated herpesvirusthat mediate the ubiquitination of major histocompatibilitycomplex class I (MHC I) molecules and subsequent internalization.Here, we found that MIR1, but not MIR2, promoted down-regulationof MHC I molecules lacking lysine residues in their intracytoplasmicdomain. In the presence of MIR1, these MHC I molecules wereubiquitinated, and their association with ubiquitin was sensitiveto ß2-mercaptoethanol, unlike lysine-ubiquitin bonds.This form of ubiquitination required a cysteine residue in theintracytoplasmic tail of MHC I molecules. An MHC I moleculecontaining a single cysteine residue in an artificial glycineand alanine intracytoplasmic domain was endocytosed and degradedin the presence of MIR1. Thus, ubiquitination can occur on proteinslacking accessible lysines or an accessible N terminus.
Department of Molecular and Cell Biology, 142 Life Sciences Addition Room 3200, Berkeley, CA 94720, USA.
* To whom correspondence should be addressed. E-mail: lcoscoy{at}berkeley.edu
Ubiquitination is a highly regulated process conserved in alleukaryotes (1, 2) that regulates many fundamental cellular processes.Many pathogens mimic, block, or redirect the activity of theubiquitin system. The modulators of immune recognition (MIR)1 and 2, two proteins encoded by Kaposi's sarcomaassociatedherpesvirus (KSHV), specifically down-regulate the expressionof MHC I from the surface of infected cells, presumably to preventlysis of infected cells by cytotoxic T lymphocytes (36).MIR1 and MIR2 are highly homologous structurally and functionally,and they belong to a large family of E3 ubiquitin ligases (3,7). E3 ubiquitin ligases function as adaptors to facilitatepositioning and transfer of ubiquitin (Ub) from an E2 enzymedirectly onto the E3-bound substrate (1). The nature of thebond between Ub and its substrate has been well characterized:The Ub C-terminal glycine carboxy group forms an isopeptidebond with the -amino group of lysine residues or, less commonly,with the amino group at the N terminus of the substrate protein(8). MIR proteins recruit E2 enzymes with their N-terminal RING-CHdomain (3). Either direct or indirect interactions between thetransmembranes of the MIRs and MHC I molecules ultimately leadto the ubiquitination of lysine residues present in the MHCI intracytoplasmic tail (3, 9). Ubiquitinated molecules arethen endocytosed and degraded by the lysosome (3, 7, 1012).Mutating all the lysines to arginines in the intracytoplasmicdomain of HLA.B7 (henceforth referred to as the HLA.B7 2R mutantor lysineless HLA.B7) abolishes internalization mediated byMIR2 (3).
However, in the presence of MIR1, the cell surface expressionof both wild-type (wt) HLA.B7 and HLA.B7 2R was strongly down-regulated,even in cells expressing low levels of MIR1 (Fig. 1). In contrast,even high levels of MIR2 (Fig. 1) did not induce HLA.B7 2R down-regulation.Thus, the MIR1 protein can mediate the down-regulation of MHCI molecules lacking lysines. Similar results were observed inHeLa cells, suggesting that HLA.B7 2R down-regulation by MIR1is not restricted to B cells. In the presence of MIR1, HLA.B72R molecules are endocytosed, translocated toward the lysosome,and degraded, which is similar to the effects of MIR1 on HLA.B7wt molecules.
Fig. 1. MIR1, but not MIR2, down-regulates the MHC I allele HLA.B7 in the absence of intracytoplasmic lysines. BJAB cells stably expressing wt HLA.B7 or the HLA.B7 2R mutant lacking the two intracytoplasmic lysines were transiently transfected with a vector expressing MIR1 or MIR2 fused to enhanced green fluorescent protein (EGFP). Cells were stained with a phycoerythrin-conjugated monoclonal antibody against HLA.B7 and analyzed by flow cytometry.
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To test whether a particular motif encoded in the intracytoplasmicdomain of HLA.B7 2R was required for MIR1-mediated down-regulation,we generated a set of HLA.B7 2R molecules lacking differentparts of the intracytoplasmic domain (Fig. 2A) and tested theirsusceptibility to MIR1-mediated down-regulation. Deletion ofthe last seven amino acids in HLA.B7 2R did not prevent down-regulation(HLA.B7 C), whereas further truncations (constructs HLA.B7 ,A, and B) inhibited internalization (Fig. 2C). Thus, a criticaldeterminant for MIR1-mediated down-regulation is encoded inthe last seven residues of HLA.B7 C.
Fig. 2. An intracytoplasmic cysteine residue is critical for lysine-independent down-regulation by MIR1. (A) Polymerase chain reaction (PCR) mutagenesis was used to create serial deletion mutants in the intracytoplasmic tail of HLA.B7 2R. (B) We generated several mutations within the intracytoplasmic region of HLA.B7 and HLA.A2 so as to analyze the requirement of the cysteine residue unique to HLA.B7. (C) BJAB cells stably expressing the mutants in (A) were transiently transfected with a construct expressing MIR1-EGFP and analyzed for surface expression of HLA.B7 by flow cytometry. (D) BJAB cells stably expressing MIR1-EGFP along with the various HLA.B7 mutants were analyzed for surface HLA.B7 expression by flow cytometry. (E) HeLa cells stably expressing MIR1-EGFP and various HLA.A2 mutants were analyzed for surface HLA.A2 expression. No down-regulation is indicated by cells stably expressing HLA.A2 and EGFP alone.
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Although we observed down-regulation of lysineless HLA.B7 byMIR1, a lysine-less HLA.A2 molecule is not down-regulated byMIR1 (7). Within the region identified above, HLA.B7 encodesa cysteine in the same position that HLA.A2 encodes a serine(Fig. 2B). We generated a HLA.B7 mutant lacking both cysteineand lysine in its cytoplasmic tail, which we call HLA.B7 2RS(Fig. 2B). Mutation of the cysteine decreased the extent ofMIR1-mediated endocytosis (Fig. 2D). We then introduced by mutagenesisa cysteine into the intracytoplasmic tail of HLA.A2 in whichall the intracytoplasmic lysines were previously mutated (Fig. 2B).HLA.A2 without lysines (HLA A2 3R) was slightly down-regulatedin the presence of MIR1, and introduction of the cysteine inHLA.A2 3R (HLA.A2 3RC) allowed full down-regulation (Fig. 2E).We also substituted the last arginine residue of HLA.B7 2RS(HLA.B7 without lysines or cysteines) with a cysteine and observedthat this mutant was as susceptible as HLA.B7 wt to MIR1-mediateddown-regulation (Fig. 2, B and D). This strongly suggested thatthe cysteine was not acting within a linear motif. Thus, inaddition to the lysine- and Ub-dependent pathway, MIR1 can down-regulatesurface molecules in a lysine-independent manner through a processthat requires a cysteine in the intracytoplasmic tail of thetarget molecule. Other determinants may also be important, becauseHLA.B7 2RS and HLA.A2 3R, neither of which contains lysinesor cysteines, are both partially down-regulated (Fig. 2, D and E).
To further demonstrate that a single cysteine was sufficientto promote MIR1-mediated down-regulation, we replaced the intracytoplasmictail of HLA.B7 by a stretch of glycine and alanine residues(GA stretch) (Fig. 3A). To this GA stretch, we added each ofthe 20 amino acids at position X (Fig. 3B). As expected, theGA stretch did not allow down-regulation, whereas the presenceof a lysine did. Thus, lysine is sufficient to promote ubiquitination-mediateddown-regulation independent of surrounding motifs. The samephenotype was observed in the presence of a cysteine (Fig. 3B).None of the other amino acids lead to down-regulation in thepresence of MIR1 (Fig. 3B), except serine. The extent of thedown-regulation in the presence of a serine was modest but highlyreproducible. This is consistent with the fact that HLA.B7 2R(which does not have lysines but has a cysteine) is stronglydown-regulated, and HLA.B7 2RS (no lysines or cysteine) is partiallydown-regulated (Fig. 2D). Indeed, HLA.B7 2RS contains nine serineresidues in its cytoplasmic tail. Overall, it appears that MHCI molecules can be down-regulated independently of lysines,in a cysteine-dependent (and possibly serine-dependent) fashion.
Fig. 3. One lysine or cysteine residue is sufficient to promote down-regulation of HLA.B7 by MIR1. (A) Amino acid sequence of the intracytoplasmic tail of HLA.B7 mutants where the tail has been replaced by a random GA stretch. Each of the 20 amino acids was substituted at position X. (B) BJAB cells stably expressing the HLA.B7 GA mutants were transfected with MIR1-EGFP and an EGFP control, then analyzed for surface expression of HLA.B7 using flow cytometry.
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We examined the possibility that lysineless MHC I moleculescould be ubiquitinated in the presence of MIR1. We used thehamster CHO cell line, which is permissive for MIR1-mediateddown-regulation and does not express endogenous human MHC Imolecules. We stably transduced CHO cells with the differentHLA.B7 constructs and MIR1. After selection, human MHC I heavychains were specifically immunoprecipitated, and their ubiquitinationstatus was analyzed. No ubiquitinated forms were observed inthe absence of MIR1, or when MIR1 was coexpressed with the HLA.B7construct lacking almost all its intracytoplasmic domain, HLA.B7 (Fig. 4A). However, in cells expressing MIR1, ubiquitinationof HLA.B7 wt and, to a lesser extent, HLA.B7 2R (no lysines)was readily detectable, because it produced a characteristicheterogeneous array. In addition, a small but detectable degreeof ubiquitination was observed in HLA.B7 2RS (no lysines orcysteine), consistent with the lower level of down-regulationobserved (Fig. 4B). Thus, a residue other than lysine was beingubiquitinated by MIR1.
Fig. 4. A novel form of ubiquitination is detectable on HLA.B7 2R. (A) Lysates from CHO cells stably expressing wt HLA.B7, HLA.B7 2R, HLA.B7 2RS, and HLA.B7 with or without stable expression of MIR1 were used in an immunoprecipitation reaction. The reaction was carried out using the antibody against human MHC I w6/32 (which recognizes only properly folded human MHC I molecules), and ubiquitinated species were detected by Western blot with an antibody against ubiquitin. (B) Lysates from CHO cells stably expressing wt HLA.B7 or HLA.B7 2R with MIR1 were immunoprecipitated with an antibody against MHC I, eluted in the presence of the reducing agent ß2-mercaptoethanol at either pH 8 or pH 11, and analyzed by Western blot using an antibody against ubiquitin. (C) WtHLA.B7 and HLA.B7 2R were immunoprecipitated as above, and the presence of HLA.B7 was determined by staining with the antibody against human MHC I, HC10.
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We next examined the possibility that this cysteine was theubiquitination site for HLA.B7 2R. We immunoprecipitated wtHLA.B7, as well as HLA.B7 2R, from CHO cells expressing MIR1,and we incubated these immunoprecipitates in the presence ofß2-mercaptoethanol at pH 11 in order to break potentialthiol-ester bonds (cysteine-Ub bond) but not isopeptide bonds(lysine-Ub bond). Ubiquitination of HLA.B7 2R, but not HLA.B7wt, was completely eliminated by this treatment (Fig. 4, B and C).Similarly, treatment drastically diminished the cysteine-Ubbond from the E2 enzyme UBE2E3 (fig. S1).
Altogether, our results show that in the absence of lysine,HLA.B7 molecules are ubiquitinated in a cysteine-dependent manner.Moreover, the bond between ubiquitin and the lysineless HLA.B7shares the same chemical property as the bond between ubiquitinand E2s, which strongly suggests that cysteine is the ubiquitin-attachmentsite for HLA.B7 2R. Direct visualization of the cysteine-ubiquitinbond by mass spectrometry is hindered by the small amount ofubiquitinated molecules available for purification.
The foregoing shows that the side chain of residues other thanlysine can serve as receptors for substrate ubiquitination.It is puzzling that, although ubiquitination has been extensivelystudied, in particular using large-scale proteomic, such a modificationhas never been observed in the past. A thiol-ester bond (cysteine-ubiquitin)is more labile than an isopeptide bond (lysine-ubiquitin), whichcertainly hinders its detection. This may explain why the levelof ubiquitination detected with HLA.B7 2R is not as robust asthe one observed with HLA.B7 wt (Fig. 4A). In addition, we believethat this form of ubiquitination might be restricted to a subfamilyof E3 ubiquitin ligases, such as the MIR1 E3 ubiquitin ligasefamily (MIR1 and its homologs) (13) (SOM text and fig. S2).The regulation processes mediated by ubiquitination may be morecomplex because nonlysine residues are also targets of ubiquitination.For example, the number of potential substrates could be extendedto molecules that do not contain accessible lysines or an accessibleN terminus, and/or transient ubiquitination of substrates mayoccur, because thiolester bonds (Ub-cysteine) are more labilethan isopeptide bonds (Ub-lysine). It will be important to determinewhether this alternate form of ubiquitination requires the samecellular cofactors as the ones involved in lysine ubiquitination.The physiological relevance, for the virus, of this alternateform of ubiquitination is still unclear. An attractive hypothesisis that the ability of MIR1 to act on lysineless molecules allowsit to broaden its potential targets.
16. We thank N. Jarousse, M. Schlissel, and N. Shastri for helpful discussions and critical reading of the manuscript. This work has been supported by the PEW scholars program in the biological sciences, the Hellman family, and a grant (1R01CA108447-01) from the National Cancer Institute.
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