Available online at www.sciencedirect.com

ScienceDirect Transport and quality control of MHC class I molecules in the early secretory pathway Sebastian Springer Folding and peptide binding of major histocompatibility complex (MHC) class I molecules have been thoroughly researched, but the mechanistic connection between these biochemical events and the progress of class I through the early secretory pathway is much less well understood. This review focuses on the question how the partially assembled forms of class I (which lack high-affinity peptide and/or the light chain beta-2 microglobulin) are retained inside the cell. Such investigations offer researchers exciting chances to understand the connections between class I structure, conformational dynamics, peptide binding kinetics and thermodynamics, intracellular transport, and antigen presentation. Address Jacobs University Bremen, Germany Corresponding author: Springer, Sebastian ([email protected])

Current Opinion in Immunology 2015, 34:83–90 This review comes from a themed issue on Antigen processing Edited by Nilabh Shastri and Jonathan Yewdell

http://dx.doi.org/10.1016/j.coi.2015.02.009 0952-7915/# 2015 Elsevier Ltd. All rights reserved.

Which forms of partially assembled class I molecules exist in the cell? Class I heavy chains are co-translationally inserted into the endoplasmic reticulum (ER) and fold with the help of calnexin or BiP [1,2]. These folded free heavy chains (Figure 1, form ) then associate with the light chain, beta-2 microglobulin (b2m [3]), followed by the dissociation of calnexin. The resulting heavy chain/b2m dimers (form ) then bind to the peptide loading complex (PLC [4]), which consists of the transporter associated with antigen processing (TAP [5]), the lectin chaperone calreticulin [6], the protein disulfide isomerase ERp57 [7], and the class I-specific assembly factor tapasin [6]. In the absence of key PLC proteins, and probably before binding to the PLC, class I molecules may bind to low-affinity [8]). Interaction with the PLC (form peptides (form ) leads to the binding of high-affinity peptides [9] and, eventually, release from the PLC [10] (form ). In the www.sciencedirect.com

context of this review, I refer to forms , , , and as ‘partially assembled class I molecules’, and to the two and , which predominate in TAP-deficient forms, cells such as RMA-S or T2, as ‘suboptimally loaded dimers’.

Which cellular locations do the partially assembled forms of class I molecules reach? Like most transmembrane surface proteins, peptidebound class I molecules are transported from the ER in COPII-coated vesicles to the ER-Golgi intermediate compartment (ERGIC) and then via the Golgi apparatus to the cell surface [11]. Some review articles still state that class I molecules are only exported from the ER after binding high-affinity peptides (form ), but it was shown already twenty years ago that suboptimally loaded dimers can leave the ER to accumulate in the ERGIC/cis-Golgi [12], and that they even reach the cell surface. Indeed, the flux of H-2Kb through the trans-Golgi is the same in RMA-S cells as in the corresponding wild type, RMA [13]. It is known today that this is also true for human class I molecules [14]. Three reasons may explain why ER export (and cell surface transport) of suboptimally loaded dimers is not widely appreciated. First, all partially assembled surface class I molecules are endocytosed and destroyed with a short half-life, and so their steady-state levels at the cell surface at 37 8C are low [15,16]. Second, in immunoprecipitations that are part of pulse-chase experiments, overnight incubations of the detergent cell lysate — as done frequently for preclearing — dissociate suboptimally loaded dimers and make them undetectable for conformation-dependent antibodies such as W6/32, which leads to the wrong assumption that suboptimally loaded dimers are not exported [17,18]. Third, the glycans on class I molecules accumulated in, or cycling through, the ERGIC and the cis-Golgi are still sensitive to digestion with glycosidases EndoH and EndoF1, since a-mannosidase II, which confers EndoH resistance, is located in the medial or trans-Golgi [19]. Thus, in TAP-deficient cell lines such as RMA-S or T2, suboptimally loaded dimers are almost entirely EndoH-sensitive at steady state, and still extensive class I export from the ER to the ERGIC takes place [20]. Thus, in the absence of TAP, class I molecules can generally reach the cis-Golgi and even the cell surface. The absence of TAP does not necessarily mean that they are completely empty of peptide (form ), since some Current Opinion in Immunology 2015, 34:83–90

84 Antigen processing

Figure 1

short half-life

long half-life

HC

HC

HC bm

bm

bm

cell surface

ERp57 SS

CRT

HC

HC

in

as

HC

HC

tap

HC

ERGIC / cis-Golgi bm

bm

bm

bm

ERp57 SS

CRT

bm

3

HC

4

bm

2

HC bm

1

HC

in as tap

HC bm

HC

ER

5

suboptimally loaded dimers partially assembled class I molecules

Current Opinion in Immunology

Assembly and maturation of an MHC class I molecule (left-to-right) and transport of the individual forms to the cell surface (bottom-to-top). See the text.

class I molecules (such as HLA-A*02:01) can bind signal peptides whose translocation into the ER lumen is independent of TAP [21], and this is why class I molecules in TAP-deficient cells are better referred to as ‘suboptimally loaded’ (see Figure 1). Many suboptimally loaded dimers that travel to the Golgi apparatus seem to accumulate in the cis-Golgi region Current Opinion in Immunology 2015, 34:83–90

[12,20], either because of a bottleneck in their anterograde transport, or because they are held there to be eventually returned to the ER (i.e. ‘recycled’) by a quality control mechanism. This Golgi quality control involves calreticulin, and in calreticulin-deficient cells, most class I molecules escape to the surface with suboptimal peptides, only to be rapidly endocytosed and destroyed. This shows that in wild type cells, retrieval of suboptimally www.sciencedirect.com

MHC class I trafficking Springer 85

loaded class I from the Golgi apparatus contributes to the quality of the bound peptide cohort [22,23]. In cells devoid of tapasin, trafficking of class I is also compromised, but in a different way than in TAP-deficient cells. The lack of tapasin, which links class I to the other proteins of the PLC, seriously decreases the cell surface transport (and thus the surface expression) of some (‘tapasin-dependent’) allotypes, such as HLAB*44:02 [24]. In tapasin-deficient cells, B*44:02 does not seem to reach the Golgi apparatus at all, suggesting that it may be stringently retained in the ER and not even cycle through the cis-Golgi [25]. Tapasin-independent allotypes such as HLA-A*02:01 and HLA-B*44:05, in contrast, travel to the cell surface normally in the absence of tapasin. Intermediate phenotypes exist, such as HLAB*27:05 [26]. The serious phenotype of tapasin-dependent allotypes in the absence of tapasin point toward a more fundamental problem, perhaps their inherent inability to fold the peptide binding site (see below). In the absence of the light chain b2m, the free heavy chains (form ) of several (but not all) murine allotypes have been detected at the cell surface, and some can even present antigen, albeit very inefficiently [27,28]. For human class I heavy chains, this is less well investigated; those free heavy chains on the surface of human T cells that have been detected by binding of exogenous b2m [29–31] might have originated from the surface decay of peptide-bound trimers instead.

What features of partially assembled forms of class I lead to their retention inside the cell? It is reasonable to assume that the intracellular retention of partially assembled forms of class I is caused by specific structural properties that are recognized by cellular factors. The study of the structure of suboptimally loaded dimers is complicated by their tendency to aggregate in vitro, which prevents crystallization [32]. Still, the existence of at least transiently stable suboptimally loaded dimers can be demonstrated by their ability to bind exogenous peptide both in cell lysates [33], where they might originate from the dissociation of high-affinity complexes, and in vitro, where empty peptide-receptive molecules of H-2Kb can be produced by refolding without peptide [34]. The inability of suboptimally loaded dimers to form crystals may indicate a partial unfolding of the peptide binding site, such that they are characterized not by one specific rigid conformation of the peptide binding groove (e.g. with the alpha helices collapsed onto each other, or widely separated), but instead by a strong conformational fluctuation. This view is supported by a recent nuclear magnetic resonance study of a peptideempty HLA-C allotype that found the a1/a2 superdomain largely unstructured but the a3 domain properly folded [35]. Theory evidence in support has come from molecular dynamics simulations that have shown excessive www.sciencedirect.com

mobility of the alpha helices in empty class I on the nanosecond time scale [36,37,38]. But the picture is slightly more complicated: while class I molecules that are entirely devoid of ligand (form ) may be natively ) such as short unfolded, suboptimal ligands (form peptides, down to dipeptides, can significantly stabilize the binding site [39,14]. Importantly, so far, in vitro studies of class I peptide-induced stability have not included its glycans (with one exception: [40]), which likely contribute to the conformational stability of all partially assembled class I molecules in cells [41]. Without peptide, the conformation of the class I peptide binding site may be unstable, but the effect of the lack of tapasin might be more severe. Several groups have found that in the absence of tapasin, the strongly tapasin-dependent allotype HLA-B*44:02 displays serious molecular disorder. It associates weakly with b2m, and is unfolded as judged by the partial reduction of the disulfide bond in the a2 domain [42,43,25,44]. A similar phenotype has been shown for the partially tapasin-dependent allotype B*27:05 [45,26]. This suggests that some class I molecules, even when they are in the ER and surrounded by ligand peptide, are not sufficiently folded to recognize and bind it, but instead they prefer to unfold, and this unfolded state is detected by the quality control system, preventing their exit to the surface (see above). The conformational flexibility of partially assembled class I molecules may lead to their recognition by an ER-Golgi quality control system. One way in which such specific recognition of flexible states of class I might work was demonstrated recently by Margulies and collaborators, who demonstrated that the flexibility of peptide-free H2Ld allows the movement of a tryptophan residue and thus the binding of the antibody 64-3-7, which is specific for suboptimally loaded dimers of Ld [46,47]. There is, however, currently not much stringent evidence that the conformational flexibility of suboptimally loaded class I really is recognized by the ER/Golgi quality control machinery. We recently sought to reduce conformational fluctuations in H-2Kb by introducing a disulfide bond between the alpha helices beyond the C terminus of the peptide, in the F pocket region; the resulting ‘disulfide mutant’ traveled to the surface rapidly in TAP-deficient cells, but it also showed an increased b2m affinity. This leaves open the possibility that stable b2m association is sufficient for surface transport [48]. Since the binding of b2m and peptide to the class I heavy chain is cooperative, stable b2m association also reports on the binding of peptide [49]. Finally, in addition to conformational flexibility and weak — or no — association with b2m, a third feature of partially assembled class I molecules is their peptide Current Opinion in Immunology 2015, 34:83–90

86 Antigen processing

binding site, which — if folded — is either empty or filled with a low-affinity ligand that can be easily displaced. Thus, a quality control protein may also recognize some feature of the empty binding groove such as the empty hydrophobic F pocket, which is common to almost all class I molecules. For such direct recognition of a hydrophobic patch, tapasin, which binds to suboptimally loaded dimers, remains a candidate.

What cellular factor retains partially assembled class I molecules inside the cell? Tapasin itself, in addition to being an assembly and peptide optimization chaperone, is usually credited with retaining suboptimally loaded dimers inside the cell, since it binds to them and is itself retrieved from the Golgi apparatus due to its C-terminal –KKXX sequence [50]. How tapasin recognizes its suboptimally loaded substrates is not well understood; it may bind into the empty binding groove or recognize some unfolding-specific feature of class I, as discussed above. Since the proteins of the PLC are mostly found in the ER at steady-state and since the N-terminal extensions of TAP [51] as well as calreticulin and ERp57 (both – KDEL) contain their own ER localization signals, it is generally assumed that PLC-bound class I molecules (form ) are restricted to the ER; however, reports of ER export, post-ER presence, and/or post-ER activity of calreticulin [22], TAP [52], and tapasin [50] suggest that the PLC components, or the entire PLC, may reach the Golgi apparatus, albeit at low efficiency. In most (especially human) tapasin-deficient cells, tapasin-dependent class I molecules are efficiently kept inside the cell, which shows that a mechanism of retention other than tapasin exists. So far, the prime candidate for recognition of any conformationally unstable and (partly) unfolded protein in the ER, ERGIC, and cis-Golgi is the UDP-glucose:glycoprotein glucosyltransferase (UGT1/ UGGT1), the main actor of cellular glycoprotein quality control. It transfers a glucose residue onto the first branch of an N-linked glycan tree, rendering the protein a binding partner for the lectins calnexin and calreticulin, which are strictly localized to pre-medial Golgi compartments through their respective –KKXX and –KDEL Cterminal sequences. UGT1 is counteracted by the nonspecific glucosidase II, which leads to a cycle of unfolding-dependent reglucosylation (the UGT cycle) that can keep an unfolded protein inside the cell [53]. Cresswell and collaborators have shown that UGT1 is indeed involved in class I quality control [54,55], but the effect of a UGT1 deletion on murine class I is surprisingly light, with only a small reduction of surface levels ([55]; Janßen et al., in press); compared with the severe effect of a calreticulin knockout (see above), it thus appears that UGT1 is not the only mediator of calreticulin function. Perhaps the function of calreticulin in the PLC, which may not require UGT1 processing of class I, accounts for Current Opinion in Immunology 2015, 34:83–90

the difference; alternatively, calreticulin may be able to bind to unfolded class I molecules even if they are not monoglucosylated [56]. Canonical cellular glycoprotein control also surveys the assembly and ligand loading of the class I-related CD1d protein [57].

Are peptide-bound class I molecules specifically recognized for ER export? Many proteins have specific transport receptors that support their packaging into COPII ER-to-ERGIC transport vesicles and thus enhance their export from the ER [58– 60]. It is therefore natural to ask whether perhaps peptide-bound class I trimers are recognized by such transport receptors. The prime candidate for such a protein, Bap31, is a multifunctional protein with roles in ER-associated protein degradation, ER–mitochondrial contact, and apoptosis [61,62]. Despite several investigations, a universal role in specific export of peptide-bound trimers or more globally in antigen presentation has not been established for Bap31 [63,64], nor for any other transport receptor. In an unbiased approach, we have therefore compared the packaging efficiencies of peptide-bound trimers versus suboptimally loaded dimers from the ER into COPII vesicles in an in vitro vesicle generation (’budding’) assay, and we found no difference between them [20]. The simplest interpretation of the current literature is that suboptimally loaded dimers and high, , and ) affinity peptide-bound trimers (forms all exit the ER with the same efficiency. Those transport signals that have been identified in the cytosolic tail of several class I (and class Ib) allotypes are not known to be specific for peptide-bound class I molecules [65,66]; the same is true for the formation of oligomers at ER exit sites [67]. The newly described tapasin-like protein TAPBPR may also be an export-promoting factor (even though it slows down the surface transport of HLA-A allotypes), since it accompanies class I through the secretory pathway [68]. In addition to these export signals, the exit rate of all forms of class I from the ER may be determined by their binding to ER chaperones such as calnexin, calreticulin, and the entire PLC. Such binding, if it occurs, need not entirely block ER exit of any of these forms, for two reasons: first, these chaperone proteins themselves leave the ER to some extent; and second, binding of class I to these chaperones is likely dynamic, with on-rates and offrates in the same time frame as secretory protein transport, such that different binding strengths may well result in differential export rates. This general concept was first proposed by Jennifer Lippincott-Schwartz as the ‘dynamic matrix model’ [69]. A similar dynamic matrix interaction may cause the dramatically different apparent surface transport rates of class I allotypes such as www.sciencedirect.com

MHC class I trafficking Springer 87

H-2Dk versus H-2Kk or H-2Db versus H-2Kb in wild type cells; to be differentially exported, they would only need to have different affinities to the ER chaperones, but not necessarily different rates of folding [70,71].

Is there a functional role for the ER-Golgi cycle of suboptimally loaded class I? In cells that lack calreticulin and thus functional Golgi quality control, class I peptide loading and antigen presentation are severely compromised [23]. This is not primarily due to a loss of function of the PLC, since calreticulin without its C-terminal –KDEL retrieval sequence supports a functional PLC but not class I retrieval and shows the same antigen presentation deficiencies [22]. Thus, the ER-Golgi cycle contributes to loading class I molecules with high-affinity peptides, perhaps by allowing enough time for tapasin to optimize the peptide load. In a viral infection, where a rapid response is crucial, the ER-Golgi cycle may guide class I molecules to a cellular location that is best for loading peptides from freshly synthesized proteins. A large, if not the largest, fraction of peptides loaded onto class I is now thought to derive from defective ribosomal products (DRiPs), that is, proteins that fail to complete translation, to fold, or to associate with other subunits [72]. Such DRiPs can arise during the RNA quality control mechanism of pioneer translation, which takes place inside or just outside the nucleus [73]. Since the ERGIC and the cis-Golgi are small organelles (compared to the ER) that lie very close to the nucleus, the ER-Golgi cycle may concentrate suboptimally loaded class I molecules in that region of the cell where pioneer-translated DRiPs are most frequent. This makes sense in the light of the (presumably) short life-times of peptides in the cytosol [74], and perhaps it is the explanation for the ribosome-to-class I peptide channeling that was observed in a model system [75]. Such peptide loading outside the ER would only work efficiently if sufficient quantities of the other PLC proteins exit the ER, perhaps even in complex with class I (form ); the TAP transporter is certainly necessary. Exit of TAP and tapasin from the ER via the secretory pathway, and even TAP activity outside the ER, have been reported in some cases [50,52] but not universally, and they are almost certain to vary between different cell types. In phagocytic cells, the ERGIC provides PLC proteins, including TAP, to phagosomes by way of Sec22-mediated direct fusion between the organelles; this enables the loading of class I in endocytic compartments known as crosspresentation [76,77]. In non-phagocytic cells, peptide loading and exchange in post-ER compartments also occur [78]. The TAPL transporter, a homolog of TAP, may provide peptide transport into the lysosomes of such cells [79]. www.sciencedirect.com

Class I molecules form homomeric clusters of perhaps 50 proteins in ER exit sites [67] and at the cell surface [80] [81]. In a model system, surface clustering was peptidespecific, which suggests that clusters originate during peptide loading in the ER and persist through the entire secretory pathway [82]. The functional role of such clusters (T cell recognition?) is currently unknown, as is their impact on transport rates and the mechanics of ER-Golgi cycling. It is also unknown what the immunological role of the wide difference in the rates of progress to the cell surface that different allotypes show (as mentioned above) may be. Perhaps it accommodates the different cellular infection kinetics of different virus types. Or perhaps it is just the consequence of different degrees of tapasin dependence, that is, native unfolding, which in turn may be correlated with different abilities to select peptides. In an interesting new study that may support this idea, slow progression of HIV-infected patients to AIDS was tentatively correlated with HLA allotypes that are slow-folding and tapasin-dependent [83].

What comes next? Techniques are crucial The unanswered questions above show that the study of class I trafficking has by no means faded into the rearview mirror, as was recently quoted for MHC class II transport [84]. Class I trafficking connects molecular immunology and cell biology and addresses open questions in both. As with any quantitative approach, proper interpretation of the data requires thorough practical knowledge of the techniques that generated them. Individual methods have limits and pitfalls that can sometimes be avoided by careful planning and controls; for example, in radiolabeling-pulse-chase experiments, some conformations, or some glycan forms, may be precipitated with lower efficiencies or become lost altogether, and thus, the observed cell surface transport rate may be biased (discussed in detail in [18]). When different methods are combined in an investigation, it is important to be aware that some report on steady-state pool sizes of proteins (e.g. flow cytometry, immunoblotting, and microscopy) and others yield flux rates between compartments (e.g. pulse-chase and vesicle budding experiments) [13,20,70]. Pool sizes and flux rates can be manipulated in cells by temperature and by inhibitors to generate, in extreme cases, defined intermediates for biochemical investigations. I believe that theory simulations, based on — or controlled by — such diverse laboratory data will have a great impact on our understanding of class I antigen presentation in the future. As an example, molecular dynamics simulations were mentioned above. For proteins other than class I whose trafficking is medically relevant, most notably the cystic fibrosis transmembrane conductance regulator (CFTR), integrated systems biology approaches Current Opinion in Immunology 2015, 34:83–90

88 Antigen processing

are now being used to link protein folding kinetics and thermodynamics to the rate and efficiency of ER export in a global fashion [85]. Such models will be especially useful for class I if they take all aspects of antigen processing into account, such as the efficiency of peptide generation and transport, the protein expression levels of class I heavy chains, tapasin, TAP, and b2m in the cell type of interest, as well as the peptide binding motif of each particular allotype and its degree of tapasin dependence. Beginnings of such approaches exist already [86– 88,89]. They will eventually allow us to predict immune responses to specific pathogens.

Acknowledgements I thank Uschi Wellbrock for drawing the figure, and Susanne Fritzsche, Caroline Hoppe, and Hannah Behrens for reading the manuscript. I apologize to those authors whose work could not, or not completely, be cited. Research in my laboratory is currently supported by the Bundesministerium fu¨r Bildung und Forschung, by the Deutsche Forschungsgemeinschaft, by the German Academic Exchange Service, and by the To¨njes Vagt Foundation.

10. Ortmann B, Androlewicz MJ, Cresswell P: MHC class I/beta 2microglobulin complexes associate with TAP transporters before peptide binding. Nature 1994, 368:864-867. 11. Barlowe CK, Miller EA: Secretory protein biogenesis and traffic in the early secretory pathway. Genetics 2013, 193:383-410. 12. Hsu VW, Yuan LC, Nuchtern JG, Lippincott SJ, Ha¨mmerling GJ, Klausner RD: A recycling pathway between the endoplasmic reticulum and the Golgi apparatus for retention of unassembled MHC class I molecules. Nature 1991, 352: 441-444. 13. Day PM, Esquivel F, Lukszo J, Bennink JR, Yewdell JW: Effect of TAP on the generation and intracellular trafficking of peptidereceptive major histocompatibility complex class I molecules. Immunity 1995, 2:137-147. 14. Saini SK, Ostermeir K, Ramnarayan VR, Schuster H, Zacharias M, Springer S: Dipeptides promote folding and peptide binding of  MHC class I molecules. Proc Natl Acad Sci U S A 2013, 110:15383-15388. Shows that incubation with allotype-specific dipeptides can reversibly stabilize suboptimally loaded human class I molecules that reach the cell surface. The effect is analogous to the cold stabilization of suboptimally loaded murine class I, and it may be used for similar experimental purposes, for example, the study of endocytosis. 15. Merzougui N, Kratzer R, Saveanu L, van Endert P: A proteasomedependent, TAP-independent pathway for cross-presentation of phagocytosed antigen. EMBO Rep 2011, 12:1257-1264.

I appreciate learning from Stefan Jentsch, Alain Townsend, and Randy Schekman. This review is dedicated to them.

16. Montealegre S, Venugopalan V, Fritzsche S, Kulicke C, Hein Z, Springer S: Dissociation of beta-2 microglobulin determines the surface quality control of MHC class I proteins (accepted).

References and recommended reading

17. Elvin J, Cerundolo V, Elliott T, Townsend A: A quantitative assay of peptide-dependent class I assembly. Eur J Immunol 1991, 21:2025-2031.

Papers of particular interest, published within the period of review, have been highlighted as:  of special interest  of outstanding interest 1.

Degen E, Williams D: Participation of a novel 88-Kd protein in the biogenesis of murine class I histocompatibilty molecules. J Cell Biol 1991, 112:1099.

2.

Nossner E, Parham P: Species-specific differences in chaperone interaction of human and mouse major histocompatibility complex class I molecules. J Exp Med 1995, 181:327-337.

3.

Williams DB, Barber BH, Flavell RA, Allen H: Role of beta-2 microglobulin in the intrcellular transport and surface expression of murine class I histocompatibility molecules. J Immunol 1989, 142:2796-2806.

4.

Neefjes J, Ha¨mmerling G, Momburg F: Folding and assembly of major histocompatibility complex class I heterodimers in the endoplasmic reticulum of intact cells precedes the binding of peptide. J Exp Med 1993, 178:1971-1980.

5.

Neefjes JJ, Momburg F, Hammerling GJ: Selective and ATPdependent translocation of peptides by the MHC-encoded transporter. Science 1993, 261:769-771.

6.

Sadasivan B, Lehner PJ, Ortmann B, Spies T, Cresswell P: Roles for calreticulin and a novel glycoprotein, tapasin, in the interaction of MHC class I molecules with TAP. Immunity 1996, 5:103-114.

18. Fritzsche S, Springer S: Investigating MHC class I folding and trafficking with pulse-chase experiments. Mol Immunol 2013,  55:126-130. A thorough discussion of the pulse-chase experimental technique and its possible pitfalls that may compromise interpretation. 19. Velasco A, Hendricks L, Moremen KW, Tulsiani DR, Touster O, Farquhar MG: Cell type-dependent variations in the subcellular distribution of alpha-mannosidase I and II. J Cell Biol 1993, 122:39-51. 20. Garstka M, Borchert B, Al-Balushi M, Praveen PV, Kuhl NM, Majoul I, Duden R, Springer S: Peptide-receptive MHC class I molecules cycle between endoplasmic reticulum and cisGolgi in wild type lymphocytes. J Biol Chem 2007, 282: 30680-30690. 21. Wei ML, Cresswell P: HLA-A2 molecules in an antigen processing mutant cell contain signal sequence-derived peptides. Nature 1992, 356:443-446. 22. Howe C, Garstka M, Al-Balushi M, Ghanem E, Antoniou AN, Fritzsche S, Jankevicius G, Kontouli N, Schneeweiss C, Williams A et al.: Calreticulin-dependent recycling in the early secretory pathway mediates optimal peptide loading of MHC class I molecules. EMBO J 2009, 28:3730-3744. 23. Gao B, Adhikari R, Howarth M, Nakamura K, Gold MC, Hill AB, Knee R, Michalak M, Elliott T: Assembly and antigen-presenting function of MHC class I molecules in cells lacking the ER chaperone calreticulin. Immunity 2002, 16:99-109. 24. Grandea AG 3rd, Golovina TN, Hamilton SE, Sriram V, Spies T, Brutkiewicz RR, Harty JT, Eisenlohr LC, Van Kaer L: Impaired assembly yet normal trafficking of MHC class I molecules in Tapasin mutant mice. Immunity 2000, 13:213-222.

7.

Hughes EA, Cresswell P: The thiol oxidoreductase ERp57 is a component of the MHC class I peptide-loading complex. Curr Biol 1998, 8:709-712.

8.

Sugita M, Brenner MB: An unstable beta-2-microglobulin: major histocompatibility complex class I heavy chain intermediate dissociates from calnexin and then is stabilized by binding peptide. J Exp Med 1994, 180:2163-2171.

25. Garstka MA, Fritzsche S, Lenart I, Hein Z, Jankevicius G, Boyle LH, Elliott T, Trowsdale J, Antoniou AN, Zacharias M et al.: Tapasin dependence of major histocompatibility complex class I molecules correlates with their conformational flexibility. FASEB J 2011, 25:3989-3998.

9.

Williams AP, Peh CA, Purcell AW, McCluskey J, Elliott T: Optimization of the MHC class I peptide cargo is dependent on tapasin. Immunity 2002, 16:509-520.

26. Abualrous ET, Fritzsche S, Hein Z, Al-Balushi MS, Reinink P, Boyle LH, Wellbrock U, Antoniou AN, Springer S: F pocket  flexibility influences the tapasin dependence of two

Current Opinion in Immunology 2015, 34:83–90

www.sciencedirect.com

MHC class I trafficking Springer 89

differentially disease-associated MHC class I proteins. Eur J Immunol 2015. B*27:05, statistically associated with ankylosing spondylitis, is shown to be partially tapasin-dependent and to have a tendency to unfold in cells. 27. Machold RP, Andree S, Van Kaer L, Ljunggren HG, Ploegh HL: Peptide influences the folding and intracellular transport of free major histocompatibility complex class I heavy chains. J Exp Med 1995, 181:1111-1122. 28. Schell TD, Mylin LM, Tevethia SS, Joyce S: The assembly of functional beta(2)-microglobulin-free MHC class I molecules that interact with peptides and CD8(+) T lymphocytes. Int Immunol 2002, 14:775-782. 29. Abdel Motal UM, Zhou MX, Siddiqi AR, Jondal M: Regulation of MHC class I membrane expression by beta 2-microglobulin. Scand J Immunol 1993, 38:395-400. 30. Anderson KS, Alexander J, Wei M, Cresswell P: Intracellular transport of class I MHC molecules in antigen processing mutant cell lines. J Immunol 1993, 151:3407-3419. 31. Otten GR, Bikoff E, Ribaudo RK, Kozlowski S, Margulies DH, Germain RN: Peptide and beta 2-microglobulin regulation of cell surface MHC class I conformation and expression. J Immunol 1992, 148:3723-3732. 32. Theodossis A: On the trail of empty MHC class-I. Mol Immunol 2013, 55:131-134. 33. Townsend A, Ohlen C, Bastin J, Ljunggren HG, Foster L, Karre K: Association of class I major histocompatibility heavy and light chains induced by viral peptides. Nature 1989, 340:443-448. 34. Saini SK, Abualrous ET, Tigan AS, Covella K, Wellbrock U, Springer S: Not all empty MHC class I molecules are molten globules: tryptophan fluorescence reveals a two-step mechanism of thermal denaturation. Mol Immunol 2013, 54:386-396. 35. Kurimoto E, Kuroki K, Yamaguchi Y, Yagi-Utsumi M, Igaki T,  Iguchi T, Maenaka K, Kato K: Structural and functional mosaic nature of MHC class I molecules in their peptide-free form. Mol Immunol 2013, 55:393-399. This NMR study of an HLA-C allotype is the first direct experimental demonstration of the natively unfolded peptide binding site of a suboptimally loaded class I molecule. 36. Zacharias M, Springer S: Conformational flexibility of the MHC class I alpha1-alpha2 domain in peptide bound and free states: a molecular dynamics simulation study. Biophys J 2004, 87:2203-2214. 37. Narzi D, Becker CM, Fiorillo MT, Uchanska-Ziegler B, Ziegler A,  Bockmann RA: Dynamical characterization of two differentially disease associated MHC class I proteins in complex with viral and self-peptides. J Mol Biol 2012, 415:429-442. A thorough comparison of the dynamic properties of HLA-B*27:05 and B*27:09 with molecular dynamics simulations. 38. Bailey A, van Hateren A, Elliott T, Werner JM: Two polymorphisms facilitate differences in plasticity between two chicken major histocompatibility complex class I proteins. PLOS ONE 2014, 9:e89657. 39. Glithero A, Tormo J, Doering K, Kojima M, Jones EY, Elliott T: The crystal structure of H-2D(b) complexed with a partial peptide epitope suggests a major histocompatibility complex class I assembly intermediate. J Biol Chem 2006, 281:12699-12704. 40. Springer S, Do¨ring K, Skipper JC, Townsend AR, Cerundolo V: Fast association rates suggest a conformational change in the MHC class I molecule H-2Db upon peptide binding. Biochemistry 1998, 37:3001-3012. 41. Ryan SO, Cobb BA: Roles for major histocompatibility complex glycosylation in immune function. Semin Immunopathol 2012, 34:425-441. 42. Howarth M, Williams A, Tolstrup AB, Elliott T: Tapasin enhances MHC class I peptide presentation according to peptide halflife. Proc Natl Acad Sci U S A 2004, 101:11737-11742. 43. Zernich D, Purcell AW, Macdonald WA, Kjer-Nielsen L, Ely LK, Laham N, Crockford T, Mifsud NA, Bharadwaj M, Chang L et al.: www.sciencedirect.com

Natural HLA class I polymorphism controls the pathway of antigen presentation and susceptibility to viral evasion. J Exp Med 2004, 200:13-24. 44. Kienast A, Preuss M, Winkler M, Dick TP: Redox regulation of peptide receptivity of major histocompatibility complex class I molecules by ERp57 and tapasin. Nat Immunol 2007, 8:864-872. 45. Fussell H, Nesbeth D, Lenart I, Campbell EC, Lynch S, Santos S, Gould K, Powis SJ, Antoniou AN: Novel detection of in vivo HLAB27 conformations correlates with ankylosing spondylitis association. Arthritis Rheum 2008, 58:3419-3424. 46. Mage MG, Dolan MA, Wang R, Boyd LF, Revilleza MJ, Robinson H,  Natarajan K, Myers NB, Hansen TH, Margulies DH: A structural and molecular dynamics approach to understanding the peptide-receptive transition state of MHC-I molecules. Mol Immunol 2013, 55:123-125. This remarkable paper shows that peptide-empty H-2Ld is conformationally flexible with the movement of a tryptophan residue in the 310 helix that allows binding of the 64-3-7 antibody. 47. Mage MG, Dolan MA, Wang R, Boyd LF, Revilleza MJ, Robinson H, Natarajan K, Myers NB, Hansen TH, Margulies DH: The peptidereceptive transition state of MHC class I molecules: insight from structure and molecular dynamics. J Immunol 2012, 189:1391-1399. 48. Hein Z, Uchtenhagen H, Abualrous ET, Saini SK, Janssen L, Van Hateren A, Wiek C, Hanenberg H, Momburg F, Achour A et al.:  Peptide-independent stabilization of MHC class I molecules breaches cellular quality control. J Cell Sci 2014, 127: 2885-2897. Connecting the a2 and a2 helices of class I by a disulfide bond leads to reduced conformational flexibility, increased b2m affinity, and rapid transport without high-affinity peptide. 49. Townsend A, Elliott T, Cerundolo V, Foster L, Barber B, Tse A: Assembly of MHC class I molecules analyzed in vitro. Cell 1990, 62:285-295. 50. Paulsson KM, Jevon M, Wang JW, Li S, Wang P: The double lysine motif of tapasin is a retrieval signal for retention of unstable MHC class I molecules in the endoplasmic reticulum. J Immunol 2006, 176:7482-7488. 51. Hulpke S, Tomioka M, Kremmer E, Ueda K, Abele R, Tampe R: Direct evidence that the N-terminal extensions of the TAP complex act as autonomous interaction scaffolds for the assembly of the MHC I peptide-loading complex. Cell Mol Life Sci 2012, 69:3317-3327. 52. Ghanem E, Fritzsche S, Al-Balushi M, Hashem J, Ghuneim L, Thomer L, Kalbacher H, van Endert P, Wiertz E, Tampe R et al.: The transporter associated with antigen processing (TAP) is active in a post-ER compartment. J Cell Sci 2010, 123:4271-4279. 53. Tannous A, Pisoni GB, Hebert DN, Molinari M: N-linked sugarregulated protein folding and quality control in the ER. Semin Cell Dev Biol 2014 http://dx.doi.org/10.1016/j.semcdb.2014. 12.001. 54. Zhang W, Wearsch PA, Zhu Y, Leonhardt RM, Cresswell P: A role  for UDP-glucose glycoprotein glucosyltransferase in expression and quality control of MHC class I molecules. Proc Natl Acad Sci U S A 2011, 108:4956-4961. Shows that the UGT1 glucosyltransferase optimizes class I antigen presentation in cells. 55. Wearsch PA, Peaper DR, Cresswell P: Essential glycan dependent interactions optimize MHC class I peptide loading. Proc Natl Acad Sci U S A 2011, 108:4950-4955. Demonstrates how class I association with the PLC is regulated by its glycosylation state. 56. Ireland BS, Brockmeier U, Howe CM, Elliott T, Williams DB: Lectin-deficient calreticulin retains full functionality as a chaperone for class I histocompatibility molecules. Mol Biol Cell 2008, 19:2413-2423. 57. Kunte A, Zhang W, Paduraru C, Veerapen N, Cox LR, Besra GS,  Cresswell P: Endoplasmic reticulum glycoprotein quality control regulates CD1d assembly and CD1d-mediated antigen presentation. J Biol Chem 2013, 288:16391-16402. Demonstrates that efficient lipid antigen presentation through CD1d requires the canonical cellular glycoprotein quality control. Current Opinion in Immunology 2015, 34:83–90

90 Antigen processing

58. Campbell JL, Schekman R: Selective packaging of cargo molecules into endoplasmic reticulum-derived COPII vesicles. Proc Natl Acad Sci U S A 1997, 94:837-842. 59. Appenzeller C, Andersson H, Kappeler F, Hauri HP: The lectin ERGIC-53 is a cargo transport receptor for glycoproteins. Nat Cell Biol 1999, 1:330-334. 60. Dancourt J, Barlowe C: Protein sorting receptors in the early secretory pathway. Annu Rev Biochem 2010, 79:777-802. 61. Geiger R, Andritschke D, Friebe S, Herzog F, Luisoni S, Heger T, Helenius A: BAP31 and BiP are essential for dislocation of SV40 from the endoplasmic reticulum to the cytosol. Nat Cell Biol 2011, 13:1305-1314.

75. Lev A, Princiotta MF, Zanker D, Takeda K, Gibbs JS, Kumagai C, Waffarn E, Dolan BP, Burgevin A, Van Endert P et al.: Compartmentalized MHC class I antigen processing enhances immunosurveillance by circumventing the law of mass action. Proc Natl Acad Sci U S A 2010, 107:6964-6969. 76. Guermonprez P, Saveanu L, Kleijmeer M, Davoust J, Van Endert P, Amigorena S: ER-phagosome fusion defines an MHC class I cross-presentation compartment in dendritic cells. Nature 2003, 425:397-402.

62. Iwasawa R, Mahul-Mellier AL, Datler C, Pazarentzos E, Grimm S: Fis1 and Bap31 bridge the mitochondria–ER interface to establish a platform for apoptosis induction. EMBO J 2011, 30:556-568.

77. Nair-Gupta P, Baccarini A, Tung N, Seyffer F, Florey O, Huang Y,  Banerjee M, Overholtzer M, Roche PA, Tampe R et al.: TLR signals induce phagosomal MHC-I delivery from the endosomal recycling compartment to allow crosspresentation. Cell 2014, 158:506-521. The results of this exciting study suggest that class I molecules for crosspresentation originate from endosomes, whereas PLC components for their loading come from the ERGIC.

63. Paquet ME, Cohen-Doyle M, Shore GC, Williams DB: Bap29/31 influences the intracellular traffic of MHC class I molecules. J Immunol 2004, 172:7548-7555.

78. Del Val M, Iborra S, Ramos M, Lazaro S: Generation of MHC class I ligands in the secretory and vesicular pathways. Cell Mol Life Sci 2011, 68:1543-1552.

64. Abe F, Van Prooyen N, Ladasky JJ, Edidin M: Interaction of Bap31 and MHC class I molecules and their traffic out of the endoplasmic reticulum. J Immunol 2009, 182:4776-4783.

79. Demirel O, Jan I, Wolters D, Blanz J, Saftig P, Tampe R, Abele R: The lysosomal polypeptide transporter TAPL is stabilized by interaction with LAMP-1 and LAMP-2. J Cell Sci 2012, 125:4230-4240.

65. Boyle LH, Gillingham AK, Munro S, Trowsdale J: Selective export of HLA-F by its cytoplasmic tail. J Immunol 2006, 176: 6464-6472. 66. Cho S, Ryoo J, Jun Y, Ahn K: Receptor-mediated ER. export of human MHC class I molecules is regulated by the C-terminal single amino acid. Traffic 2011, 12:42-55. 67. Pentcheva T, Edidin M: Clustering of peptide-loaded MHC class I molecules for endoplasmic reticulum export imaged by fluorescence resonance energy transfer. J Immunol 2001, 166:6625-6632.

80. Chakrabarti A, Matko J, Rahman NA, Barisas BG, Edidin M: Selfassociation of class I major histocompatibility complex molecules in liposome and cell surface membranes. Biochemistry 1992, 31:7182-7189. 81. Damjanovich S, Vereb G, Schaper A, Jenei A, Matko J, Starink JP, Fox GQ, Arndt-Jovin DJ, Jovin TM: Structural hierarchy in the clustering of HLA class I molecules in the plasma membrane of human lymphoblastoid cells. Proc Natl Acad Sci U S A 1995, 92:1122-1126.

68. Boyle LH, Hermann C, Boname JM, Porter KM, Patel PA, Burr ML,  Duncan LM, Harbour ME, Rhodes DA, Skjodt K et al.: Tapasinrelated protein TAPBPR is an additional component of the MHC class I presentation pathway. Proc Natl Acad Sci U S A 2013, 110:3465-3470. Characterizes the mysterious novel tapasin-like protein TAPBPR and its influence on class I trafficking.

82. Lu X, Gibbs JS, Hickman HD, David A, Dolan BP, Jin Y, Kranz DM, Bennink JR, Yewdell JW, Varma R: Endogenous viral antigen  processing generates peptide-specific MHC class I cellsurface clusters. Proc Natl Acad Sci U S A 2012, 109: 15407-15412. Ingeniously demonstrates formation of homomeric peptide-specific clusters of class I molecules during antigen presentation.

69. Nehls S, Snapp EL, Cole NB, Zaal KJ, Kenworthy AK, Roberts TH, Ellenberg J, Presley JF, Siggia E, Lippincott-Schwartz J: Dynamics and retention of misfolded proteins in native ER membranes. Nat Cell Biol 2000, 2:288-295.

83. Rizvi SM, Salam N, Geng J, Qi Y, Bream JH, Duggal P, Hussain SK,  Martinson J, Wolinsky SM, Carrington M et al.: Distinct assembly profiles of HLA-B molecules. J Immunol 2014, 192:4967-4976. Shows that some HLA-B allotypes correlated with rapid disease progression in HIV infection are tapasin-dependent.

70. Williams D, Swiedler S, Hart G: Intracellular transport of membrane glycoproteins: two closely related histocompatibility antigens differ in their rates of transit to the cell surface. J Cell Biol 1985, 101:725-734.

84. Cresswell P, Roche PA: Invariant chain-MHC class II complexes: always odd and never invariant. Immunol Cell Biol 2014, 92:471-472.

71. Fritzsche S, Abualrous ET, Borchert B, Momburg F, Springer S:  Release from endoplasmic reticulum matrix proteins controls cell surface transport of MHC class I molecules. Traffic 2015. (in press). A careful and comprehensive study of the possible molecular causes of different surface transport rates of murine class I molecules. Shows that neither class I folding rates nor any single known factor in the ER are responsible. 72. Bourdetsky D, Schmelzer CE, Admon A: The nature and extent of contributions by defective ribosome products to the HLA peptidome. Proc Natl Acad Sci U S A 2014, 111:E1591-E1599. 73. Apcher S, Millot G, Daskalogianni C, Scherl A, Manoury B,  Fahraeus R: Translation of pre-spliced RNAs in the nuclear compartment generates peptides for the MHC class I pathway. Proc Natl Acad Sci U S A 2013, 110:17951-17956. A striking demonstration of the role of pioneer translation in epitope peptide generation for MHC class I molecules, which is one possible molecular explanation for the DRiP phenomenon. 74. Neijssen J, Herberts C, Drijfhout JW, Reits E, Janssen L, Neefjes J: Cross-presentation by intercellular peptide transfer through gap junctions. Nature 2005, 434:83-88.

Current Opinion in Immunology 2015, 34:83–90

85. Wiseman RL, Powers ET, Buxbaum JN, Kelly JW, Balch WE: An adaptable standard for protein export from the endoplasmic reticulum. Cell 2007, 131:809-821. 86. Yewdell JW, Reits E, Neefjes J: Making sense of mass destruction: quantitating MHC class I antigen presentation. Nat Rev Immunol 2003, 3:952-961. 87. Schneeweiss C, Garstka M, Smith J, Hutt MT, Springer S: The mechanism of action of tapasin in the peptide exchange on MHC class I molecules determined from kinetics simulation studies. Mol Immunol 2009, 46:2054-2063. 88. Neefjes J, Jongsma ML, Paul P, Bakke O: Towards a systems understanding of MHC class I and MHC class II antigen presentation. Nat Rev Immunol 2011, 11:823-836. 89. Dalchau N, Phillips A, Goldstein LD, Howarth M, Cardelli L,  Emmott S, Elliott T, Werner JM: A peptide filtering relation quantifies MHC class I peptide optimization. PLoS Comput Biol 2011, 7:e1002144. A tour de force attempt to construct an all-encompassing mathematical model of class I peptide selection.

www.sciencedirect.com