Nucleotide sequence of a rat class I cDNA clone

Polymorphism of thePaGene

PROBLEM

This study was undertaken to identify the number of alleles of the Pa gene at the DNA level and to correlate the presence of the different alleles with the ability of a strain to elicit an anti-Pa antibody response when mated with a WF female. The Pa gene is present in both Pa+ and Pa- strains of rats, but it has unique restriction fragment length polymorphisms (RFLP) in the two types of strains: 1.7 kb in Pa- and 1.8 kb in Pa+XbaI digests using a probe derived from the Pa gene.

RESULTS

Examination of DNA from a variety of strains using different enzymes showed that there were characteristic RFLP patterns for Pa+ and Pa- strains. Strains of the b haplotype, however, had an intermediate RFLP pattern, and all of these strains had a relatively low level of reactivity with anti-Pa antibody.

CONCLUSIONS

Thus, there are three alleles of the Pa gene based on their level of expression: Paa, high; Pab, low; and Pa-, none.

Characterisation of RT1-E2, a multigenic family of highly conserved rat non-classical MHC class I molecules initially identified in cells from immunoprivileged sites

BACKGROUND

So-called "immunoprivileged sites" are tissues or organs where slow allograft rejection correlates with low levels of expression of MHC class I molecules. Whilst classical class I molecules are recognised by cytotoxic T lymphocytes (CTL), some MHC class I molecules are called "non-classical" because they exhibit low polymorphism and are not widely expressed. These last years, several studies have shown that these can play different, more specialised roles than their classical counterparts. In the course of efforts to characterise MHC class I expression in rat cells obtained from immunoprivileged sites such as the central nervous system or the placenta, a new family of non-classical MHC class I molecules, which we have named RT1-E2, has been uncovered.

RESULTS

Members of the RT1-E2 family are all highly homologous to one another, and the number of RT1-E2 loci varies from one to four per MHC haplotype among the six rat strains studied so far, with some loci predicted to give rise to soluble molecules. The RT1n MHC haplotype (found in BN rats) carries a single RT1-E2 locus, which lies in the RT1-C/E region of the MHC and displays the typical exon-intron organisation and promoter features seen in other rat MHC class I genes. We present evidence that: i) RT1-E2 molecules can be detected at the surface of transfected mouse L cells and simian COS-7 cells, albeit at low levels; ii) their transport to the cell surface is dependent on a functional TAP transporter. In L cells, their transport is also hindered by protease inhibitors, brefeldin A and monensin.

CONCLUSIONS

These findings suggest that RT1-E2 molecules probably associate with ligands of peptidic nature. The high homology between the RT1-E2 molecules isolated from divergent rat MHC haplotypes is particularly striking at the level of their extra-cellular portions. Compared to other class I molecules, this suggests that RT1-E2 molecules may associate with well defined sets of ligands. Several characteristics point to a certain similarity to the mouse H2-Qa2 and human HLA-G molecules.

Physical mapping of the E/C and grc regions of the rat major histocompatibility complex

Alignment of class I-hybridizing cosmids from an R21 (AlBlDlEugrc+) genomic DNA library gave two contigs: one [150 kilobases (kb)] encompassed the E/C region, or a large part thereof, and the other (110 kb) contained the grc region which has genes influencing resistance to chemical carcinogens (rcc), fertility (ft), and growth (dw-3). Amplification of gene sequences in the four cosmids in the E/C region using Eu-specific and LW2 (RT1.C)-specific primers showed that each cosmid contained both Eu-like and C-like genes. They are clearly different but closely associated, and they show some variation from the prototypic E (Eu) and C (LW2) genes, respectively. Comparison of DNA from grc+ and grc- strains of rats showed that the deletion in the grc- strains was approximately 50 kb, and that it was located on two of the three cosmids in the grc-region contig. The use of specific class I probes showed that the grc region contained tandemly duplicated RT1.O-RT1.N genes and that the RT.BM1 loci lay outside of the grc region. Neither contig reacted with probes specific for class II, TNFA, Hsp70, or RT1.M genes. The data presented here and the previous data in the literature (summarized in Gill et al. 1995) suggest that the gene order in the major histocompatibility complex (MHC) and MHC-linked region of the rat is: A-E/C-grc-M.

Nucleotide sequence and structural analysis of the rat RT1.Eu and RT1.Aw3l genes, and of genes related to RT1.O and RT1.C

A cDNA library was constructed using mRNA isolated from the R21 strain of rats which have the major histocompatibility complex (MHC) haplotype RT1.AlBlDlEu and the growth and reproduction complex (grc) genotype grc+. The cDNA clones that hybridized with the class I probes pAG64c and pARI.5 and were 1.3-1.7 kilobases were selected. Full-length clones were identified by sequencing partially the 5' and 3' ends of each clone, by the presence of a start codon at the 5' end, and by a polyadenylation sequence at the 3' end. The full-length cDNA clones were examined for in vitro transcription by transfection into human CIR cells using electroporation, and expression was detected by flow cytometry using monoclonal antibodies specific to the heavy chains and polyclonal antibody to beta 2-microglobulin. The RT1.Eu gene was transcribed and expressed optimally, and its nucleotide and deduced amino acid sequences differed significantly from the RT1.Aa, RT1.A(l), RT.Au, LW2, and 11/3R genes but only slightly from the RT1.K gene. The high level of sequence similarity between RT1.Eu and RT1.K suggests that the two genes may have originated from a common ancestral gene. In addition, three new genes (RT1.Aw3l, RT1.C-type, and RT1.O-type) were identified. The RT1.Aw3l gene is almost identical to RT1.A(l) with the exception of an in frame deletion of 21 nucleotides in exon 2 leading to a 7 amino acid deletion in the alpha 1 domain of the deduced amino acid sequence and 11 nucleotide substitutions and insertions in the rest of the sequence. It transcribed optimally, but no significant expression was detected. The RT1.C-type gene 119 is very similar (97%) to the LW2 gene in the 3' untranslated region, which suggests that it is in the RT1.C region. It transcribed optimally, but no significant expression was detected. The RT1.O-type gene 149 has all the features of a class Ib gene, but a premature stop codon in the alpha 1 domain causes incomplete translation. Its in vitro transcription was very low, and no expression was detected. These studies, combined with previous work, indicate that in the MHC of the R21 strain three class Ia genes (Eu, A(l), Aw3l) and three class Ib genes (C-type, O-type, N) are transcribed but only two class Ia genes (Eu, A(l)) are expressed.

Genomic structure and organization of a Q-like gene in the GRC-G/C region of the rat

In the rat homologue of the mouse Q/TL region, grc-G/C, a TL-like gene (RT1.N) has been identified recently. This paper reports on a Q-like gene, designated RT1.0, that maps in the same region. It contains a 5' untranslated region (UT), signal peptide, alpha 3 domain, transmembrane region, cytoplasmic domain (three exons) and 3'UT region. Comparison with mouse class-I genes shows that the greatest similarity is to the H-2Q, K, D and L genes; it is very different from the TL genes of the mouse and rat. A sequence that includes many CT repeats occurs in the 3'UT region of RT1.0 and in three to five other class I-hybridizing fragments. Thus, the MHC-linked region of the rat contains both Q-like and TL-like class-I genes.

Heterogeneity of HLA-G genes identified by polymerase chain reaction/single strand conformational polymorphism (PCR/SSCP)

A genomic HLA-G clone named 7.0E was isolated from a Japanese placenta. The deduced amino acid sequence of the 7.0E was identical to two HLA-G genomic clones and two cDNA clones previously described. The DNA sequences of alpha 1 and alpha 2 domains of the HLA-G gene from 5 cell lines also encoded the same amino acids. However, a 14 bp insertion, ATTTGTTCATGCCT, was present in the 3' untranslated region of 7.0E compared with the originally described HLA-G clone (HLA 6.0). Polymerase chain reaction (PCR)/single strand conformational polymorphism (SSCP) analysis of exon 8 allowed the HLA-G gene to be classified into two alternative types, G6.0 and 7.0 E, those correlated to the absence or the presence of the 14 bp stretch. Each group had minor sequence variant(s), and the alleles of the 7.0E-type were more heterogeneous than those of the G6.0-type. The 14 bp deletion is present only in the G6.0-type of HLA-G alleles among HLA class I genes. Thus it was suggested that G6.0 alleles were generated after diversification of the HLA-G.

Characterization of a class Ib gene of the rat major histocompatibility complex

The cDNA and a partial genomic sequence of a rat class I major histocompatibility (RT1) gene, 11/3R, is reported here. The sequence contains several unique amino acid residues at certain positions, mutations in exon 7 (which is not expressed), a mutation of the canonical exon 8 stop codon to a sense codon, and includes a long 3' untranslated region (utr). The structure of exon 7 differs from that found in most rat class I genes and resembles exon 7 of most H-2K,D,L,Q genes. Parts of the 3' noncoding region are homologous to the RT1.A-4 and certain H-2 genes. Expression is detectable by northern blot analysis in mitogen-stimulated lymphocytes only, by polymerase chain reaction (PCR) in each tissue tested. After transfection into L cells 11/3R can be shown to be expressible at the cell surface. Probes derived from the 3' noncoding part crosshybridize with a number of restriction fragments which map to the RT1.C region, thus defining a subfamily of RT1.C region genes. Several members of this subfamily are deleted in the lm1 RT1 mutant. The 11/3R gene presents typical features of a class Ib gene. Aspects of evolution and the potential function of the gene are discussed.

Genomic DNA sequence and organization of a TL-like gene in the grc-G/C region of the rat

Genes in the grc-G/C region, which is linked to the rat major histocompatibility complex, influence the control of growth, development, and susceptibility to chemical carcinogens. As an initial approach to analyzing the structure and organization of these genes, a class I hybridizing fragment designated RT(5.8) was isolated from an R21 genomic DNA library and sequenced from overlapping restriction enzyme fragments. The RT(5.8) clone has 5788 base pairs and contains the eight exons characteristic of a class I gene. There are CAAT and TATA boxes upstream of the signal peptide, and the recognition sequence that precedes the site of polyadenylation is located downstream from the third cytoplasmic domain. Comparison of the RT(5.8) gene with representative class I genes from the rat and other species shows that the nucleotide sequences of RT(5.8) have a high level of similarity to those of TL region genes of several strains of mice. The peptide sequence deduced from the RT(5.8) clone is distinct from all previously published class I gene sequences, and at many positions there are amino acid residues that are unique to the RT(5.8) sequence. Probes have been isolated from the third exon and from the 5' and 3' flanking regions of the RT(5.8) clone, and Southern blot analysis with genomic DNA of various rat strains shows that these probes are specific for the RT(5.8) fragment. Northern blot analysis shows that the gene is transcribed in the thymus but not in the liver or spleen. The RT(5.8) sequence is more similar to some mouse TL genes (especially in the alpha 2 and cytoplasmic domains and in the 5' and 3' untranslated regions) than it is to other rat class I genes. Hence, TL-like genes are not restricted to the mouse.

Analysis of the expression and immunostimulatory capacity of class I major histocompatibility antigens on rat trophoblast cell lines

In rat strains expressing the a and other major histocompatibility complex (MHC) haplotypes, subpopulations of placental trophoblast cells synthesize the nonclassical class I Pa antigen in preference to the classical RT1.Aa antigen. In this study, a rat trophoblast cell line, R8RP.3, which was derived from midgestation placentas of PVG.R8 (RT1.Aa) rats, was shown to express class I antigens similarly to those of trophoblast cells in situ. Both unstimulated and IFN-gamma-exposed metabolically labeled R8RP.3 cells synthesized more Pa than RT1.Aa antigen. The reverse was true for labeled spleen cells from PVG.R8 rats. The R8RP.3 cells failed to stimulate allogeneic lymphocyte proliferation even when high levels of both classical and nonclassical class I MHC antigens were expressed on their membranes after incubation with IFN-gamma. These experiments thus supply the first evidence that the inductive phase of the immune response is not promoted by trophoblast cell class I MHC antigens, which could explain the failure of mothers to mount immune responses to class I MHC positive trophoblast cells.

Evolution of the major histocompatibility complex: molecular cloning of major histocompatibility complex class I from the amphibian Xenopus

Class I major histocompatibility complex (MHC) cDNA clones have been isolated from an expression library derived from mRNA of an MHC homozygous Xenopus laevis. The nucleotide and predicted amino acid sequences show definite similarity to MHC class I molecules of higher vertebrates. The immunoglobulin-like alpha-3 domain is more similar to the immunoglobulin-like domains of mammalian class II beta chains than to those of mammalian class I molecules, and a tree based on nucleotide sequences of representative MHC genes is presented.

Expression and analysis of the rat placental class I cDNA clone encoding the Pa antigen

The previously sequenced cDNA clone pARI.5 was recloned into the mammalian expression vector pcEXV3, and transient and permanent transfectants were prepared in COS7 green monkey kidney fibroblasts. The transfectants were analyzed by indirect immunofluorescence using monoclonal and polyclonal antibodies raised in specifically selected rat strain combinations. These studies showed that pARI.5 encodes the Pa antigen and that the Pa molecule is distinct from the Aa molecule. Probes were derived from the pARI.5 clone and used to study the genomic DNA from Pa-positive and Pa-negative strains. Two probes derived from the 3' untranslated region (3'apARI.5 and 3'bpARI.5) and one probe derived from the 5' region (5'pARI.5) hybridized nonspecifically in all strains under moderate stringency conditions. By contrast, an Xba I restriction fragment unique to the Pa gene was detected with the 5'pARI.5 probe under high stringency conditions. This probe hybridized with a 1.8 kilobase (kb) fragment in the Pa-positive strains and with a 1.7 kb band in the Pa-negative strains. These studies suggest that the gene encoding the Pa antigen, or a fragment thereof, is present in both Pa-positive and Pa-negative strains but may not be expressed in the latter.

Concerted evolution of class I genes in the major histocompatibility complex of murine rodents

Full-length cDNA sequences of two class I major histocompatibility complex molecules from the DA strain of Rattus norvegicus are reported. One codes for the classical class I restriction element RT1.Aa, which maps to the locus in the rat major histocompatibility complex homologous to H-2K in the mouse. The other probably codes for a soluble nonclassical class I molecule present in DA rat serum; a short deletion in the fifth exon implies that the translated product will terminate in the membrane-spanning region. These sequences have been compared with mouse classical class I sequences as well as with three published rat class I cDNA partial sequences. The results show, first, that "locus-specific" substitutions from the H-2K, H-2D, and H-2L data set are scrambled in the RT1.Aa molecule; a majority of these substitutions have H-2D/L-specific features. Second, the data show that the four rat sequences are strikingly similar to one another regardless of locus or haplotype of origin; they share a number of apparently species-specific features that distinguish them all from mouse classical class I sequences, which likewise share distinctive features of their own. The results suggest that segmental sequence exchange plays a major role in determining the evolution of sequence in class I major histocompatibility complex molecules.

Biochemical analysis of the rat MHC class I antigens RT1.Aa, RT1.Fa and Pa

In DA strain rats, there are two other MHC class I loci (Pa and RT1.Fa) in the vicinity of the classical class I locus RT1.Aa. The Pa antigen is the pregnancy-associated antigen, and it was detected by antibodies elicited in WF females pregnant by DA males without any other immunization. The Fa antigen was detected by a monoclonal antibody raised by alloimmunization. In the present work, the Aa, Fa and the Pa antigens have been compared by HPLC peptide mapping and by isoelectric focusing after their isolation by appropriate monoclonal antibodies. All the three antigens are identical in primary structure with respect to lysine, methionine, asparagine and the aromatic amino acid residues, but they differ from one another with respect to glutamic acid and/or aspartic acid residues. The pI values of the antigens differ slightly. All three antigens have two identical N-linked glycans, but the Fa antigen has an additional N-linked glycan. Based on the available amino acid sequence of the Pa antigen, it can be concluded that both Aa and Pa antigens are devoid of glycosylation in the second domain. This lack of glycosylation of the classical antigen Aa is unique for the rat, since classical class I antigens of the mouse show glycosylation in the first and second, and sometimes in the third domain, and those in the human, in the first domain only. The high degree of similarity among the Aa, Fa, and Pa molecules that this study indicates is also unique for the rat, since antigens encoded by different class I genes of the same haplotype are quite disparate in the mouse and human.

Major histocompatibility complex class I antigens expressed on rat trophoblast cells

There is controversy about the size of the major histocompatibility complex antigens of trophoblast cells from placenta. There are some reports that the heavy chains of these molecules are smaller (39-43 kd) than those of the classical class I antigens (45-46 kd), while there are others which show that both the light and the heavy forms of class I antigens occur in the trophoblast cells. In order to investigate this problem, we studied the classical class I antigen (RT1.Aa) and the pregnancy-associated class I antigen (Pa) of the rat from 125I-labeled basal trophoblast cells, isolated from the placenta of WF females pregnant by DA males, using very mild conditions. These antigens were compared with those of the syngeneic (DA x DA) trophoblast cells or paternal (DA) lymphocytes by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Both the Aa and Pa antigens, precipitated from the two trophoblast preparations, showed a heavy chain of 46 kd associated with a 12 kd beta 2-microglobulin component, as did the same molecules precipitated from the lymphocytes. Heavy chains in the range of 39-43 kd could not be detected in any of the samples. The results suggest that the smaller molecular weight heavy chains are methodological artifacts and could arise from loss of a glycan(s) during isolation.

The rat as an experimental animal

The development and characterization of many inbred, congenic, and recombinant strains of rats in recent years has led to the detailed genetic description of this species, especially in regard to its major histocompatibility complex. This information has contributed substantially to the study of comparative genetics and has greatly enhanced the utility of the rat in a variety of areas of biomedical research. This article focuses on the use of the rat in immunogenetics, transplantation, cancer-risk assessment, cardiovascular diseases, and behavior.