PMCCPMCCPMCC

Search tips
Search criteria 

Advanced

 
Logo of nihpaAbout Author manuscriptsSubmit a manuscriptHHS Public Access; Author Manuscript; Accepted for publication in peer reviewed journal;
 
Mol Immunol. Author manuscript; available in PMC 2010 December 1.
Published in final edited form as:
PMCID: PMC2788069
NIHMSID: NIHMS150407

The chimpanzee Mhc-DRB region revisited: gene content, polymorphism, pseudogenes, and transcripts

Abstract

In humans, great apes, and different monkey species, the major histocompatibility complex (MHC) class II DRB region is known to display considerable copy number variation. The microsatellite D6S2878 has been shown to be a valuable marker for haplotyping the DR region in humans and macaque species. The present report illustrates that chimpanzee haplotypes also can be discriminated with this marker. The analyses resulted in the description of nine different region configurations, of which seven are present within the West African chimpanzee population studied. The region configurations vary in gene content from two up to five DRB genes. Subsequent cDNA sequencing increased the number of known full-length Patr-DRB sequences from 3 to 32, and shows that one to three Patr-DRB genes per haplotype apparently produce functional transcripts. This is more or less comparable to humans and rhesus macaques. Moreover, microsatellite analysis in concert with full-length DRB gene sequencing showed that the Patr-DRB*W9 and -DRB3*01/02 lineages most likely arose from a common ancestral lineage: hence, the Patr-DRB*W9 lineage was renamed to Patr-DRB3*07. Overall, the data demonstrate that the D6S2878 microsatellite marker allows fast and accurate haplotyping of the Patr-DRB region. In addition, the limited amount of allelic variation observed at the various Patr-DRB genes is in agreement with the fact that chimpanzees experienced a selective sweep that may have been caused by an ancient retroviral infection.

Keywords: HLA, HIV, Microsatellite, Patr

Introduction

Chimpanzees (Pan troglodytes) are the closest living relative of humans, and both species share approximately 98.7% similarity at the nonrepetitive DNA level (Fujiyama et al., 2002). The split between the ancestors of humans and chimpanzees happened about 5–6 million years ago (Fujiyama et al., 2002). Chimpanzees can be divided into four different subspecies, designated as Pan troglodytes troglodytes (P.t.t.), P.t. schweinfurthii (P.t.s.), P.t. verus (P.t.v.), and P. t. vellerosus (Gonder et al., 1997; Morin et al., 1994).

The major histocompatibility complex (MHC) is a multigene family, which is present in most vertebrate species, and two clusters of cell-surface proteins are recognised. MHC class I gene products are expressed on nucleated cells, whereas the MHC class II proteins are expressed on B cells, macrophages, and other antigen-presenting cells. The MHC plays a key role in generating adaptive immunological responses, and the main function is the binding of pathogen-derived peptides and presenting them on the cell surface for T-cell recognition. The MHC class II gene products in humans and chimpanzees are designated HLA-DP, -DQ, and -DR, and Patr-DP, -DQ, and -DR, respectively. All three loci possess one A gene and at least one B gene. The DR region is the most complex, and several B genes are characterised in humans: they have been named HLA-DRB1 to -DRB9 (Marsh et al., 2005). In chimpanzees, the orthologues of these genes are described, and as in humans, the -DRB2 and -DRB6 to -DRB9 are considered to be pseudogenes (Bontrop et al., 1999). Chimpanzees, however, seem to have lost during their evolution the equivalent of the HLA-DRB1*04 lineage. In both species, the various types of DRB loci display different levels of polymorphism, and most of this variation is confined to exon 2. Additionally, the unique number of DRB genes present per region configuration differs and ranges from one to four in humans and from two to five in chimpanzees (de Groot et al., 2008b; Doxiadis et al., 2007). Allelic variation is observed within region configurations, and as a consequence different haplotypes can be discriminated per region configuration.

A complex dinucleotide repeat, D6S2878, located in close proximity of exon 2 of most HLA-DRB genes (Andersson et al., 1987; Epplen et al., 1997; Riess et al., 1990), was found to represent an accurate and valuable marker for haplotyping humans and two macaque species (de Groot et al., 2008a; Doxiadis et al., 2007). The genetic profile of this microsatellite showed its usefulness in the description of Patr-DRB1 alleles (Bak et al., 2006). In humans, the HLA-DRB1, -DRB3, -DRB4, and -DRB5 genes produce functional transcripts that are translated into products. To date there are limited data available on the actual transcription of Patr-DRB alleles (Fan et al., 1989), and even a thorough chimpanzee population study is lacking.

Chimpanzees are known to have very effective cytotoxic T-cell (CTL) responses against human immunodeficiency virus type 1 (HIV-1) infection (Balla-Jhagjhoorsingh et al., 2003). Moreover, like particular human individuals, chimpanzees in general are relative resistant to developing acquired immunodeficiency syndrome (AIDS) after natural or experimental infection with HIV-1 or chimpanzee-derived simian immunodeficiency virus (SIVcpz, the closest relative of HIV-1) (Heeney et al., 2006; Keele et al., 2009; Novembre et al., 1997). In humans, resistance to AIDS is strongly associated with the presence of the HLA-B*2705 or -B*5701 molecules (Goulder and Watkins, 2008); also in chimpanzees CTL responses are found that are directed against conserved HIV-1 epitopes in the context of particular Mhc class I molecules (Balla-Jhagjhoorsingh et al., 1999). Based on these observations, and on the fact that chimpanzees possess a reduced Mhc class I repertoire, we hypothesised that the Mhc class I gene repertoire reduction may have been caused by SIVcpz or a related ancestral retrovirus. As such, the contemporary chimpanzee populations have modified MHC class I repertoires but are able to cope with their natural environment and with (retro)viral infections such as HIV-1/SIVcpz (de Groot et al., 2002). Evidence for such a selective sweep was further substantiated by the analyses of the MIC locus, which maps near Patr-B (de Groot et al., 2005), and by comparative genomics using different microsatellite markers mapping inside and outside the MHC region (de Groot et al., 2008b).

MHC class II molecules play a pivotal role in providing CD4+ T-cell-mediated help and antibody production. This effector function is also important for the development and maintenance of CD8+ memory T cells (Williams et al., 2006). Although the MHC class I repertoire of chimpanzees is reduced, these animals do mount effective CTL responses against various pathogens such as HCV, HIV-1, and malaria (Balla-Jhagjhoorsingh et al., 2003; Bottius et al., 1996; Erickson et al., 1993). We aimed to characterise the Mhc-DRB region of a P.t.verus colony thoroughly and to investigate which different Patr-DRB alleles may play a role in providing immunological help to CD8+ memory T cells.

Material and methods

Source of RNA and DNA

Thirty-five chimpanzees originating from Sierra Leone represent the founder population that is the basis of the West African chimpanzee colony studied. The colony increased to more than 200 animals, covering three generations. The offspring was pedigreed based on serological specificities (Patr-A and -B) and molecular-defined class I and II polymorphisms (Bontrop et al., 1995; de Groot et al., 2000). Epstein-Barr virus- transformed B-cell lines were used to obtain RNA and genomic DNA (gDNA). Human DNA samples, originating from unrelated Caucasoid individuals, were provided by the department of Immunohaematology and Blood Bank of the Leiden University Medical Centre (Doxiadis et al., 2007) and were included for comparison. In addition, samples of four P.t.t. and two P.t.s. animals were included in the panel.

Patr-DRB short tandem repeat (STR) genotyping and sequencing

The microsatellite marker D6S2878 was used for DRB genotyping. The genotyped cohort comprised of 114 different chimpanzee DNA samples of founder animals and offspring. The relevant DNA segment was amplified with the primers (0.2 μM) described for the human samples and the genotyping techniques were performed as published (de Groot et al., 2008a; Doxiadis et al., 2007).

Forty three (31 P.t.v and 12 P.t.t/P.t.s.) different Patr-DRB alleles were sequenced from exon 2 to intron 2, and this area included the microsatellite. The same primers are used as described for humans (Doxiadis et al., 2007). The PCR products were purified using the QIAquick Gel Extraction Kit (Qiagen) and were subsequently blunt-end ligated into the vector pJET1.2/blunt vector (Fermentas, St. Leon-Rot, Germany). Transformation of the XL1Blue E. coli cells was performed with the TransformAid Bacterial Transformation Kit (Fermentas). A minimum of 32 clones were examined per PCR reaction. The sequence samples were prepared using 1 μl of ABI Prism BigDye Terminator v3.1 Cycle Sequencing mixture (Applied Biosystems, Foster City, CA), 0.2 μM of pJET1.2 forward or reverse primer (Fermentas), and 2 μl of 5Χ sequencing dilution buffer (400mM Tris-HCL, 10mM MgCl2) in a 10 μl reaction, and sequenced on an ABI 3130xl genetic analyser (Applied Biosystems). The data were analysed using the programmes Lasergene SeqMan Pro version 7.2.1 (Dnastar, Inc Madison, USA) and MacVector version 10.0.2. (MacVector, Inc Cambridge, UK). At least two independent PCR reactions were performed and/or the alleles were confirmed by their presence in different animals.

Patr-DRB cDNA sequencing

For 21 different animals (17 P.t.v. and 4 P.t.t.), covering most of the genotyped Mhc-DRB haplotypes, RNA was extracted using the RNeasy mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s recommendations. An RT-PCR reaction (Promega, Madison, WI, USA) in accordance with the manufacturer’s recommendation was performed using Mhc-DRB specific primers described previously (Lekutis and Letvin, 1995). The purification of the PCR products, the ligation, transformation, and sequencing was performed as described above.

Phylogenetic analysis and detection of transposable elements

Neighbor-Joining (NJ) trees were constructed with the PAUP* programme version 4.0b10 for Macintosh (Swofford, 2002). Pairwise distances were calculated using the Kimura-2 parameter method. Bootstrap values were calculated based on 1000 replicates. Alleles of the Patr-DRB3*01/02 and -DRB*W9 lineages were analysed for their repetitive elements using the CENSOR software tool from the Genetic Information Research Institute website (http://www.girinst.org/censor) (Kohany et al., 2006).

Nomenclature and re-designation of the Patr-DRB*W9 lineage

Allele names were assigned according to a standardized protocol (Ellis et al., 2006; Klein et al., 1990; Robinson et al., 2003). The full-length DRB sequences are deposited at the EMBL database, and received accession numbers FN424191 to FN424222. The newly described exon 2 sequence Patr-DRB1*0215 received accession number FN424223. All sequences are documented at the IPD-MHC-NHP-database (www.ebi.ac.uk/ipd/mhc/nhp).

Based on gDNA and cDNA sequences, the Patr-DRB*W9 lineage seems to be highly related to the -DRB3*01/02 lineages. The present data elucidated that the above- mentioned lineages possess a highly similar microsatellite. Furthermore, an analysis of the introns of the Patr-DRB3*01/02 and -DRB*W9 alleles in the CENSOR database showed that intron 1 is similar in length and possesses the same Alu inserts (Kohany et al., 2006). The similarity observed between the Patr-DRB*W9 and -DRB3*01/02 lineages must reflect the common ancestry. Thus, the alleles that were given the Patr-DRB*W9 designations in the past are more likely alleles of a lineage of the Patr-DRB3 locus. For a more consistent nomenclature, we renamed the Patr-DRB*W9 alleles as follows: Patr-DRB*W901 became -DRB3*0701, -DRB*W902 became -DRB3*0702, and -DRB*W903 became -DRB3*0703. The renaming is documented at the IPD-MHC-NHP-database (www.ebi.ac.uk/ipd/mhc/nhp).

Results and discussion

Patr-DRB haplotype definition by microsatellite analysis

In the past, restriction fragment length polymorphism (RFLP) followed by sequencing of the exon 2 segment of the DRB loci and Denaturing Gradient Gel Electrophoresis (DGGE) were used as techniques to describe the Patr-DRB profile of the West African chimpanzee colony, and resulted in the description of six different region configurations (Bontrop et al., 1990; de Groot et al., 2008b; Kenter et al., 1992). The region configurations and haplotypes were firmly established based on segregation analyses. The present analyses, using the D6S2878 marker, showed that all exon 2- positive Patr-DRB genes possess the DRB-STR repeat. In the chimpanzee samples, 6 to 10 DRB-STR amplicons could be detected, which have highly variable lengths ranging from 135 to 226 base pair (bp). Subsequent sequencing of exon 2/DRB-STR alleles made it possible to link unequivocally a microsatellite to a particular exon 2. This approach resulted in a more accurate definition of Patr-DRB haplotypes (Table 1), and for the P.t.v. colony seven different region configurations can now be distinguished (Fig. 1A). The analyses of the P.t.t. and P.t.s. animals resulted in the detection of two additional region configurations (Fig. 1B), each composed of an exclusive combination of Patr-DRB genes: the combination of DRB-STR alleles seems to be unique for a given haplotype. Additionally, some DRB-STR alleles are highly predictive for the presence of a particular DRB allele. For example, the 157 fragment is observed in combination with Patr-DRB1*0701, the 155 fragment is observed in combination with Patr-DRB6*0305, and the 135 fragment segregates in combination with Patr-DRB7*0101 (Table 1). There are also a few haplotypes in which the microsatellite displays length differences for a particular Patr-DRB allele: for instance, the DRB1*0201-linked DRB-STR of haplotype Ia (Table 1A). These slight length differences originate from different founder haplotypes, as was confirmed by segregation analysis.

Figure 1
A) DRB region configurations in the P.t.v. subspecies. The haplotypes are arranged based on DRB1 locus lineages; therefore, haplotype VII is situated between haplotype II and III. B) Additional DRB region configurations detected in the P.t.t. and P.t.s. ...
Table 1
Patr-DRB haplotypes defined by DRB-STR genotyping and exon 2 sequencing for the P.t.v. subspecies (A) and P.t.t. (B) and P.t.s. subspecies (C)

In humans, five DRB region configurations are recognised and all display an abundant amount of allelic variation for the DRB1 locus. Another situation is detected in rhesus and cynomolgus macaques. The latter species possess a high number of region configurations that display hardly any allelic variation within a given configuration (de Groot et al., 2008a; Doxiadis et al., 2007). The present data demonstrate that chimpanzees show a moderate amount of allelic variation within certain - but not all nine - described region configurations (Table 1). In general, the situation involving chimpanzees seems to resemble more closely the one found for the HLA-DRB region configurations. The human and chimpanzee region configurations contain similar DRB genes, illustrating that these genes must have been present in a common ancestor. For instance, region configuration IV is completely identical between humans and chimpanzees, indicating that it was present in a common ancestor and inherited ‘untouched’ during primate evolution. The stability of this region configuration may be due to an antisense integration of a retroviral insert within the DRB7 pseudogene (Doxiadis et al., 2008a). Moreover, all p.t.v. region configurations are found to contain a DRB1 gene, which is comparable to humans. In the p.t.t. and p.t.s. animals analysed region configuration IX was found to lack a DRB1 gene, but most likely the prominent task of the HLA-DRB1 gene was taken over by one of the other genes on this region configuration. Chimpanzee region configuration I shows the highest degree of polymorphism and this is mostly due to the allelic variation within the Patr-DRB5*03 lineage. Haplotype Ii is only observed in one animal, and contains an allele of the Patr-DRB3*01 lineage, whereas all the other haplotypes of region configuration I possess an allele of the Patr-DRB3*02 lineage (Table 1A). Nevertheless, a similar haplotype is present in the chimpanzee genome database (contig NM_01236523), thus confirming the existence of haplotype Ii. Another lineage that possesses several alleles is the Patr-DRB1*03 lineage. It is the most polymorphic lineage, and distinct alleles are present on three different region configurations in the p.t.v. population studied (Table 1A). A similar observation has been made with regard to the Patr-DRB3 locus, which is present on several different region configurations and shows lineage and allelic polymorphism. The different Patr-DRB alleles were analysed phylogenetically together with HLA-DRB alleles from a Caucasoid population (Fig. 2A). The results equal the earlier published phylogenetic analysis on DRB exon 2 sequences (Kenter et al., 1992), and demonstrate that chimpanzee and human alleles of identical lineages/loci cluster tightly together. In addition, the composition of the corresponding microsatellites is shown. The DRB-STR is a composite microsatellite, and the comparison of different DRB sequences of several primate species indicated that the ancient structure of the microsatellite most likely must have been (GT)x(GA)y (Bergstrom et al., 1999; Doxiadis et al., 2007; Kriener et al., 2000; Riess et al., 1990). Thus far, most DRB gene-associated microsatellites encountered are constructed of four sections: namely, a (GT)x, a (GA)z-mix, a (GA)y, and a (GC)n part. The 5′ (GT)x repeat represents the longest segment, is mostly uninterrupted by other nucleotides, and is therefore known to evolve rapidly. For example, the HLA-DRB5*010101 allele can be detected with different DRB-STR lengths, (GT)18–24 (Fig. 2B). This illustrates that the repeat itself evolves faster, due to a higher mutation rate, than the adjacent exon 2 sequence. Interruption of a repeat by other nucleotides usually results in more stablility. This is, for instance, evidenced by the Patr-DRB5 alleles, which all have a highly similar (GT)x part that is interrupted by a GA (Fig. 2B). The (GA)z-mix part is mostly shorter and interrupted by other dinucleotides, and appears to correlate with the different DRB lineages (Fig. 2B). Identical/similar color codes highlight that within particular lineages the relevant microsatellite is quite similar between humans and chimpanzees (Fig. 2B). Thus, not only the exon 2 sequences but also the DRB-STR alleles appear to reflect the common ancestry of DRB lineages. The (GA)y part often correlates with lineages as well, although this is less prominent. The (GC)n part forms the 3′ end of the repeat. The Patr-DRB1*1001 allele was found not to cluster together with its human equivalent, and both the HLA- and Patr-DRB1*1001 alleles appear to possess a different microsatellite (Fig. 2). These observations suggest that the HLA- and Patr-DRB1*1001 alleles belong to different lineages, and therefore the Patr-DRB1*1001 allele is currently under investigation to unravel its evolutionary history. The presence of two different Patr-DRB6 loci on one chromosome is unique for haplotype VII (Table 1A). The compositions of the microsatellites of the loci vary (Fig. 2B); indicating that most likely the haplotype arose via recombination rather then via duplication of one of the DRB6 genes.

Figure 2
A) Rooted phylogenetic comparison of the exon 2 sequences of DRB alleles detected in chimpanzees (Patr, blue) and humans (HLA, red). The common marmoset allele Caja-DRB*W1601 is taken as an outgroup (Doxiadis et al., 2006). Relevant bootstrap values are ...

As compared to Patr-DRB typing strategies used earlier, the DRB-STR typing protocol appears to be an accurate and speedy method. The present analysis illustrates that next to humans and old world monkeys (de Groot et al., 2008a; Doxiadis et al., 2007), great ape species can also be haplotyped with the D6S2878 microsatellite marker. With the DRB-STR protocol it is possible to haplotype several different kinds of species for the Mhc-DRB region; hence, this microsatellite may find its application in pedigree analysis and can be used for conservation biology and breeding management in zoos.

Full-length cDNA analysis of Patr-DRB alleles

To determine which Patr-DRB alleles are transcribed, a panel of cell lines of different animals was selected that covered most of the known haplotypes (Table 1A/B). All Patr-DRB1 and -DRB5 alleles present on the different haplotypes were found to produce bona fide transcripts. For the Patr-DRB3 locus, we detected transcripts for the -DRB3*0102, -DRB3*0103, -DRB3*0201, -DRB3*0214, and -DRB3*07 alleles. For the Patr-DRB3*0208 and -DRB3*0209 alleles, no transcripts were observed. The Patr-DRB3*0309 is observed only on one haplotype and for only one animal a cell-line was available to analyse this allele. Thus, there is a possibility that due to primer inconsistencies the allele was not amplified, and therefore this allele needs further investigation. The Patr-DRB3*0208 allele appears to be a pseudogene, as sequencing analysis on genomic DNA resulted in the detection of a premature stopcodon in exon 3 (Doxiadis et al., 2008b). No transcripts were detected for the Patr-DRB4*0104 and -DRB7*0101 alleles, present on region configuration IVa/b (Table 1A/B). Patr-DRB4*0104 was deemed to represent a non-functional allele because of the presence of a premature stopcodon at the end of exon 2, whereas the -DRB7*0101 allele is considered to be a pseudogene because of the presence of deletions and a premature stopcodon (Doxiadis et al., 2008a; Kenter et al., 1992). However, the Patr-DRB4*0201 allele, representing the other lineage within the Patr-DRB4 locus, produces a transcript. Previously, it was described that this allele most likely arose from a recombination event between a Patr-DRB4*01 allele and an unknown donor allele (Kenter et al., 1992). The data indeed illustrate that the composition of the DRB-STR is different between the alleles of the HLA- and Patr-DRB4*01 and Patr-DRB4*02 lineages (Fig. 2B). The comparison of the full-length sequences of the HLA-DRB4*0101 and Patr-DRB4*0201 alleles shows that the sequences diverged, and only a small motif in exon 2 characteristic for the DRB4 locus is shared between the alleles. These observations suggest a hybrid character for the Patr-DRB4*0201 allele, and therefore currently the introns of this allele are sequenced to unravel its evolutionary history. Moreover, with the primer set used, no full-length transcripts are observed for the DRB6 locus. This is expected, as this locus lacks its exon 1 and is therefore considered to be a pseudogene (Kenter et al., 1992; Mayer et al., 1993). Taken together, the present communication increases the number of known full-length Patr-DRB sequences from 3 to 32. The full-length sequences of the Patr-DRB1*0201, -DRB3*0201, and -DRB5*0301 alleles are identical to the earlier published sequences W1, C4-2, and B3-5, respectively (Fan et al., 1989).

The Patr-DRB5*0313 allele (present on haplotype Ij) detected in one of the p.t.t. animals is very similar to Patr-DRB5*0306 (present on haplotype Ib and IIc). Although, at position 13 in exon 2 of the Patr-DRB5*0313 allele, the triplet TGT coding for a cysteine is substituted by CAT, which encodes for a histidine. A histidine is rare at this position and is only observed in alleles of the HLA-DRB1*04 and Patr-DRB4*01 lineages (Fig. 3). However, chimpanzees are known to lack the equivalent of the HLA-DRB1*04 lineage, and Patr-DRB4*01 seems to represent a non-functional lineage. As such, the substitution of the cysteine by a histidine in the Patr-DRB5*0313 allele suggests the rescue of a residue, most probably by recombination, originating from a different functional chimpanzee lineage.

Figure 3
Deduced protein alignment of the beginning of exon 2 of a representative allele of the HLA-DRB1*04 lineage and representative alleles of the different Patr-DRB lineages. The HLA-DRB1*010101 is taken as consensus from the IMGT/HLA database (www.ebi.ac.uk/imgt/hla ...

In humans, only haplotypes with one or two transcribed DRB alleles are known (Robinson et al., 2003). Most chimpanzee haplotypes of the P.t.v. subspecies possess two transcribed DRB alleles. Only haplotype IVa contains one, whereas haplotypes Ia, Ie, Ii, and IIa to IIc contain three DRB alleles that are potentially translated into a polypeptide (Table 1A). The analysed animals of the P.t.t. subspecies possess haplotypes with one (r.c. IVb) or two (r.c. IIIe, VIIIa, and IXa) transcribed DRB allele(s) (Table 1B). In comparison, rhesus macaques, which possess haplotypes with up to six different Mamu-DRB genes, are known to transcribe one to three DRB genes/alleles (de Groot et al., 2004). In humans, the presence of only one transcribed DRB gene per haplotype (HLA-DR1 and -DR8 serotypes) does not seem to have any disadvantage, as HLA-DR1 and DR8 homozygous individuals are not rare and appear to be healthy (Marsh, 2000; Robinson et al., 2003). Nonetheless, the transcription of three DRB alleles per haplotype is most probably the limit, as more DRB transcripts per haplotype have not yet been reported. This assumption seems to be plausible if one envisages that the expression of too many MHC class II molecules would result in a high number of T cells that would be deleted during thymic education. As a consequence, such individuals would possess a reduced T-cell repertoire and therefore may become susceptible to infectious diseases.

The complete cDNA sequences of the analysed Patr-DRB alleles and particular HLA-DRB alleles were subjected to phylogenetic analysis (Fig. 4). The analysis confirms the results of the exon 2 phylogenetic comparison (Fig. 2A and (Kenter et al., 1992)), and illustrates that for most of the full-length HLA- and Patr-DRB genes a transspecies mode of evolution is observed (von Salome et al., 2007). Even if intron sequences of both species are compared, the footprint of a transspecies mode of evolution is retained. This is, however, different from the situation observed in rhesus macaques. The Mamu-DRB exon 2 sequences represent old entities that predate primate speciation, whereas these exons are embedded in genes that appear to represent relatively young entities (Doxiadis et al., 2008b). The full-length sequence of Patr-DRB3*0103 appears to cluster with Patr-DRB3*0201 (Fig. 4). This is different from what observed in the exon 2 phylogenetic comparison (Fig. 2A), and indicates that also in chimpanzees exon 2 shuffling in the Patr-DRB genes may appear. This seems to be, however, a rare event.

Figure 4
Rooted phylogenetic comparison of the full-length chimpanzee (Patr, blue) cDNA sequences. Particular HLA-DRB alleles (red) extracted from the IMGT/HLA-database were included (Robinson et al., 2003), the sequences of HLA-DRB1*110201 and -DRB1*030201 were ...

Chimpanzee DRB alleles and their potential contribution to resistance to AIDS

Analysis of the MHC region revealed that chimpanzees experienced a selective sweep affecting mainly the Mhc class I repertoire. This selective sweep may have been caused by a HIV-1/SIVcpz-like retrovirus (de Groot et al., 2002). In addition to Mhc class I, other parts within the Mhc region also show signs of a repertoire reduction, such as the major histocompatibility chain-related gene (MIC), located centromeric of the Mhc-B locus (de Groot et al., 2005; Kulski et al., 2002). Comparative genomics showed that the strongest repertoire reduction maps to the chimpanzee Mhc class I region. However, different parts in the Mhc class II region show signs of a repertoire reduction as well (de Groot et al., 2008b).

A recent study performed in a cohort of Kenyan sex workers reported that particular HLA-DRB alleles are associated with resistance or susceptibility to HIV-1 mediated disease (Lacap et al., 2008). We compared these alleles with the Patr-DRB alleles present in our cohort. Equivalents of the HLA-DRB1*070101, -DRB1*1503, and -DRB5*010101, associated with susceptibility, can be found in chimpanzees (Fig. 4). For the HLA-DRB1*010101 and 010201 alleles, associated with resistance, no apparent equivalents are detected in chimpanzees. The HLA-DRB1*1102 allele, associated with resistance, seem to cluster phylogenetically together with alleles of the Patr-DRB1*03 lineage. However, the HLA-DRB1*030201 allele, associated with susceptibility, seems to cluster as well with the Patr-DRB1*03 lineage. This suggests that it is difficult to define a contribution of the Patr-DRB lineages in HIV-1/SIVcpz infection based on phylogenetic comparisons of sequences. Indeed, in humans it has recently been shown that each of the nine antigens of the HLA-B44 supertype possess unique peptide binding motifs (Hillen et al., 2008). This observation, together with the knowledge that the peptide binding affinity of a MHC class II molecule is less stringent than the binding affinity of a MHC class I molecule, corroborates the notion that caution must be exercised in drawing conclusions based only on the similarity observed in phylogenetic comparisons (Hammer et al., 1993; Rammensee et al., 1993). With the availability of the full-length cDNAs of different Patr-DRB alleles, we are now able to construct single antigen-expressing cell lines and study in detail the function and the MHC/peptide interaction of the Patr-DRB molecules.

Nevertheless, the human study indicated that the DRB-specific CD4+ T-cell responses are an important factor in resistance/susceptibility to HIV-1 infection (Lacap et al., 2008). For chimpanzees, it is known that they maintain CD4+ T-cell responses after HIV-1/SIVcpz infection. Comparing the HLA- and Patr-DRB region, it is obvious that both species have a slightly different number of region configurations, but the region configurations possess identical DRB genes. Humans on the one hand seem to have acquired a large amount of allelic variation within the different DRB region configurations, whereas chimpanzees on the other hand, although known to be an older species, show only limited allelic variation. Additionally, chimpanzees lack the equivalent of the HLA-DRB1*04 lineage. These observations support that the chimpanzee MHC class II region may have experienced a reduction in the repertoire as well. The contemporary MHC class II alleles were most likely positively selected due to genetic linkage to the MHC class I alleles that survived the selective sweep. The presently available repertoire of Patr-DRB alleles seems to contribute efficiently to the maintenance of the CD4+ T-cell responses, and therefore chimpanzees seem to have successful combinations of CD4+/CD8+ T-cell responses that are able to cope with pathogens of their natural habitat and with HIV-1/SIVcpz infection.

Acknowledgments

The authors wish to thank D. Devine for editing the manuscript, H. van Westbroek for preparing the figures, and Drs F. Claas and I. Doxiadis for providing the human DNA samples. This study was supported in part by NIH/NIAID contract number HHSN266200400088C and 5R24RR016038-05.

Footnotes

Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

References

  • Andersson G, Larhammar D, Widmark E, Servenius B, Peterson PA, Rask L. Class II genes of the human major histocompatibility complex. Organization and evolutionary relationship of the DR beta genes. J Biol Chem. 1987;262:8748–58. [PubMed]
  • Bak EJ, Ishii Y, Omatsu T, Kyuwa S, Tetsuya T, Hayasaka I, Yoshikawa Y. Identification and analysis of MHC class II DRB1 (Patr-DRB1) alleles in chimpanzees. Tissue Antigens. 2006;67:134–42. [PubMed]
  • Balla-Jhagjhoorsingh SS, Koopman G, Mooij P, Haaksma TG, Teeuwsen VJ, Bontrop RE, Heeney JL. Conserved CTL epitopes shared between HIV-infected human long-term survivors and chimpanzees. J Immunol. 1999;162:2308–14. [PubMed]
  • Balla-Jhagjhoorsingh SS, Verschoor EJ, de Groot N, Teeuwsen VJ, Bontrop RE, Heeney JL. Specific nature of cellular immune responses elicited by chimpanzees against HIV-1. Hum Immunol. 2003;64:681–8. [PubMed]
  • Bergstrom TF, Engkvist H, Erlandsson R, Josefsson A, Mack SJ, Erlich HA, Gyllensten U. Tracing the origin of HLA-DRB1 alleles by microsatellite polymorphism. Am J Hum Genet. 1999;64:1709–18. [PubMed]
  • Bontrop RE, Broos LA, Pham K, Bakas RM, Otting N, Jonker M. The chimpanzee major histocompatibility complex class II DR subregion contains an unexpectedly high number of beta-chain genes. Immunogenetics. 1990;32:272–80. [PubMed]
  • Bontrop RE, Otting N, de Groot NG, Doxiadis GG. Major histocompatibility complex class II polymorphisms in primates. Immunol Rev. 1999;167:339–50. [PubMed]
  • Bontrop RE, Otting N, Slierendregt BL, Lanchbury JS. Evolution of major histocompatibility complex polymorphisms and T-cell receptor diversity in primates. Immunol Rev. 1995;143:33–62. [PubMed]
  • Bottius E, BenMohamed L, Brahimi K, Gras H, Lepers JP, Raharimalala L, Aikawa M, Meis J, Slierendregt B, Tartar A, Thomas A, Druilhe P. A novel Plasmodium falciparum sporozoite and liver stage antigen (SALSA) defines major B, T helper, and CTL epitopes. J Immunol. 1996;156:2874–84. [PubMed]
  • de Groot N, Doxiadis GG, De Groot NG, Otting N, Heijmans C, Rouweler AJ, Bontrop RE. Genetic makeup of the DR region in rhesus macaques: gene content, transcripts, and pseudogenes. J Immunol. 2004;172:6152–7. [PubMed]
  • de Groot N, Doxiadis GG, de Vos-Rouweler AJ, de Groot NG, Verschoor EJ, Bontrop RE. Comparative genetics of a highly divergent DRB microsatellite in different macaque species. Immunogenetics. 2008a;60:737–48. [PMC free article] [PubMed]
  • de Groot NG, Garcia CA, Verschoor EJ, Doxiadis GG, Marsh SG, Otting N, Bontrop RE. Reduced MIC gene repertoire variation in West African chimpanzees as compared to humans. Mol Biol Evol. 2005;22:1375–85. [PubMed]
  • de Groot NG, Heijmans CM, de Groot N, Otting N, de Vos-Rouweller AJ, Remarque EJ, Bonhomme M, Doxiadis GG, Crouau-Roy B, Bontrop RE. Pinpointing a selective sweep to the chimpanzee MHC class I region by comparative genomics. Mol Ecol. 2008b;17:2074–88. [PubMed]
  • de Groot NG, Otting N, Arguello R, Watkins DI, Doxiadis GG, Madrigal JA, Bontrop RE. Major histocompatibility complex class I diversity in a West African chimpanzee population: implications for HIV research. Immunogenetics. 2000;51:398–409. [PubMed]
  • de Groot NG, Otting N, Doxiadis GG, Balla-Jhagjhoorsingh SS, Heeney JL, van Rood JJ, Gagneux P, Bontrop RE. Evidence for an ancient selective sweep in the MHC class I gene repertoire of chimpanzees. Proc Natl Acad Sci U S A. 2002;99:11748–53. [PubMed]
  • Doxiadis GG, de Groot N, Bontrop RE. Impact of endogenous intronic retroviruses on major histocompatibility complex class II diversity and stability. J Virol. 2008a;82:6667–77. [PMC free article] [PubMed]
  • Doxiadis GG, de Groot N, Claas FH, Doxiadis II, van Rood JJ, Bontrop RE. A highly divergent microsatellite facilitating fast and accurate DRB haplotyping in humans and rhesus macaques. Proc Natl Acad Sci U S A. 2007;104:8907–12. [PubMed]
  • Doxiadis GG, de Groot N, de Groot NG, Doxiadis II, Bontrop RE. Reshuffling of ancient peptide binding motifs between HLA-DRB multigene family members: old wine served in new skins. Mol Immunol. 2008b;45:2743–51. [PubMed]
  • Doxiadis GG, van der Wiel MK, Brok HP, de Groot NG, Otting N, t Hart BA, van Rood JJ, Bontrop RE. Reactivation by exon shuffling of a conserved HLA-DR3-like pseudogene segment in a New World primate species. Proc Natl Acad Sci U S A. 2006;103:5864–8. [PubMed]
  • Ellis SA, Bontrop RE, Antczak DF, Ballingall K, Davies CJ, Kaufman J, Kennedy LJ, Robinson J, Smith DM, Stear MJ, Stet RJ, Waller MJ, Walter L, Marsh SG. ISAG/IUIS-VIC Comparative MHC Nomenclature Committee report, 2005. Immunogenetics. 2006;57:953–8. [PubMed]
  • Epplen C, Santos EJ, Guerreiro JF, van Helden P, Epplen JT. Coding versus intron variability: extremely polymorphic HLA-DRB1 exons are flanked by specific composite microsatellites, even in distant populations. Hum Genet. 1997;99:399–406. [PubMed]
  • Erickson AL, Houghton M, Choo QL, Weiner AJ, Ralston R, Muchmore E, Walker CM. Hepatitis C virus-specific CTL responses in the liver of chimpanzees with acute and chronic hepatitis C. J Immunol. 1993;151:4189–99. [PubMed]
  • Fan WM, Kasahara M, Gutknecht J, Klein D, Mayer WE, Jonker M, Klein J. Shared class II MHC polymorphisms between humans and chimpanzees. Hum Immunol. 1989;26:107–21. [PubMed]
  • Fujiyama A, Watanabe H, Toyoda A, Taylor TD, Itoh T, Tsai SF, Park HS, Yaspo ML, Lehrach H, Chen Z, Fu G, Saitou N, Osoegawa K, de Jong PJ, Suto Y, Hattori M, Sakaki Y. Construction and analysis of a human-chimpanzee comparative clone map. Science. 2002;295:131–4. [PubMed]
  • Gonder MK, Oates JF, Disotell TR, Forstner MR, Morales JC, Melnick DJ. A new west African chimpanzee subspecies? Nature. 1997;388:337. [PubMed]
  • Goulder PJ, Watkins DI. Impact of MHC class I diversity on immune control of immunodeficiency virus replication. Nat Rev Immunol. 2008;8:619–30. [PMC free article] [PubMed]
  • Hammer J, Valsasnini P, Tolba K, Bolin D, Higelin J, Takacs B, Sinigaglia F. Promiscuous and allele-specific anchors in HLA-DR-binding peptides. Cell. 1993;74:197–203. [PubMed]
  • Heeney JL, Rutjens E, Verschoor EJ, Niphuis H, ten Haaft P, Rouse S, McClure H, Balla-Jhagjhoorsingh S, Bogers W, Salas M, Cobb K, Kestens L, Davis D, van der Groen G, Courgnaud V, Peeters M, Murthy KK. Transmission of simian immunodeficiency virus SIVcpz and the evolution of infection in the presence and absence of concurrent human immunodeficiency virus type 1 infection in chimpanzees. J Virol. 2006;80:7208–18. [PMC free article] [PubMed]
  • Hillen N, Mester G, Lemmel C, Weinzierl AO, Muller M, Wernet D, Hennenlotter J, Stenzl A, Rammensee HG, Stevanovic S. Essential differences in ligand presentation and T cell epitope recognition among HLA molecules of the HLA-B44 supertype. Eur J Immunol. 2008;38:2993–3003. [PubMed]
  • Keele BF, Jones JH, Terio KA, Estes JD, Rudicell RS, Wilson ML, Li Y, Learn GH, Beasley TM, Schumacher-Stankey J, Wroblewski E, Mosser A, Raphael J, Kamenya S, Lonsdorf EV, Travis DA, Mlengeya T, Kinsel MJ, Else JG, Silvestri G, Goodall J, Sharp PM, Shaw GM, Pusey AE, Hahn BH. Increased mortality and AIDS-like immunopathology in wild chimpanzees infected with SIVcpz. Nature. 2009;460:515–9. [PMC free article] [PubMed]
  • Kenter M, Otting N, Anholts J, Jonker M, Schipper R, Bontrop RE. Mhc-DRB diversity of the chimpanzee (Pan troglodytes) Immunogenetics. 1992;37:1–11. [PubMed]
  • Klein J, Bontrop RE, Dawkins RL, Erlich HA, Gyllensten UB, Heise ER, Jones PP, Parham P, Wakeland EK, Watkins DI. Nomenclature for the major histocompatibility complexes of different species: a proposal. Immunogenetics. 1990;31:217–9. [PubMed]
  • Kohany O, Gentles AJ, Hankus L, Jurka J. Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics. 2006;7:474. [PMC free article] [PubMed]
  • Kriener K, O’HUigin C, Tichy H, Klein J. Convergent evolution of major histocompatibility complex molecules in humans and New World monkeys. Immunogenetics. 2000;51:169–78. [PubMed]
  • Kulski JK, Shiina T, Anzai T, Kohara S, Inoko H. Comparative genomic analysis of the MHC: the evolution of class I duplication blocks, diversity and complexity from shark to man. Immunol Rev. 2002;190:95–122. [PubMed]
  • Lacap PA, Huntington JD, Luo M, Nagelkerke NJ, Bielawny T, Kimani J, Wachihi C, Ngugi EN, Plummer FA. Associations of human leukocyte antigen DRB with resistance or susceptibility to HIV-1 infection in the Pumwani Sex Worker Cohort. Aids. 2008;22:1029–38. [PubMed]
  • Lekutis C, Letvin NL. Biochemical and molecular characterization of rhesus monkey major histocompatibility complex class II DR. Hum Immunol. 1995;43:72–80. [PubMed]
  • Marsh SG, Albert ED, Bodmer WF, Bontrop RE, Dupont B, Erlich HA, Geraghty DE, Hansen JA, Hurley CK, Mach B, Mayr WR, Parham P, Petersdorf EW, Sasazuki T, Schreuder GM, Strominger JL, Svejgaard A, Terasaki PI, Trowsdale J. Nomenclature for Factors of the HLA System, 2004. Hum Immunol. 2005;66:571–636. [PubMed]
  • Marsh SG, Parham P, Barber LD. The HLA FactsBook. Academic Press; London, UK: 2000.
  • Mayer WE, O’HUigin C, Klein J. Resolution of the HLA-DRB6 puzzle: a case of grafting a de novo-generated exon on an existing gene. Proc Natl Acad Sci U S A. 1993;90:10720–4. [PubMed]
  • Morin PA, Moore JJ, Chakraborty R, Jin L, Goodall J, Woodruff DS. Kin selection, social structure, gene flow, and the evolution of chimpanzees. Science. 1994;265:1193–201. [PubMed]
  • Novembre FJ, Saucier M, Anderson DC, Klumpp SA, O’Neil SP, Brown CR, 2nd, Hart CE, Guenthner PC, Swenson RB, McClure HM. Development of AIDS in a chimpanzee infected with human immunodeficiency virus type 1. J Virol. 1997;71:4086–91. [PMC free article] [PubMed]
  • Rammensee HG, Falk K, Rotzschke O. MHC molecules as peptide receptors. Curr Opin Immunol. 1993;5:35–44. [PubMed]
  • Riess O, Kammerbauer C, Roewer L, Steimle V, Andreas A, Albert E, Nagai T, Epplen JT. Hypervariability of intronic simple (gt)n(ga)m repeats in HLA-DRB genes. Immunogenetics. 1990;32:110–6. [PubMed]
  • Robinson J, Waller MJ, Parham P, de Groot N, Bontrop R, Kennedy LJ, Stoehr P, Marsh SG. IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex. Nucleic Acids Res. 2003;31:311–4. [PMC free article] [PubMed]
  • Swofford D. PAUP*: Phylogenetic Analysis Using Parsimony (*and other methods) Sinauer Associates; Sunderland, MA: 2002. Version 4.
  • von Salome J, Gyllensten U, Bergstrom TF. Full-length sequence analysis of the HLA-DRB1 locus suggests a recent origin of alleles. Immunogenetics. 2007;59:261–71. [PubMed]
  • Williams MA, Holmes BJ, Sun JC, Bevan MJ. Developing and maintaining protective CD8+ memory T cells. Immunol Rev. 2006;211:146–53. [PubMed]