Of the seven human and nine chimpanzee lineage III KIR
genes, only KIR2DS4
are orthologous. All other lineage III KIR
are the products of species-specific evolution that occurred after the separation of human and chimpanzee ancestors. In humans the genes encoding activating KIR outnumber by 2.5 to one those encoding inhibitory KIR, the latter consisting of KIR2DL1
. Whereas KIR2DL1 is exquisitely specific for C2 epitopes, the KIR2DL2 and KIR2DL3 allotypes of the KIR2DL2/3
locus are less specific; they principally react with C1, but exhibit crossreactivities with some C2-bearing allotypes (31
). These crossreactions are more apparent for KIR2DL2, a stronger receptor than KIR2DL3. By contrast to the human situation, in chimpanzees the activating KIR are outnumbered twofold by the inhibitory KIR, for which the functions and specificities have been the focus of this investigation. Thus the ratio of inhibitory to activating KIR in these two closely related species differs by a factor of five ().
On the basis of genomic and cDNA analysis we identified six chimpanzee lineage III KIR
genes that encode inhibitory receptors with potential specificity for MHC class I. Despite the considerable sequence divergence in the human and chimpanzee KIR, all six chimpanzee KIR were demonstrated to have functional specificities for MHC-C epitopes that were essentially the same as the established C1 and C2 specificities of human KIR2DL. Like human KIR2DL3, chimpanzee Pt-KIR2DL6 and 2DL8 are C1-specific and have lysine at position 44, the specificity-determining position. Four chimpanzee KIR have similar C2 specificity to human KIR2DL1, but three of them differ from KIR2DL1 in distinctive structural features. Pt-KIR3DL4 and 3DL5 provide the first examples of MHC-C specific KIR that have three extracellular domains, and Pt-KIR2DL9 exhibits C2 specificity although its specificity determining residue is glutamate, rather than the methionine found in other C2 receptors. Only Pt-KIR2DL7 has the same domain structure and specificity-determining residue as KIR2DL1. In our experiments, these differences had no detectable effects on the capacity to bind MHC-C and inhibit the function of effector NKL cells function, nor did mutagenesis to add or remove the D0 domain. One interpretation of the latter result is that the D0 domain is of marginal benefit, which could explain why the exon encoding this domain has been silenced in all human and a majority of chimpanzee lineage III KIR. Alternatively, D0 may have functions that are not well replicated by the NKL cell line, or pertain to the role of inhibitory MHC-C receptors in NK cell development (43
Pt-KIR2DL6 and 2DL8 both resembled KIR2DL3 in their functional specificity for C1 and thus a potentially significant difference between the species is that no chimpanzee equivalent of KIR2DL2 was identified. Human KIR
haplotypes are divided into two broad groups, A
, according to gene content (26
). KIR2DS4, which has a chimpanzee ortholog, is the only activating lineage III KIR of the A
haplotype. In contrast, the human specific activating lineage III KIR are only present on B
haplotypes and the same is true for KIR2DL2
. Thus the formation of KIR2DL2
, which likely involved recombination between KIR2DL1
, as well as the emergence of A
haplotypes, could also be products of human-specific evolution, as is consistent with the absence of A
- and B
-like differences between chimpanzee KIR
haplotypes (L. Abi-Rached, manuscript in preparation).
Reconstructing the sequence of the common ancestor of the hominoid lineage III KIR showed that it had lysine 44 as its specificity-determining residue. This result strongly indicates that the first MHC-C receptor was C1-specific. Supporting this conclusion are studies of the orangutan, a species in which the MHC-C
locus is not fixed (44
), as it is in humans and chimpanzees. That all known orangutan MHC-C are C1, suggests this epitope is ancestral, and C2 evolved subsequently. Ancestral reconstruction also showed that C2-specific KIR with methionine and glutamate at position 44 independently evolved from C1-specific KIR by point mutation. Today, all modern human populations have both C1 and C2 indicating the presence and persistence of selection pressures that retain them.
One possible explanation for the independent evolution of C2 receptors with methionine and glutamate at position 44 is that they are functionally different and complementary. Our results show that their specificity and avidity for C2-bearing MHC allotypes is similar, suggesting that if such difference exists, it does not involve ligand binding but another aspect of their function not investigated in this study. An alternative possibility is that in some circumstances (as appears for the chimpanzee) there is advantage to having two genes encoding C2 receptors, because this would increase the proportion of NK cells expressing C2 receptors (45
). Such selection would not necessarily discriminate between receptors having glutamate or methionine at position 44, but pick the first two variants to emerge, which by chance happened to be one with glutamate 44 and one with methionine 44. In other circumstances, either population bottleneck or selection could cause the loss of one the C2 receptors, explaining the absence of inhibitory C2 receptors having glutamate 44 in humans.
loci emerged from a common ancestor during hominoid evolution. In humans the C1 and C2 epitopes are almost exclusively carried by HLA-C allotypes. Notable, and informative, exceptions are HLA-B*4601 and B*7301, which both carry the C1 epitope and interact with human and chimpanzee C1-specific KIR. These two allotypes have very different histories. HLA-B*4601 was relatively recently formed in South East Asia by gene conversion (46
). Subsequently it has reached allele frequencies of nearly 20% in some South East Asian populations. In contrast, HLA-B*7301 is a rare but geographically widespread allotype (47
) that appears to be the last survivor of an old and divergent lineage of MHC-B
alleles, distinguished from the dominant lineage by having valine at position 76, an essential feature of the C1 epitope. Contrasting with the strong bias for HLA-B allotypes not to have valine 76, the Patr-B
locus has a diverse and substantial representation of valine 76-containing allotypes that we demonstrate are ligands for C1-specific KIR. In the panel of chimpanzees we studied ~50% of individuals express a Patr-B allotype that carries the C1 epitope.
Thus in the chimpanzee Patr-B and Patr-C are both substantial contributors of C1 ligands. During human evolution this function of MHC-B was lost as the frequency of B allotypes with valine 76 declined. In this context, the formation and selection of B*4601 can be seen as a reacquisition through gene conversion of a valine-76-containing B allotype. Thus in humans, the epistatic interaction between lineage III KIR and HLA-B that was lost due to selection or drift, has been restored in particular populations. Notably, B*4601 contributes an additional C1-ligand in populations that already have high frequencies of C1 within HLA-C ().
We have shown here that humans and chimpanzees have a similar system of C1 and C2 ligands that interact with cognate lineage III inhibitory KIR. This system existed in the common ancestor and has been preserved throughout ~8 million years of independent evolution. During this time significant differences also occurred in the human and chimpanzee lineages. The overall trend during human evolution has been to concentrate the C1 and C2 epitopes at the HLA-C locus, which can be seen as becoming increasingly specialized in the regulation of NK cells via their KIR. In the chimpanzee the specialization appears to have been less extreme, as a diversity of both Patr-B and Patr-C allotypes can serve as ligands for inhibitory lineage III KIR. In humans the inhibitory C1 and C2 receptors are encoded by single-copy genes, which are essentially fixed. Related activating receptors evolved and now define the A and B groups of KIR haplotypes, which are associated with C1 receptors of different strength and crossreactivity with C2. An equivalent bifurcation of KIR haplotypes is not apparent in the chimpanzee, where there is a multiplicity of inhibitory C1 and C2 specific KIR and fewer activating lineage III KIR.
Environmental and behavioral differences have most likely shaped the distinctive MHC and KIR systems we describe in humans and chimpanzees. Humans differ from the extant apes in their capacity to populate new and varying habitats by dispersal and adaptive radiation. Human-specific traits such as increased post-breeding lifespan and shorter interbirth intervals (48
) enable rapid population growth following periods of restricted population size due to migration, disease or resource depletion (49
). Human reproductive strategy likely evolved under constraints, which became increasingly lifted following the advent of recent (post-neolithic) modern human behavior patterns (49
). In the case of extreme population bottleneck, as likely occurred during the evolution of pre-modern humans when genetic diversity diminished (50
), subsequent population expansion favors rapid evolution of crucial epistatic interactions and selection for new variants (51
The extensive species differences in inhibitory KIR and MHC frequencies could also be a reflection of species-specific expansion within the chimpanzee, as suggested by their unusually high number of positively selected genes (52
). While chimpanzee populations have likely remained stable in terms of geographic distribution and total population numbers (53
), behavioral adaptations may have contributed specific selection on immune loci. For example, hunting and consumption of other primate species exposes chimpanzees to broad array of trans-species pathogenic infections and superinfections (54
). This in turn can render chimpanzees a resource for infectious diseases that emerge in humans, such as human immunodeficiency virus type-1 (56