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*
Basel Institute for Immunology, Basel, Switzerland; and
Centre de Recherche d’Immunologie et d’Hématologie, Strasbourg, France
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Abstract |
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 Top Abstract IntroductionMaterials and MethodsResultsDiscussionReferences |
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2-glycoprotein, subversion of NK
cytolytic activity by the CMV UL18 gene product, and, finally, crucial
involvement in iron homeostasis of the HFE gene. A recently described
member of this family is the MHC class-I related (MR1) gene. The most
notable feature of MR1 is undoubtedly its relatively high degree of
sequence similarity to the MHC-encoded classical class I genes. The
human chromosome 1q25.3 MR1 locus gives rise not only to the originally
reported 1,263-bp cDNA clone encoding a putative 341-amino acid
polypeptide chain, but to many additional transcripts in various
tissues as well. Here we define the molecular identity of all human and
murine MR1 isoforms generated through a complex scenario of alternative
splicing, some encoding secretory variants lacking the Ig-like 3
domain. Moreover, we show ubiquitous transcription of these MR1
variants in several major cell lineages. We additionally report the
complete 18,769-bp genomic structure of the MR1 locus, localize the
murine orthologue to a syntenic segment of chromosome 1, and provide
evidence for conservation of a single-copy MR1 gene throughout
mammalian evolution. The 90% sequence identity between the human and
mouse MR1 putative ligand binding domains together with the ubiquitous
expression of this gene favor broad immunobiologic
relevance. |
Introduction |
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TopAbstractIntroductionMaterials and MethodsResultsDiscussionReferences |
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ß of
CD8+ T lymphocytes (1). They are highly polymorphic,
ubiquitously expressed, membrane-bound heterodimers formed by
noncovalent association of a 45-kDa heavy chain and the 12-kDa
ß2m (2). The heavy chain is encoded by a small number of
genes, i.e., HLA-A, -B, and -C in man and H2-K, -D, and -L in mouse,
located within the MHC on human chromosome 6p21.3 and murine chromosome
17 (3, 4). The MHC of various species contains, in addition to these
well-defined classical MHC-I (also known as MHC-Ia), a rather diverse
collection of so-called nonclassical genes (also referred to as
MHC-Ib), including HLA-E (5), HLA-F (6), and HLA-G (7) in man and the
H2-Q, -T, and -M loci in mice (8, 9, 10). These show a restricted pattern
of tissue expression, are not polymorphic, and have not been shown to
consistently interact with a defined T cell population. A long-standing
body of work has, however, implicated some of these MHC-Ib genes in
unique immunologic functions. These include presentation of
N-formulated peptides (of bacterial or mitochondrial origin)
by H2-M3 (11) and leader sequence peptides by HLA-E (12) and Qa-1 (13);
presence (and therefore probable function) at the maternal-fetal
interface for HLA-G (14) and in the mucosa for some TL molecules (15);
existence as both glycosylphosphatidylinositol-anchored and soluble
versions capable of binding a diverse peptidic array for Qa-2 (16);
and, finally, restriction of several 
T cell clones for
H2-T10b (17) and H2-T22b (18). Despite these
apparently special features, the high degree of sequence similarity
between the MHC-Ia and -Ib molecules defines them as members of the
same gene lineage, derived from a common ancestor through gene
duplication and minimal diversification, late in speciation.
The past decade has clearly shown that beside this first lineage
of MHC-I genes, vertebrate genomes harbor a growing number of highly
divergent MHC-I-like structures (19). The prototype of this category of
molecules is undoubtedly CD1 (20). Initially recognized through
serologic analysis, further work characterized CD1 as a
ß2m-associated MHC-I-like chain (21, 22). There are five
CD1 isotypes (CD1A–E) on human chromosome 1q21–23 (23) and two CD1
genes (CD1.1 and CD1.2) on murine chromosome 3 (24). Despite featuring
an extracellular tri-domain structure (1–3) like typical MHC-I
molecules, CD1 is at crossroads between MHC-I and -II at the level of
both amino acid composition and function. The molecule is equally
homologous to MHC-I and -II, exhibits a tissue-specific pattern of
expression, and engages Ag through an endocytic pathway as does MHC-II
(20). However, in sharp contrast to peptide presenting MHC-I and -II,
CD1 molecules have an unusually hydrophobic ligand binding groove (25)
and seem to specialize in presentation of lipidic/glycolipidic moieties
of bacterial origin to TCR-ß and -
CD4-CD8- T cells (20). The neonatal Fc
receptor (FcRn) is the second well-characterized member of
non-MHC-I-like structures. The human chromosome 19q13.3 (murine
chromosome 7) FCGRT gene encodes a highly divergent 48-kDa heavy chain
bound to ß2m at the gut epithelial brush border where it
acts as a transepithelial shuttle delivering maternal IgG from the
intestinal lumen into the bloodstream, providing passive neonatal
immunity (26, 27). The Zn2gp (AZGP1) is another MHC-I
like structure. A soluble single-chain 41-kDa molecule of as yet
unknown function, Zn2gp was first purified from plasma,
although it is more prevalent in exocrine secretions, especially those
of the mammary gland. The gene has been mapped to human chromosome
7q22.1 and mouse chromosome 5 (28, 29, 30). Highly divergent MHC-I genes
are not all encoded outside the MHC; in particular, a novel highly
divergent multigene class I family termed MIC (MHC class I chain
related) is located within the MHC class I region (31). The MICA gene
in this family is unusually polymorphic (32) (compared with mono-,
oligomorphic MHC-Ib genes) and encodes a highly glycosylated
single-chain, membrane-bound protein almost exclusively expressed in
epithelia (33). HFE is yet another example of a drastically divergent
MHC-I gene, adjacent to the MHC itself (approximately 4 megabases
telomeric to HLA-F) (34). Surprisingly, the murine HFE orthologue does
not map to the H2 complex, but is located within a paralogous locus on
chromosome 13 (35, 36). A typical class I gene by domain structure, HFE
displays only 30% overall homology to typical MHC-I molecules, but
requires dimerization with ß2m before surface expression
(37). Nevertheless the role of an MHC-I molecule in iron homeostasis
remains a complete mystery and exemplifies yet another fascinating
aspect of MHC-Ib biology. The complete sequencing of three viral
genomes, i.e., human and mouse CMV and Molluscum contagiosum
virus, has revealed the existence of a distinct MHC-I gene within each
of them (38, 39, 40). The significance and possible function of these
molecules are not yet understood, although the CMV-encoded UL18
molecule has been shown to bind endogenously derived peptides and
interact with NK cell receptors (41, 42).
In summary, a restricted collection of diverse, yet structurally related, MHC-I genes located on various chromosomes perform highly disparate, yet essential, functions. The latest addition to the group of non-MHC-encoded class I genes is the human MHC class I-related (MR1) gene (43). Discovered by degenerate PCR, MR1 was subsequently mapped to human chromosome 1q25.3. Northern blotting experiments using a number of human tissues revealed ubiquitous expression of multiple MR1 transcripts; a cDNA clone of 1263 bp encoding a putative polypeptide of 341-amino acid sequence (calculated Mr of 39 kDa) resembling an authentic MHC-I was originally reported (43). Perhaps the most interesting feature of MR1 is that despite being located outside the MHC, the molecule shows the highest degree of homology to the classical MHC-I molecules (43). This opens the possibility of analogous function for MR1 and raises enticing questions as to the scenario of genome-wide MHC-I dispersion.
Here we present the cDNA sequences of all human and murine MR1 isoforms and show evidence for their uniform expression in various cell lineages and tissues. Moreover, we define the genomic structure of MR1, localize the gene by fluorescence in situ hybridization (FISH) in the mouse genome, and study the extent of phylogenetic conservation of this molecule.
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Materials and Methods |
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TopAbstractIntroductionMaterials and MethodsResultsDiscussionReferences |
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A full-length human MR1 cDNA clone was obtained by RT-PCR using oligonucleotides derived from published sequence (43) and human intestinal total RNA (Clontech, Palo Alto, CA) as template, employing standard procedures (44, 45). The oligonucleotides used were as follow: RT, 5'-TGACTCTATGGGGGACAGAG-3'; and PCR, 5'-GGACTATGGGGGAACTGATG-3' and 3'-CTAACGTCTAGGGAGAAAAGG-5'. The full-length cDNA clone of 1.3 kb was subsequently used as a probe to sequentially screen approximately 106 phage clones of the following cDNA libraries: human fetal spleen and murine (C57/BL6) spleen (Stratagene, San Diego, CA). This led to isolation of several cDNA clones from each species, which were subsequently analyzed by sequence determination. The full-length human MR1 cDNA probe was also used to screen approximately 6 x 105 phage clones of the 129/SvJ mouse genomic library (Stratagene). This yielded the isolation of several genomic clones that were subsequently characterized by blot hybridization of restriction-mapped fragments (isolation of the bacteriophage P1 containing the MR1 gene is detailed below). Cross-species screenings were conducted as follows. In brief, overnight hybridization was performed at 42°C in a solution containing 50% formamide, 5x Denhart’s solution, 5x SSPE, 0.1% SDS, and 100 µg/ml of denatured salmon sperm DNA (Sigma, St. Louis, MO). The nitrocellulose filters were subsequently treated in a final wash solution containing 2x SSC/0.1% SDS at 45°C. High stringency screening of the human cDNA library with an isogenic probe was performed using standard conditions (44, 45).
The 18,769-bp full-length MR1 gene sequence was assembled as follows.
Almost 13 kb was derived from the available 
clones (directly or
after subcloning); the remaining 5' 6 kb encoding exon 1 and a large
part of intron 1 were obtained employing the following pair of
oligonucleotides, 5'-GGTTGATGATGCTCCTGTTACC-3' (derived from leader
peptide sequence of murine cDNAs) and 3'-CGGCAATTCTCGGTCAGAGAAC-5'
(pan-ultimate sequence within by then available DNA), in a PCR
reaction using the Expand Long Template kit (Boehringer Mannheim,
Mannheim, Germany) and P1 DNA as template following the manufacturer’s
recommendations (see below for P1 isolation). Finally, upstream
sequence from exon 1 was obtained using the Human GenomeWalker kit
(Clontech) following the manufacturer’s recommendations and employing
the following exon 1-located nested oligonucleotides:
3'-GTAACACAATTACCACTTCGTGTCGCTA-5' and
3'-CTTGACTACCGCAAGGACAATGGAGAGT-5'. Double-strand sequencing of
cloned DNA fragments (plasmid, , or P1) was performed using flanking
vector sites and custom-synthesized oligonucleotides (primer walking).
The chain termination method was conducted using either the Thermo
Sequenase cycle sequencing kit (Amersham, Aylesbury, U.K.) and
[35S]dATPS (Amersham, UK) or the ABI PRISM Dye
Terminator Cycle Sequencing Ready Reaction kit with AmpliTaq DNA
polymerase, FS (Perkin-Elmer, Foster City, CA) according to the
manufacturer’s protocol. In the latter technique, the reactions were
run on an ABI 373XL DNA Sequencer STRETCH (Perkin-Elmer-Applied
Biosystems, Foster City, CA), and the results were analyzed using ABI
PRISM Sequencing Analysis, Factura, and Sequence Navigator software
(all from Perkin-Elmer-Applied Biosystems). Further sequence analysis
employed the EditSeq and MegAlign (default parameters) programs of the
LaserGene Navigator (DNAstar, Madison, WI).
RNA blots
All cell lines were purchased from American Type Culture
Collection (Manassas, VA) and grown in the recommended medium at 37°C
in an atmosphere supplemented with 5% CO2. Total RNA was
isolated from approximately 107 cells after lysis in a
solution containing 4.0 M guanidinium thiocyanate, 0.1 M Tris (pH 7.5),
and 1% ß-ME, followed by ultracentrifugation (33,000 rpm, 16 h)
on a cushion of 5.7 M CsCl/0.01 M EDTA (pH 7.5). Twenty micrograms of
total RNA was subjected to electrophoresis on a 1%
agarose/formaldehyde gel (44, 45). Upon transfer onto Zeta-Probe GT
(Bio-Rad, Richmond, CA), the membrane was hybridized to a randomly
[-32P]dCTP-labeled MR1 cDNA probe
(Ready · To · Go DNA Labelling Kit, Pharmacia, Uppsala, Sweden)
in a solution containing 10% dextran sulfate, 1.5x SSPE, and 0.5%
SDS overnight at 65°C. The membrane was subsequently washed at 65°C
in a solution containing 0.2x SSC/0.1% SDS. The wet membrane was
exposed for 4 days at -80°C to X-OMAT AR film (Eastman Kodak,
Rochester, NY) opposing an intensifying screen. The mouse
poly(A)+ multiple tissue Northern blot was purchased from
Clontech and hybridized to a full-length murine MR1 cDNA probe under
stringent conditions according to the manufacturer’s specifications.
The blot was subsequently exposed for 72 h to an intensifying
screen at -70°C. The loading control probe consisted in both cases
of a 2-kb human ß-actin cDNA fragment (Clontech) and required 2
h of exposure at room temperature.
Zoo blots
Eight micrograms of various high m.w. genomic DNA were digested with HindIII (HindIII/BglII for mouse DNA) and analyzed by standard Southern blotting employing the full-length human MR1 cDNA as a probe. DNA from the following species were used in this study: human (a gift from Dr. A. Meyer, Strasbourg, France); primates: bonobo (Pan paniscus), gorilla (Gorilla gorilla), and gibbon (Hylobates lar; all provided by Dr. M. Chorney, Hershey, PA); dog, bovine, porcine, rat (all purchased from Clontech); and finally DBA/2-C57/BL6 F1 mouse (Basel Institute for Immunology animal facility, Basel, Switzerland). Hybridization and low stringency wash of the blot were performed as described above. The membrane was subsequently exposed for 1 wk to Kodak X-OMAT AR films opposing an intensifying screen.
Bacteriophage P1 cloning and FISH
The following two oligonucleotides, 5'-CAGACCTGTGTGGTGGTGTC-3' and 3'-CTAATACACCGAGTGTAGTG-5', amplifying a unique 275-bp genomic fragment within exon 3 of the murine MR1 gene, were used to PCR screen a 129/SvJ mouse embryonic stem cell genomic P1 library (Genome Systems, St. Louis, MO) following published protocols (45, 46, 47). This yielded isolation of two P1 clones. The identity of one of these was ascertained through amplification and sequence analysis employing the same primer pair mentioned above. This clone, called F298, was subsequently used to FISH-localize the MR1 locus (Genome Systems, St. Louis, MO). In brief, DNA from clone F298 was labeled with digoxigenin dUTP by nick translation. Labeled probe was combined with sheared mouse DNA and hybridized to normal metaphase chromosomes derived from mouse embryo fibroblast cells in a solution containing 50% formamide, 10% dextran sulfate, and 2x SSC. Specific hybridization signals were detected by incubating the hybridized slides in fluoresceinated antidigoxigenin Abs followed by counterstaining with 4',6-diamidino-2- phenylindole, dihydrochloride. The initial experiment resulted in specific labeling of the distal portion of the largest chromosome pair. A second experiment was conducted in which a probe specific for the centromeric region of chromosome 1 was cohybridized with clone F298. This experiment resulted in the specific labeling of the centromere and the distal portion of chromosome 1. Measurements of 10 specifically hybridized chromosomes 1 demonstrated that F298 is located at a position that is 75% of the distance from the heterochromatic-euchromatic boundary to the telomere of chromosome 1, an area that corresponds to band 1G1–2. A total of 80 metaphase cells were analyzed, with 76 exhibiting specific labeling.
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Results |
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TopAbstractIntroductionMaterials and MethodsResultsDiscussionReferences |
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To define the genomic structure of MR1, a PCR-cloned human cDNA
encompassing the entire coding sequence was used to isolate orthologous
genomic clones from a murine bacteriophage library. However,
because of the lack of the entire transcriptional unit within the
obtained clones, a murine bacteriophage P1 library (average insert
size, 90–100 kb) was PCR-screened employing MR1-specific primers.
Double-stranded sequence analysis identified MR1 within 18,769 bp of
mouse genomic DNA (Figs. 1
and
2; GenBank accession no.
AF035672). The structure of the gene is that of a typical MHC-I gene,
with respective 1, 2, and 3 extracellular domains, and
transmembrane and cytoplasmic sequences encoded by separate exons.
Particularities include an unusually large first intron of 8,857 bp. As
in other MHC-I and -II genes, each domain starts with a composite codon
where the first nucleotide is contributed by the previous exon (type I
splicing) (44) and is flanked by intronic sequences harboring the
canonical GT/AG splice junctions. Finally, sequence analysis of 1384 bp
putative promoter sequence of human MR1 gene did not reveal any obvious
similarity to other MHC-I promoters (see GenBank accession no.
AF039526).
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A). To map the gene
within the mouse genome, a bacteriophage P1 clone was used to
FISH-localize a single MR1 locus within bands G1–2 of mouse chromosome
1, syntenic to human 1q25.3,5
the location of the orthologous locus (Fig. 3B).
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A).
Finally, to ascertain a similar situation in the mouse, a
multiple tissue Northern blot revealed, as predicted, a broad range of
expression for the murine gene, once again present in multiple isoforms
(Fig. 4B).
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, 6, and
7). In humans, we identified one
RT-PCR-cloned transcript identical with the original 1263-bp cDNA clone
reported by Hashimoto and colleagues (43), hereafter called hMR1A, as
well as three other cDNA species, respectively designated hMR1B, hMR1C,
and hMR1D (Figs 5 and 6). Interestingly, all newly described
transcripts lack the Ig-like 3 domain. Moreover, the 1578-bp hMR1C
transcript bears a stop codon a few amino acids after the end of the
2 domain and therefore encodes a putative soluble isoform, whereas
the 776-bp hMR1B and the 2046-bp hMR1D remain putative integral
transmembrane proteins (Figs. 5 and 6). In the mouse, six distinct cDNA
species were delineated (Fig. 7). The mMR1A cDNA of 2406 bp encodes a
bonafide MHC-I molecule organized similar to the human orthologue.
However, due to the presence of a cryptic splice donor site 77 bp
inside the 1 domain and through a scheme best described as partial
exon skipping, several transcripts containing aborted open reading
frames were generated through splicing of this initial exon 2 fragment
directly to the beginning of exon 3. These include the mMR1B, -C, -E,
and -F of 2130, 1641, 1115, and 2854 bp, respectively. The mMR1D is a
3219-bp truncated, partially spliced transcript carrying part of intron
3 (Figs. 5 and 7). Finally, the extensive length heterogeneity observed
among both human and murine MR1 transcripts is due to the respective
sizes of their 3' untranslated regions, a fact readily visible on
Northern blot experiments (see above).
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1,
90%; 2, 89%; and 3, 73%; see Figs. 8 and 9). The same
comparison including representatives of other MHC-I molecules reveals,
as expected, conservation of almost all so-called invariant residues,
mostly thought to maintain the class I scaffold (48, 49). Moreover,
this analysis defines at least three novel pan-MHC-I conserved amino
acids (underlined hereafter). These residues are P20, G26, V28, D29,
S38, P47, W51, W60, E/D61, T64, and the N86XS glycosylation site within
the 1 domain; G91, H93, Q96, M98, G100, C101, G112, Y118, D119,
G120, W133, C164, L168, R170, L172,
and G175 throughout the 2 domain (Fig. 8); and P185, C203, F208, Y209, P210,
P235, D238, C259, V261, and H263 in the Ig-like 3 domain.
Among the eight residues defined by high resolution crystallographic
analysis to contact peptide termini in MHC-Ia molecules (50), only
three are conserved in MR1, i.e., Y7, T143, and W147 (Figs. 8 and 9). Finally, homologous residues to
positions 223 to 229, 245, and 247 of the MHC-Ia 3 domain,
indispensable for interaction with the CD8 coreceptor and present in
both human and mouse MHC-encoded class I molecules (51, 52) (with the
exception of MICA/B genes), are clearly absent from human and mouse MR1
(Fig. 8).
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Discussion |
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TopAbstractIntroductionMaterials and MethodsResultsDiscussionReferences |
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1)/62(2)% for CD1, 59/74%
for Zn2gp, 69/66% for FcRn, and 78/76% for HFE, or in
the MHC-encoded class Ia and Ib molecules, which have average
human-mouse similarities of 69/70% and 51/41%, respectively (Fig. 9
).
This outstanding degree of trans-species sequence identity in MR1
should naturally include preservation of key structural/functional
residues. Keeping this in mind, examination of such positions reveals
interesting information. As previously noted, most if not all
structural residues conserved across all vertebrate MHC-I molecules are
also maintained in MR1, predicting folding of the putative MR1
polypeptide chain in an analogous three-dimensional configuration.
Moreover, the N86XS glycosylation site present in all human and mouse
MHC-Ia and -Ib, HFE, and human Zn2gp, but absent from
all CD1 isotypes as well as from MICA/MICB molecules, is present in
both human and murine MR1 (Fig. 8). However, the absence of over half
the residues interacting with peptide termini from the MR1 1-2
domains as well as all CD8 binding residues from the Ig-like 3
domain favors a functional digression from the peptide binding,
CD8+ ß T cell-interacting classical class I molecules
(Fig. 8).
The genomic organization of MHC class I genes parallels their
multidomain polypeptide chain configuration. Indeed, each extracellular
domain is encoded by a separate exon, preceded by the leader sequence
and followed by transmembrane, cytoplasmic, and 3'-untranslated
sequences (one or more depending on the locus; Fig. 1) (44).
Examination of the large number of genomic structures available
reveals, with the exception of CD1, a clear dichotomy between the
structurally homogeneous HLA-A-G genes (mouse H2-K, L, D, Q, T, and M)
and those encoding the divergent (both functionally and structurally)
MICA/B, HFE, FcRn, Zn2gp, and MR1 molecules; this is
regardless of their physical location in the genome, i.e., whether they
are located within the MHC proper (Fig. 1). Indeed, the former group
averages a total gene length of 3 to 5 kb, whereas the latter easily
exceeds 6 kb, with 6.8 kb for HFE, 10 kb for Zn2gp, 11
kb for FcRn, 12 kb for MICA/B, and close to 19 kb for the MR1 gene
reported here (Fig. 1). With the exception of FcRn, where this is due
to a lengthy fourth intron (between exons 3 and 4), the extra length is
due to an unusually large first intron preceding the 1 domain,
reaching a peak stretch of 8857 bp in MR1 (Fig. 2). Whether this
unusual length has any functional repercussions, possibly at the
transcriptional level, remains to be seen. Finally, it is noteworthy
that large MHC-I genes are not exclusive to mammals, as, for instance,
several carp genes have been documented with first introns up to 14 kb
(54).
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). In man, the
apparent over-representation of transcripts lacking the Ig-like 3
domain may have functional relevance, although this can only be
verified once specific Abs to various extracellular domains are
available.
MHC-I genes constitute diverse multigenic families in various
vertebrate species (58, 59, 60). On the other hand, non-MHCencoded
class I genes are, in general, more simply arranged, although the human
Zn2gp locus contains a pseudogene in addition to the
functional locus (28), and the CD1 loci are present in various
configurations in different species (20). Within this context, both the
low complexity of genomic bands seen in our zoo blot experiments and
especially observation of single hybridization spots in both human and
mouse FISH favor the existence of a single MR1 locus throughout
mammalian evolution, in clear contrast therefore to most MHC-encoded
and to some non-MHC-I-encoded genes. Given the strong sequence
conservation between such phylogenetically distant species as
Homo sapiens and Mus musculus, these data are
largely in favor of strong selective pressure maintaining MR1
structure. Finally, the location of MR1 on human chromosome 1 might not
be fortuitous, as the relative proximity of the CD1 locus is
intriguing. Indeed, capitalizing on theories first forwarded by Ohno,
who proposed creation of the present day vertebrate genomes via
tetraploidization (61), a process recently verified through sequence
analysis of the complete yeast genome (62), Kasahara and colleagues
identified another MHC-like gene cluster outside chromosome 6 in man
and chromosome 17 in mouse (9q33–34 in man and chromosome 2 in mouse)
harboring elements resembling those found in the MHC itself, e.g.,
ATP-binding cassette transporters (such as the MHC-encoded TAP
molecules), proteasome Z subunit (such as MHC-encoded LMP2 and -7),
Grp78 stress protein (such as the MHC-encoded 70-kDa heat shock protein
genes), complement C5 gene (such as the MHC-encoded C2/Bf/C4
molecules), etc. (63). Through similar observations, this time
regarding several nonimmune genes (NOTCH and PBX), Katsanis and
co-workers added the long arm of chromosome 1 as yet an additional
paralogous locus (64). However, the true MHC signature, i.e., MHC-I and
-II genes, has not been found or noted on either 9q34 or 1q. In this
light, the relatively close proximity of human CD1 and MR1 loci might
parallel for the first time the human 6p21.3 (mouse 17) MHC-II/I
topology and therefore define an authentic MHC paralogous locus. In
this respect, it is interesting to note that through many
functional/structural aspects (see above) CD1 is more closely related
to MHC-II than to MHC-I. Given these facts, CD1 could be considered the
chromosome 1-encoded MHC-II paralogue and MR1 an authentic MHC-I
equivalent. Moreover, several other key genes chart this genomic
segment and therefore contribute to its emergence as yet another MHC
paralogous locus. These are 1) the retinoid X receptor located
between MR1 and CD1; interestingly, the two other RXRs genes are
located, respectively, in the MHC (retinoid X receptor ß) and
chromosome 9q34 (retinoid X receptor ) (65); 2) the recently mapped
proteasome ß subunit PSMB4 to 1q21 (66), in comparison to other ß
subunits encoded within 9q34 for Z (PSMB7) (63) and the MHC for LMP2/7
(PSMB9/8) (3); 3) the 1q25-q32-located tenascin-R gene (67) paralogous
to MHC-encoded tenascin-X molecule (3); and 4) the so-called regulator
of the complement activation (RCA) gene cluster comprising complement
receptors type 1 and 2, decay-accelerating factor, and C4 binding
protein, closely linked on 1q32 (65); reminiscent perhaps of a somewhat
similar organization within the MHC, where the complement genes C2, BF,
and C4 are sandwiched between MHC-I and -II loci (3) and 9q34, the
location of yet another complement subunit, C5 (65). Finally, a close
inspection of the other loci neighboring MR1 and CD1 reveals the
existence of an unusually large number of immune-related loci.
These are IL6RA, Ly9, CD48, CD3z, CD64, LYAM1, ELAM1, OX40L,
IL10, CD34, CRP, and a constellation of Fc receptors, i.e., FCGR1A,
FCER1A, FCER1G, FCGR, and FCGR3A and -B (65).
The relatively high and truly ubiquitous transcription of MR1 is unique
among the so-called nonclassical MHC-I genes (Fig. 4). Human CD1a, -b,
and -c, for instance, are mainly expressed on cortical thymocytes and
Langerhans cells, whereas both human and mouse CD1d seem to be mainly
transcribed in intestinal epithelial cells (20). The expression pattern
of neonatal FcRn is selective to the intestinal brush border and
placental syncytiotrophoblast (26). Zn2gp is highly
prevalent in breast fluids (28), and HFE expression appears to be
confined to the gut (36). Even among the MHC-encoded nonclassical genes
and with the exception of human HLA-E (5), there is an evident degree
of compartmentalization, e.g., epithelia for MICA/B (31), trophoblasts
for HLA-G (14), intestine or thymocytes for most TL genes (15), and so
on. Within this context the wide cellular expression of MR1 is clearly
reminiscent of ubiquitous classical MHC-I molecules and is therefore in
favor of a general physiologic function.
MHC-Ia molecules show an extraordinary degree of polymorphism, with
more than 300 alleles collectively defined for human HLA-A/B/C genes
(2). In clear contrast, MHC-Ib genes, with the important exception of
the MIC loci (32), are not polymorphic, a situation that has led some
authors to postulate their presentation of invariant ligands (68), for
instance glycolipidic moieties by CD1 molecules to CD4, CD8
double-negative ß, or T lymphocytes (20). Following this
rationale, the apparent monomorphism of MR1 favors possible interaction
with a putative invariant ligand.
In summary, MR1 is a broadly expressed, phylogenetically conserved, invariant class I molecule located within an MHC-paralogous locus. Although at this point any suggestions regarding MR1 function within the immune system are highly speculative, possible interaction with a growing family of orphan leukocyte Ig superfamily receptors, whose founding members interact with a diverse set of MHC-I molecules, warrants further investigation (69).
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Acknowledgments |
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Footnotes |
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2 The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession numbers AF010446 (hMR1B), AF010447 (hMR1C), AF031469 (hMR1D), AF010448 (mMR1A), AF010449 (mMR1B), AF010450 (mMR1C), AF010451 (mMR1D), AF010452 (mMR1E), AF010453 (mMR1F), AF039526 (hMR1 putative promoter sequence), and AF035672 (mouse MR1 gene).
3 Address correspondence and reprint requests to Dr. Seiamak Bahram, Centre de Recherche d’Immunologie et d’Hématologie, 4 Rue Kirschleger, 67085 Strasbourg, France. E-mail address:
4 Abbreviations used in this paper: MHC-I, MHC class I gene or protein; MHC-II, MHC class II gene or protein; FcRn, neonatal Fc receptor; MIC, MHC class I chain related; MR1, MHC class I related; FISH, fluorescence in situ hybridization.
5 A higher degree of resolution was achieved via blastn search of GenBank STS database using human MR1 cDNA clones as probes. This analysis revealed a complete match with STS_U22963 (locus G26705) positioned at 838.4 cR from the top of the chromosome 1 linkage group.
Received for publication January 30, 1998. Accepted for publication June 8, 1998.
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