Our immune system has the remarkable ability to recognize and destroy damaged cells or invading microbes while leaving the healthy cells in the body alone. Groups of proteins called ‘MHC class I molecules’ play important roles in defence against invading microbes. If a cell becomes infected with a virus or a bacterium, these molecules can recognize and bind to fragments of foreign or unusual proteins inside the cell, and display them on the surface of the cell. This allows immune cells to identify and kill the infected cells.

Cells produce many different MHC class I molecules that are able to bind to different protein fragments. Some MHC molecules can bind to a wider variety of protein fragments than others, and the number of these molecules present on the cell surface can also vary between individuals. Researchers have noticed that individuals with particular MHC molecules tend to be more or less resistant to particular diseases. For instance, individuals with certain MHC molecules tend to take longer to develop AIDS if they become infected with HIV. However, it is not clear how either the variety of protein fragments bound or the numbers of MHC class I molecules on the surface of cells could alter the immune response.

Here, Chappell, Meziane et al. studied MHC class I molecules in chickens and humans. The experiments reveal that the MHC class I molecules that can bind to a larger variety of protein fragments (so-called ‘generalists’) are present in lower numbers on the surface of cells than molecules that can bind to a smaller variety of fragments (so-called ‘specialists’).

Furthermore, generalist MHC molecules were found to provide resistance to Marek's disease in chickens—which causes paralysis—but some specialists slowed the progression of HIV infections into AIDS in humans. Chappell, Meziane et al. propose that these two types of MHC class I molecules evolved to perform different roles in immune responses. This is a new way of looking at the role of MHC molecules in fighting disease, and the next challenge is to explore the implications for medicine and evolutionary biology.

Highly polymorphic class I molecules encoded by the major histocompatibility complex (MHC) are crucial in the adaptive immune response to viruses and some intracellular bacteria, binding peptides inside the cell and presenting them on the cell surface to CD8 T lymphocytes (Blum et al., 2013; International HIV Controllers Study et al., 2013; Trowsdale and Knight, 2013). The impact of the MHC in response to human immunodeficiency virus (HIV) is well recognized, with class I alleles like HLA-B*35:01 leading to rapid onset of AIDS while HLA-B*57:01 and HLA-B*27:05 confer long-term non-progression (Carrington et al., 1999; Goulder and Walker, 2012; International HIV Controllers Study et al., 2013). Various explanations for these associations have been suggested, including antigen presentation of a particularly effective peptide or of a number of peptides to cytotoxic CD8 T cells or recognition (primarily) independent of peptide by natural killer (NK) cells (Carrington et al., 1999; Martin et al., 2002; Kosmrlj et al., 2010; International HIV Controllers Study et al., 2013). Recently, the level of cell surface expression of HLA-C alleles correlated with CD8 T cell cytotoxicity has been proposed as one important basis for control (Thomas et al., 2009; Apps et al., 2013). Understanding how cell expression level might impact on disease resistance is complicated in humans due to the presence of three class I loci, so we began by studying a simpler animal system before examining human class I alleles.

Long ago, we reported that the relative expression level of MHC class I molecules on the surface of chicken red blood cells as assessed by flow cytometry varies significantly, with cells of the MHC haplotype B21 approximately ten-fold lower than B4, B12, B15, and B19 (Kaufman et al., 1995). This finding was of interest because the level of cell surface expression is inversely correlated with the reported levels of MHC-determined resistance to Marek's disease, an economically important disease caused by the oncogenic herpesvirus, Marek's disease virus (MDV). Decades of investigation identified B21 (and other haplotypes like B2, B6, and B14) as generally conferring resistance and B19 (and other haplotypes such as B4, B12, and B15) as generally conferring susceptibility (reviewed in Plachy et al., 1992). On this basis, we proposed that MHC-determined resistance to Marek's disease could be due to the cell surface expression polymorphism of class I molecules (Kaufman et al., 1995; Kaufman and Salomonsen, 1997).

Compared to humans, the chicken MHC is relatively simple (Kaufman et al., 1999), with two classical class I genes BF1 and BF2 that flank the genes for the transporter associated with antigen presentation (TAP). The TAP transporter pumps peptides from the cytoplasm to the lumen of the endoplasmic reticulum for loading nascent class I molecules, and in typical mammals is functionally monomorphic, pumping a wide variety of peptides for all members of the polymorphic class I multigene family. In contrast, chicken TAP genes are highly polymorphic, with each haplotype encoding a TAP molecule with a peptide-translocation specificity matching the peptide-binding specificity of the dominantly expressed class I molecule encoded by the BF2 gene, with the BF1 gene expressed poorly or not at all (Wallny et al., 2006; Shaw et al., 2007; Walker et al., 2011).

In chickens, the peptide-binding specificity of the dominantly expressed class I molecule can determine resistance to infectious pathogens as well as responses to vaccines. The peptide motifs from B4, B12, B15, and B19 class I molecules are if anything more fastidious than human and mouse motifs, with only one or two amino acids found at the positions of anchor residues, with the motifs explaining the immune response to infection and vaccination (Kaufman et al., 1995). The fastidious binding of these molecules could be easily understood from wire models of the binding site, in which charged and hydrophobic residues were found in appropriate places to interact in a simple manner with the anchor residues of the bound peptides (Wallny et al., 2006). This view was confirmed from the crystal structure of the dominantly expressed class I molecule BF2*0401 from the B4 haplotype, with positive-charged residues in a narrow groove allowing only certain anchor residues from the peptide to be accommodated (Zhang et al., 2012). In contrast, much less peptide material was isolated from B21 cells, with many amino acids found in every peptide position. Crystal structures demonstrated that the dominantly expressed class I molecule BF2*2101 remodels the binding site to accommodate two peptides with completely different sequences, including the anchor residues (Koch et al., 2007). Thus, the lack of a clear peptide motif could be explained as promiscuous peptide binding due to the remodelling of the peptide-binding site.

In this paper, we find that two other haplotypes known to confer resistance to Marek's disease also have low cell surface expression and promiscuous peptide motifs, and examine the structural basis for promiscuous binding in three low expressing molecules. We show that the same relationship between cell surface expression and peptide-binding repertoire is found for four human class I molecules, associated with progression to AIDS. Finally, we propose how promiscuous peptide binding might confer resistance to some pathogens, what the basis for the cell surface expression polymorphism might be, and how these properties may relate to different strategies for resistance to pathogens.

In this article, we make three major points. First, we extend previous work showing that the chicken BF2*2101 achieves promiscuity by remodelling the peptide binding site in a way unknown for mammals, but we find that two other low expressing chicken class I molecules achieve promiscuity with the same pockets typically used in mammals. By extension, these latter results provide a potential molecular explanation for recent reports that human class I molecules vary in peptide repertoire and other reports that they vary in cell surface expression level. Second, we show that peptide-binding repertoire and level of cell surface expression are inversely correlated in both chickens and humans, indicating that this relationship is a fundamental property of class I molecules. Finally, we find that there is a clear association with resistance to infectious diseases, with the low expressing promiscuous class I molecules associated with resistance to Marek's disease in chickens but associated with faster progression to AIDS in humans. We discuss each of these points in turn.

The first point is the structural and mechanistic basis for differences in peptide repertoire of chicken class I molecules. In this article, we confirm and extend the finding (Koch et al., 2007) that BF2*2101 binds 10mer and 11mer peptides with three anchor positions, with many different amino acids with different chemical characteristics, mostly charged and polar at positions P₂ and P_c-2 (and hydrophobic at P_c), which is unlike any mammalian molecule described thus far. In contrast, we find that BF2*0201 and BF2*1401 bind 8mer and 9mer peptides with two anchor residues (much like typical mammalian class I molecules), each with a variety of amino acids at P₂ and P_c.

One question is why BF2*2101 and BF2*0201 bind in such different ways, given that both have Asp24 and Arg9 in their binding sites. In part, this may be due to the difference in residues lining the peptide-binding groove. In BF2*2101, small residues like Gly68(human position 69), Ser69(70), Ser97(99), and Gly152(155) create a big cavity in the centre of the binding groove, allowing Asp24 and Arg9 to move. In BF2*0201 and BF2*1401, the two Ser residues are replaced by the large residues Asn69(70) and Tyr97(99), creating a constricted groove much more like narrow grooves found in high expressing fastidious molecules such as BF2*0401. It is also possible that the length of peptides is determined at least in part by TAP specificity. Together, the narrower groove and the shorter peptides ensure that Asp24 and Arg9 in BF2*0201 (as well as Thr24 and Gln9 in BF2*1401) cannot reach the P₂ and P_c-2 positions, and thus they interact (if at all) with the main chain atoms of the peptide.

Another question is how chicken class I molecules BF2*0201 and BF2*1401 compare to human molecules like HLA-A2, all of which bind peptides with hydrophobic anchor residues. HLA-A2 has one of the widest peptide repertoires among human class I molecules, as assessed by peptide-binding studies (Paul et al., 2013). The anchor residues for HLA-A2 fit into narrow and specific-binding pockets, which allow almost only P₂ Met and Leu for pocket B and P_c Val and Leu for pocket F (Guo et al., 1993). Although Leu and Val in particular are relatively common in proteins (so that the number of peptides bearing these amino acids should be relatively high), there is a much larger number of hydrophobic amino acids that are accommodated by the shallower pockets in both BF2*0201 and BF2*1401. Hence, it seems likely that the peptide repertoire of the most promiscuous chicken class I molecules will be greater than the most promiscuous human class I molecules.

Finally, are there obvious mechanisms by which differences in peptide repertoire arise? In chickens, the peptides presented depend on the peptide-binding specificities of the class I molecule, but also on the peptide-translocation specificities of the TAPs and perhaps also on peptide-editing by tapasin. The genes for chicken TAP and tapasin have at least as many alleles as class I genes (Walker et al., 2005, 2011; van Hateren et al., 2013). On this basis, we propose that the difference in peptide repertoire (and in cell surface expression level) between chicken class I alleles is determined at the level of peptide loading and editing, likely to take place mostly in the peptide-loading complex. It might not be immediately apparent whether such an explanation could account for the differences in peptide repertoire and cell surface expression of human class I molecules, since human TAPs and tapasin are functionally monomorphic. However, a recent paper suggests that the assembly and cell surface expression of different HLA-B alleles is determined by interaction with the near invariant tapasin molecule, based on variation in the certain HLA-B residues (Rizvi et al., 2014). Indeed, it is striking that the rank order of expression level that we find for the four HLA-B alleles tested is exactly the same as the rank order of tapasin dependence found in this recent paper.

The second important point for discussion is why the cell surface expression would be inversely correlated with peptide-binding repertoire. A proximal explanation might be that the biochemical mechanism of peptide loading, as mentioned in the paragraph above, leads to this relationship. Another explanation, similar to the suggestion that multiple MHC molecules lead to a greater chance of autoimmunity (Kaufman et al., 1995), is that promiscuous class I molecules confer more resistance to pathogens but also lead to greater autoimmunity compared to fastidious class I molecules.

We favour a third possibility, prompted by the experimental and supporting theoretical evidence for the notion that a greater number of MHC loci would lead to greater level of negative selection in the thymus (Vidović and Matzinger, 1988; Nowak et al., 1992). In a similar way, one might expect that class I molecules presenting a lesser variety of peptides would negatively select fewer T cell clones, but class I molecules presenting a greater variety of peptides would negatively select many more T cells and create a pauperized T cell repertoire. Therefore, we propose that the peptide-binding repertoire and the cell surface expression levels are inversely correlated precisely to allow similar numbers of T cell clones to survive negative selection and be available in the periphery. In this view, low expressing and promiscuous class I molecules might present many more peptides but each individual peptide would be present on the surface at a much lower level, so that T cells would escape the negative selection that might have occurred at a higher concentration of a particular MHC-peptide complex. In essence, we propose that peptide-binding repertoires and cell surface expression levels have evolved to optimize peripheral T cell responses. Many papers have examined naïve CD8 T cell repertoire in humans and mice (for example, Alanio et al., 2010; Jenkins and Moon, 2012; Lo et al., 2014); such analyses with high and low expressing haplotypes would be informative.

The third important point for discussion is the fact that the inverse correlation between peptide binding repertoire and cell surface expression level also correlates with resistance and susceptibility to certain infectious pathogens. One important question is how it might work.

In chickens, these phenomena are correlated with MHC-determined resistance to historic Marek's disease. Many genetic loci contribute to resistance to Marek's disease, but historically the B locus (containing the MHC) was by far the most important, and under strong selection by MDV (Plachy et al., 1992; Vallejo et al., 1998). Here, we show that the low expressing promiscuous class I molecules are associated with resistance to Marek's disease, while the high expressing fastidious class I molecules are associated with susceptibility. A consequence of promiscuous binding is that these low expressing class I molecules present a larger repertoire of peptides which should activate a wider range of T cell clones, which may be beneficial in the immune response to certain pathogens. We propose that this breadth of antigen presentation leads to a breadth of T cell response that is the basis of MHC-determined resistance to Marek's disease. Conversely, a narrow T cell response to Marek's disease would be the basis for MHC-determined susceptibility, and there is already evidence for a limited repertoire of CD8 T cell clones infiltrating tumours in susceptible B19 chickens (Mwangi et al., 2011). Parenthetically, if true this model suggests that the narrowing of CD8 T cell clonality characteristic of responses in humans and mice (Yewdell and Bennink, 1999; Yewdell and Del Val, 2004; Akram and Inman, 2012) may not be a feature of responses involving promiscuous class I molecules in chickens.

For our example in humans, however, we find the opposite disease association. We find that the low expressing promiscuous HLA-B alleles are associated with rapid progression from HIV infection to AIDS, while the high expressing fastidious HLA-B alleles are found in non-progressors (Carrington et al., 1999; Goulder and Walker, 2012; International HIV Controllers Study et al., 2013). The correlation with peptide binding repertoire (as assessed by prediction) of HLA-B alleles had already been noted (Kosmrlj et al., 2010), but the relationship with cell surface expression level has not. The controller alleles HLA-B*57:01 and HLA-B*27:05 are known to bind and present particular viral peptides that are both protective and difficult for the virus to change without a loss in fitness (Gillespie et al., 2006; Schneidewind et al., 2007). Thus, particular class I molecules may be selected because their fastidious motif presents a particularly protective peptide.

Is there an obvious evolutionary basis for differences in peptide-binding repertoire? The fact that the fastidious HLA-B*57:01 confers resistance to AIDS while the promiscuous BF2*2101 confers resistance to Marek's disease may be no paradox, in that breadth of peptide presentation may be an appropriate response to some pathogens, while presentation of a particular peptide may be more suitable for other pathogens. Viewed from this perspective, the work presented in this paper has begun to define two groups (or a range between two extremes) of class I molecules that are strategically evolved for different modes of resistance.

One possible strategy is that fastidious class I molecules with pauci-clonal T cell responses might be better suited for rapidly evolving viruses with a limited scope for immune evasion, for which a particular peptide might be the most efficient way to achieve resistance. In contrast, promiscuous class I molecules might be better suited for pathogens with coding potential for many immune evasion genes and more stability over evolutionary time, such as large DNA viruses, bacteria, and even parasites. There are few reports about pathogen peptides that are presented in chickens, but the large literature on the MHC restriction of viruses, bacteria, and parasites in humans and mice (for example, Fitzmaurice et al., 2015; Goulder and Walker, 2012; Macnamara et al., 2010; Moss and Khan, 2004; Steven et al., 1997; Yim and Selvaraj, 2010) may be reinterpreted, as the peptide repertoire and cell surface expression levels of the class I molecules become known.

Another potentially fruitful way of considering the strategies of class I molecules (not necessarily exclusive of the first view) might be as generalists and specialists. There is a large literature in biology that examines the generalist/specialist paradigm at the species level, typically testing the model that ‘the jack of all trades is the master of none’ (McArthur, 1972; Futuyma and Moreno, 1988). Recent examples, among many others, include breadth of diet by insect herbivore species (Ali and Agrawal, 2012), niche breadth by bird species (Julliard et al., 2006), competition on shared hosts by aphid parasitoids (Straub et al., 2011), and weasel predation of voles (Sundell and Ylönen, 2008), as well as mathematical models to disentangle the contributions by various factors (Remold, 2012; Büchi and Vuilleumier, 2014). Indeed, the terms generalist and specialist MHC alleles have already been used for describing correlations of class II alleles of the striped mouse in Africa with number of nematode species carried (Froeschke and Sommer, 2012).

In this view, the promiscuous class I molecules would be generalists, which one might expect to suffice for protection against a wide variety of the most common pathogens. However, such generalists might not suffice for protection from a new and/or an especially virulent pathogen that suddenly appears, at which point there would be a strong selection for a specialist class I molecule that was particularly suited to deal with the new threat. The properties of fastidious class I molecules are consistent with selection as specialists for particular pathogens, perhaps including those no longer a danger in the current population.

The importance of these concepts for immunology and medicine may be clear from the discussion above, but there are also ramifications for evolutionary biology, ecology, and conservation. As one example, the number of MHC alleles is considered a key measure for population diversity in estimating the risk of extinction, both as a measure of overall genome diversity and in terms of fitness, including resilience to infection (Sommer, 2005). However, a population with a few generalist MHC alleles might remain healthy compared to a population with many inappropriate specialist MHC alleles.

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Author details

1. Paul E Chappell

   Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom

   Contribution

   PC, Acquisition of data, Analysis and interpretation of data, Drafting or revising the article

   Contributed equally with

   El Kahina Meziane

   Competing interests

   The authors declare that no competing interests exist.

2. El Kahina Meziane

   Department of Pathology, University of Cambridge, Cambridge, United Kingdom

   Contribution

   EKM, Acquisition of data, Analysis and interpretation of data, Drafting or revising the article

   Contributed equally with

   Paul E Chappell

   Competing interests

   The authors declare that no competing interests exist.

3. Michael Harrison

   Department of Pathology, University of Cambridge, Cambridge, United Kingdom

   Contribution

   MH, Acquisition of data, Analysis and interpretation of data, Drafting or revising the article

   Competing interests

   The authors declare that no competing interests exist.

4. Łukasz Magiera

   Department of Pathology, University of Cambridge, Cambridge, United Kingdom

   Contribution

   ŁM, Acquisition of data, Analysis and interpretation of data

   Competing interests

   The authors declare that no competing interests exist.

5. Clemens Hermann

   Department of Pathology, University of Cambridge, Cambridge, United Kingdom

   Contribution

   CH, Acquisition of data, Analysis and interpretation of data

   Competing interests

   The authors declare that no competing interests exist.

6. Laura Mears

   Department of Pathology, University of Cambridge, Cambridge, United Kingdom

   Contribution

   LM, Acquisition of data, Analysis and interpretation of data

   Competing interests

   The authors declare that no competing interests exist.

7. Antoni G Wrobel

   Department of Pathology, University of Cambridge, Cambridge, United Kingdom

   Contribution

   AGW, Acquisition of data, Analysis and interpretation of data

   Competing interests

   The authors declare that no competing interests exist.

8. Charlotte Durant

   Department of Pathology, University of Cambridge, Cambridge, United Kingdom

   Contribution

   CD, Acquisition of data, Analysis and interpretation of data

   Competing interests

   The authors declare that no competing interests exist.

9. Lise Lotte Nielsen

   Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark

   Contribution

   LLN, Provided unique constructs and bacterial cells

   Competing interests

   The authors declare that no competing interests exist.

10. Søren Buus

    Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark

    Contribution

    SB, Provided unique constructs and bacterial cells

    Competing interests

    The authors declare that no competing interests exist.

11. Nicola Ternette

    Target Discovery Institute, University of Oxford, Oxford, United Kingdom

    Contribution

    NT, Acquisition of data, Analysis and interpretation of data, Drafting or revising the article

    Competing interests

    The authors declare that no competing interests exist.

12. William Mwangi

    Pirbright Institute, Compton, United Kingdom

    Contribution

    WM, Acquisition of data, Analysis and interpretation of data, Drafting or revising the article

    Competing interests

    The authors declare that no competing interests exist.

13. Colin Butter

    Pirbright Institute, Compton, United Kingdom

    Contribution

    CB, Acquisition of data, Drafting or revising the article, Contributed unpublished essential data or reagents

    Competing interests

    The authors declare that no competing interests exist.

14. Venugopal Nair

    Pirbright Institute, Compton, United Kingdom

    Contribution

    VN, Acquisition of data, Drafting or revising the article, Contributed unpublished essential data or reagents

    Competing interests

    The authors declare that no competing interests exist.

15. Trudy Ahyee

    Anthony Nolan Research Institute, The Royal Free Hospital, London, United Kingdom

    Contribution

    TA, Acquisition of data, Drafting or revising the article

    Competing interests

    The authors declare that no competing interests exist.

16. Richard Duggleby

    Anthony Nolan Research Institute, The Royal Free Hospital, London, United Kingdom

    Contribution

    RD, Acquisition of data, Drafting or revising the article

    Competing interests

    The authors declare that no competing interests exist.

17. Alejandro Madrigal

    1. Anthony Nolan Research Institute, The Royal Free Hospital, London, United Kingdom
    2. University College London, London, United Kingdom

    Contribution

    AM, Acquisition of data, Drafting or revising the article

    Competing interests

    The authors declare that no competing interests exist.

18. Pietro Roversi

    Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom

    Present address

    Department of Biochemistry, University of Oxford, Oxford, United Kingdom

    Contribution

    PR, Acquisition of data, Analysis and interpretation of data

    Competing interests

    The authors declare that no competing interests exist.

19. Susan M Lea

    Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom

    Contribution

    SML, Conception and design, Analysis and interpretation of data, Drafting or revising the article

    For correspondence

    susan.lea@path.ox.ac.uk

    Competing interests

    The authors declare that no competing interests exist.

20. Jim Kaufman

    1. Department of Pathology, University of Cambridge, Cambridge, United Kingdom
    2. Pirbright Institute, Compton, United Kingdom
    3. Basel Institute for Immunology, Basel, Switzerland
    4. Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom

    Contribution

    JK, Conception and design, Acquisition of data, Analysis and interpretation of data, Drafting or revising the article, Contributed unpublished essential data or reagents

    For correspondence

    jfk31@cam.ac.uk

    Competing interests

    The authors declare that no competing interests exist.

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