Description of a new kind of MHC DNA sequence in Saguinus oedipus (cotton‐top tamarin)
Authors: Alvarez M. , Martínez‐Laso J. , García‐Torre C. , Varela P. , Pérez‐Blas M. , Moreno M. A. , Gómez‐Casado E. , Arnaiz‐Villena A. 
Published: March 2003

The MHC class I genes of the New World primate the cotton‐top tamarin (Saguinus oedipus) are an exception to the high polymorphism and variability usually displayed by this multigene family. In the present work, the cloning and sequencing of a new pseudogene, tentatively named Saoe‐Mhc‐N4, in this primate species are reported. This new sequence has two characteristic deletions at exon 2, making it very unlikely that any putative protein from this sequence was an antigen‐presenting molecule. Comparison of intron 1, intron 2, partial exon1, exon 2 and partial exon 3 showed little similarity with those of classical class I genes and pseudogenes in S. oedipus and in other primates. Phylogenetic analysis grouped this Saoe‐Mhc‐N4 sequence with other pseudogenes in S. oedipus. Thus, it seems that Saoe‐Mhc‐N4 is an inactivated gene or a pseudogene which has been originated by the common process of duplication and subsequent inactivation of MHC class I loci in this primate species.

The major histocompatibility complex (MHC) class I genes encode cell surface glycoproteins that present peptides to cytotoxic T cells. On the basis of the level of expression and polymorphism, MHC class I mammalian genes may be grouped within three different categories: (1) classical class I loci, which are highly polymorphic with products expressed on the surface of all nucleated somatic cells, (2) non‐classical class I loci, which are monomorphic or show very little polymorphism and whose products, of unknown function, have a more limited tissue distribution, and (3) class I pseudogenes which include complete genes whose expression is prevented by frameshift, premature stop codons or other defects and also gene fragments lacking one or more of the exons characteristic of expressed class I genes (Le Bouteiller, 1994).

The MHC class I genes of the New World primate cotton‐top tamarin (S. oedipus) show low polymorphism and the variation among alleles of their three described MHC class I loci is comparable to that seen for alleles at the same locus in human classical class I loci (Cadavid et al., 1996b). Additionally, the expressed MHC class I DNA sequences of cotton‐top tamarins have been shown to be more closely related to the human non‐classical HLA‐G gene (Watkins et al., 1991), and to HLA‐E (Alvarez et al., 1997), than to the human classical HLA‐A, ‐B or ‐C genes. It has been proposed that the unusually limited polymorphism in the cotton top tamarins’ MHC originated because they may come from a small founder population and recently duplicated genes have been fixed and quickly inactivated thereafter. Only three possible functional Saoe class I genes and four pseudogenes have been described so far (Cadavid et al., 1996b).

In the present work, a MHC class I sequencing study in S. oedipus was carried out to define possible new alleles or genes and investigate the nature and evolution of the MHC class I genes in these New World monkeys. A new sequence has been found, Saoe‐Mhc‐N4, which carries two deletions at exon 2 and several stop codons in exons 1 and 3; this suggests that Saoe‐Mhc‐N4 is a new pseudogene.

Genomic DNA from EBV cell lines of three different unrelated S. oedipus individuals (B95, 3F1 and 74E7) was extracted using standard methods (Arnaiz‐Villena et al., 1992). Partial exon 1, intron 1, exon 2, intron 2 and partial exon 3 from this new Saoe‐Mhc nucleotide sequence gene were obtained by polymerase chain reaction (PCR) using SAOEX1 41–60 (5'‐CGAGGGCCCTGGTCCTGAT‐3') and SAOEX3197–215 (5'‐GC C‐ C TCCAGGTAGGCTTC‐3') primers; the first primer corresponds to exon 1 of classical class I genes at base positions 41–60 and the second to exon 3 at base positions 197–215 (Alvarez et al., 1997). PCR amplification fragments had a size of 825 bp. Random sequencing of the amplified products was carried out and the PCR products purified and inserted into the pMOS ‘blue vector’ (Amersham, UK) following the manufacturers’ protocols. Double‐stranded DNA stretches were automatically sequenced in an Applied Biosystems (Foster City, CA) machine as previously described (Arnaiz‐Villena et al., 1992; Castro et al., 1996; Alvarez et al., 1997). A phylogenetic tree based on exon 2 and partial exon 3 was obtained by using the neighbour‐joining method (Saitou & Nei, 1987) and the computer program NJBOOT (kindly provided by Masatoshi Nei, Mol. Evol. Genetics, Pennsylvania, USA). The phylogenetic tree was based on a genetic distance matrix of nucleotide substitutions per site, obtained with the Kimura’s biparametric method. The bootstrap analysis for tree topology (Felsenstein, 1985) was used to evaluate the statistical significance of each internal branch of the tree.

Twenty clones were obtained from each of the following S. oedipus individuals: B95, 74e7 and 3F1, all of which were subsequently sequenced. Three, five and four clones, respectively, were identical and corresponded to a new MHC‐DNA sequence, tentatively named Saoe‐Mhc‐N4. Other sequences obtained were already described (Saoe‐G*02, *04, *06, and *08). This sequence (Fig. 1) has two characteristic deletions at exon 2, the first between codon 14 and the first base in codon 23 (28 bp), and the second one between the second base of codon 66 and codon 71 (17 bp). A putative protein resulting from a hypothetical transcription and translation would not bear part of the β sheet (amino acids 14–22) at the floor of the MHC molecule groove and seven amino acids of the α helix (amino acids 66–71); also, the expected reading frame has three premature stop codons located at position – 2 in exon 1 and positions 101 and 123 in exon 3. However, Saoe‐Mhc‐N4 has an 81‐codon open reading frame, starting at codon 5. The other two possible reading frames show also several premature stop codons. Thus, a theoretical Saoe‐Mhc‐N4 protein, if transcribed and translated, would not be an antigen‐presenting molecule.

A comparison of exon 1, exon 2 and partial exon 3 DNA sequences with those of classical class I genes and pseudogenes in S. oedipus (Fig. 1) and other primates (not shown) showed that this new sequence shows little similarity to any of them.

Introns 1 and 2 of Saoe‐Mhc‐N4 were compared with those of classical and non‐classical human class I genes to study intron sequence similarities (Geraghty et al., 1987; Cereb et al., 1996; Gomez‐Casado et al., 1997), since it has been shown that MHC gene intron‐specific motifs may be conserved for more than 33 million years (Castro et al., 1996). The nature of substitutions present in introns 1 and 2 of Saoe‐Mhc‐N4 are not conserved in any of the compared genes (Fig. 2), showing a specific deletion at intron 2 between positions 208 and 227 absent in all the MHC classical or non‐classical class I genes analysed.

The relationship of Saoe‐Mhc‐N4 exons 2 and 3 with other class I loci was further studied; 36 exon 2 and exon 3 classical and non‐classical class I DNA sequences from different primates were included to construct a relatedness NJ dendrogram (Watkins et al., 1991; Otting & Bontrop, 1993; Watkins et al., 1993; Boyson et al., 1995; Cadavid et al., 1996a,b; Castro et al., 1996; Alvarez et al., 1997) (Fig. 3). The tree showed that the Saoe‐Mhc‐N4 sequence was grouped with Saoe‐PS1 and So‐N1, two pseudogenes already found in S. oedipus; however, this grouping has a low bootstrap value and may not be definitive. Moreover, the branch length leading to Saoe‐Mhc‐N4 is longer (approximately 2‐fold) than that leading to Saoe‐PS1 and So‐N1; this suggests that the nucleotide substitution rate could be faster in Saoe‐Mhc‐N4 than in other pseudogenes found in S. oedipus, or that this pseudogene is older. In summary, Saoe‐Mhc‐N4 seems to be an inactivated gene or a pseudogene, which may be a result of the common process of duplication and subsequent inactivation of MHC class I loci in S. oedipus (Cadavid et al., 1996b) because:

1
Saoe‐Mhc‐N4 is grouped with Saoe‐PS1 and So‐N1, two previously described pseudogenes (Fig. 1), although its mutation rate seems to be much higher (probably due to a longer period of inactivation);

2 it contains deletions that would disrupt the correct folding of a putative MHC molecule;

3 it has several premature stop codons in all possible reading frames;

4 the percentage of G + C at the third codon position was low (82.8%), further suggesting that Saoe‐Mhc‐N4 is an inactivated class I gene or a pseudogene (Hughes & Nei, 1989).