DNA sequence analysis of a rat RT1 class II A beta gene

Sequencing and genetic analysis of a bovine DQB cDNA clone

A BoLA-DQB cDNA clone (BoLA-DQ beta-1) was isolated by screening a bovine lymphoblastoid cDNA library with a HLA-DQB genomic clone. The DNA and predicted protein sequences were compared to class II sequences from cattle and other species. BoLA-DQ beta-1 has 92.0% similarity to the coding regions of two previously sequenced BoLA-DQB genomic clones and 69.6% similarity to a BoLA-DR beta pseudogene. However, the first domain encoded by BoLA-DQ beta-1 has 94 amino acids; one more than the predicted size of the products encoded by two previously sequenced bovine DQB genes (BoDQ beta-Q1 and BoDQ beta-Y1). Comparing all coding regions, BoLA-DQ beta-1 has greater nucleotide similarity to HLA-DQB sequences than to I-A beta, HLA-DRB and I-E beta sequences. Like the HLA-DQB gene product, the cytoplasmic domain of the predicted protein encoded by BoLA-DQ beta-1 is eight amino acids shorter than that of I-A beta, HLA-DRB and I-E beta molecules. Six clone-specific amino acid substitutions were identified in the beta 1 domain of BoLA-DQ beta-1, including an unusual cysteine residue at position 13 which is believed to be positioned on a beta-strand and face into the antigen recognition site. Southern blot analysis of PvuII-digested genomic DNA from a paternal half-sibling family (sire, and six dam-offspring pairs) using BoLA-DQ beta-1 as a probe, revealed five allelic PvuII RFLP patterns, including two patterns not previously described, that cosegregated with serologically-defined BoLA-A (class I) alleles. The evolution, polymorphism and function of a transcriptionally active BoLA-DQB gene can now be readily studied using this DQB cDNA clone as a source of allele and locus-specific oligonucleotide primers.

Partial nucleotide sequence of a bovine major histocompatibility class II DR beta-like gene

A genomic clone containing a bovine DR beta-like gene, BoDR beta II, was isolated from a bovine genomic library and characterized by restriction enzyme mapping and nucleotide sequencing of exon regions. Alignment of this sequence with the human DR beta cDNA sequence allowed identification of exon/intron boundaries. The clone contains a 13.3-kilobase (kb) insert, and includes 1.3 kb 5' of the beta 1 exon and 6.7 kb 3' of the transmembrane (TM) exon. Open reading frames were present in the BoDR beta exons sequenced. Nucleotide identities of the bovine beta 1, beta 2 and TM exons with the corresponding human DR beta exons were 73, 91 and 83%, respectively. Nucleotide identities of these exons with those of a previously described bovine DR beta-like pseudogene, BoDR beta I, were 69, 95 and 81%, respectively. Although a limited amount of sequence data was obtained for the intron regions, a 71% identity was found within a 514-nucleotide region immediately 3' to the beta 2 exons in BoDR beta I and BoDR beta II. A series of GT residues followed by a longer series of GA residues began about 35 nucleotides 3' of the beta 1 exon in both BoDR beta I and BoDR beta II.

Position-dependent repression and promotion of DQB1 intron 3 splicing by GGGG motifs

Alternative splicing of HLA-DQB1 exon 4 is allele-dependent and results in variable expression of soluble DQbeta. We have recently shown that differential inclusion of this exon in mature transcripts is largely due to intron 3 variants in the branch point sequence (BPS) and polypyrimidine tract. To identify additional regulatory cis-elements that contribute to haplotype-specific splicing of DQB1, we systematically examined the effect of guanosine (G) repeats on intron 3 removal. We found that the GGG or GGGG repeats generally improved splicing of DQB1 intron 3, except for those that were adjacent to the 5' splice site where they had the opposite effect. The most prominent splicing enhancement was conferred by GGGG motifs arranged in tandem upstream of the BPS. Replacement of a G-rich segment just 5' of the BPS with a series of random sequences markedly repressed splicing, whereas substitutions of a segment further upstream that lacked the G-rich elements and had the same size did not result in comparable splicing inhibition. Systematic mutagenesis of both suprabranch guanosine quadruplets (G(4)) revealed a key role of central G residues in splicing enhancement, whereas cytosines in these positions had the most prominent repressive effects. Together, these results show a significant role of tandem G(4)NG(4) structures in splicing of both complete and truncated DQB1 intron 3, support position dependency of G repeats in splicing promotion and inhibition, and identify positively and negatively acting sequences that contribute to the haplotype-specific DQB1 expression.

Immunological properties of the thymopentin-like fragments of HLA-DQ

Class II human leukocyte antigens (HLA-II) are cell surface alpha beta heterodimers (M(r) approximately 60,000) that play a pivotal role in the immune response by presenting peptides derived from environmental antigens to the T-cell receptor. A 167-171 fragment of the beta 2-chain of the HLA-DQ molecule consists of the sequence RGDVY, which is very similar to thymopentin (pentapeptide RKDVY, an active fragment (32-36) of thymopoietin, an immune system activator produced in thymi), and at the same time contains the RGD sequence, known as an inhibitor of adhesion processes. We synthesized and investigated the immunomodulatory activity of series of peptide fragments of HLA-DQ containing thymopentin-like sequences. The results indicate that all synthesized peptides suppress the cellular immune response. However, RGDV, RGDVY and QRGDVY show very weak stimulatory activity in humoral immunological response tests. In contrast to the shorter peptides, the nonapeptide fragment of HLA-DQ, TPQRGDVYT, shows significant immunosuppressive activity in all tests. A possible role of these fragments of the polypeptide chain of HLA-DQ in the regulation of HLA functions is discussed.

Characterization of anti-HLA class II monoclonal antibody LGII-612.14 reacting with formalin fixed tissues

mAb LGII-612.14 derived from a BALB/c mouse immunized with interferon-gamma (IFN-gamma) treated cultured human B lymphoid cells LG-2 has been shown with serological and immunochemical assays to recognize a monomorphic determinant expressed on the beta chain of HLA-DR, -DQ and -DP antigens. The linear nature of the determinant, which is likely to be formed by residues 19-25, is indicated by the reactivity of mAb LGII-612.14 with HLA-DR, -DQ and -DP beta chains purified by electrophoresis in presence of SDS. An unusual characteristic of mAb LGII-612.14 is its reactivity with fixed tissue sections. The intensity of staining is affected by the incubation temperature, the incubation time and the fixative used. Maximal intensity of staining of formalin fixed, paraffin embedded tissue sections required an incubation time of 16 h. The intensity of staining of paraffin embedded tissues initially fixed with Bouin's solution, formalin or ethanol was similar to that of frozen tissue sections and stronger than that of tissues fixed with B5 solution. No staining was detected of paraffin embedded tissues fixed with glutaraldehyde or Zenker's solution. Comparison of the staining patterns with mAb LGII-612.14 of frozen and fixed tissue sections showed that the latter substrates provide a superior detail of tissue architecture and cellular morphology without significant loss of sensitivity. Furthermore, comparison of the characteristics of mAb LGII-612.14 with the few previously published anti-HLA class II mAb reacting with fixed tissues indicates that mAb LGII-612.14 stains formalin fixed, paraffin embedded tissues, while mAb 910D7 and TAL-1B5 stain tissues fixed with less commonly used fixatives. Furthermore, mAb LGII-612.14 is likely to yield more sensitive staining results than anti-HLA-DR, -DQ and -DP mAb KUL/05. The present results indicate that mAb LGII-612.14 represents a useful probe to apply immunohistochemical techniques to the analysis of the distribution of HLA class II antigens in fixed tissues. This will greatly facilitate the use of readily available collections of fixed tissue specimens in retrospective studies to assess the clinical significance of changes in HLA class II antigen expression which occur in various disease states.

In the presence of dexamethasone, gamma interferon induces rat oligodendrocytes to express major histocompatibility complex class II molecules

Cells that express major histocompatibility complex (MHC) class II molecules can interact directly with CD4 T lymphocytes and either activate immune reactions or become the targets of T-cell-mediated cytotoxic attack. Using rat optic nerve cultures combined with immunocytochemistry and in situ hybridization, we have shown that oligodendrocytes, the major myelin-forming cells of the central nervous system and the main casualty of the immune attacks associated with multiple sclerosis and experimental allergic encephalomyelitis, can be readily induced to express MHC class II mRNA and surface antigens in vitro by exposure to gamma interferon, provided the glucocorticoid dexamethasone is included in the culture medium. Oligodendrocytes exposed to gamma interferon without dexamethasone fail to express MHC class II molecules, which may account for the failure of previous attempts to induce expression in these cells. In the experiments reported here MHC class II expression can be demonstrated both on galactocerebroside-positive cells and on mature oligodendrocytes that express proteolipid protein. These findings expand possibilities for understanding immune-related oligodendrocyte killing and demyelination in human and experimental demyelinating diseases.

Allele-specific expression of the cytoplasmic exon of HLA-DQB1 gene

The beta chain of the HLA-DQ molecule is shorter by eight amino acid residues than other major histocompatibility complex class II beta chains due to elimination of the fifth exon coding for part of the cytoplasmic domain. This elimination is caused by one base substitution in the splice acceptor site of the exon. We found that two HLA-DQB1 alleles, DQB1*0503 and DQB1*0601, did not have this substitution, and the exon was utilized in these two alleles. However, two forms of HLA-DQB mRNA, with or without exon 5, were generated in Epstein-Barr virus-transformed cell lines homozygous for DQB1*0503 or DQB1*0601, indicating alternative mRNA splicing. The alternative splicing of DQB1*0601 mRNA was also found in peripheral blood lymphocytes and L cell transfectants. To investigate the functional relevance of the allele-specific long cytoplasmic tail of HLA-DQ beta chain, we developed three types of L cell transfectants expressing exclusively the HLA-DQw6 molecules with short cytoplasmic tail, long cytoplasmic tail, or both forms of the beta chain, and used them as antigen presenting cells for streptococcal cell wall antigen-specific T cell lines. These three types of transfectants could function almost equally well as antigen presenting cells. It was thus demonstrated that both forms of HLA-DQ beta chain, with or without eight amino acid residues coded for by the exon 5, can be associated with the HLA-DQ alpha chain, be expressed on the cell surface, and function as restriction molecules in antigen recognition by the CD4+ T cells.

The nucleotide sequence and evolution of ovine MHC class II B genes: DQB and DRB

The nucleotide sequences of one Ovar-DQB gene, excluding exon 1 and parts of the introns, and one Ovar-DRB pseudogene are presented. The structure of the Ovar-DQB gene is typical of a major histocompatibility complex (MHC) class II B gene and demonstrates considerable sequence similarity with that of humans including such characteristics as the less common polyadenylation signal, ATTAAA. The ovine sequence has a typical 5' acceptor splice signal for exon 5, thus potentially encoding a full length cytoplasmic tail. The Ovar-DRB gene identified in this study was found to be a pseudogene, lacking a defined exon 2 and containing premature termination codons in both exons 3 and 4. The 3' donor splice site of exon 3 is also atypical. A purine-pyrimidine microsatellite repeat, (dC.dA)15, in the 3' region of the pseudogene may be a hotspot for recombination within the ovine DR subregion.

Amplification of major histocompatibility complex class II gene diversity by intraexonic recombination

The roles of mutational and recombinational processes in the diversification of the exon encoding the antigen binding site in the murine major histocompatibility complex class II gene Ab were assessed by phylogenetic analysis of allelic nucleotide sequences. A total of 46 alleles of Ab exon 2 from 12 Mus species or subspecies and 2 Rattus species were sequenced after amplification by the polymerase chain reaction. Reliable allelic genealogies could not be determined by phylogenetic analyses, due to extensive homoplasy in the data set. This homoplasy results from the shuffling of polymorphisms between alleles by recombinational processes, indicating that polymorphisms in the antigen binding site encoded by Ab are generated by a combination of two processes. First, the accumulation of point mutations has produced highly divergent polymorphic sequence motifs in five regions of Ab exon 2, each encoding a portion of the binding site. Some of these motifs have persisted as polymorphisms in rodents since before the divergence of mouse and rat (greater than 10 million years ago). The second process mediating Ab diversification involves the shuffling of these polymorphic sequence motifs into numerous allelic combinations by repeated intraexonic recombination. Site-specific hyperrecombinational mechanisms are not involved in this process within the exon. We postulate that these mechanisms continuously generate new Ab alleles with highly divergent binding sites from which alleles with advantageous antigen-binding properties are selectively maintained by some form of balancing selection.

Organization of a functional chicken class II B gene

Five class II (B-L) B genes are encoded in the major histocompatibility complex (MHC) of chickens of the B12 haplotype. We report here the nucleotide sequence of one of these genes, B-LBII, as well as the primary structure of a corresponding cDNA. The organization of B-LBII, its 5' flanking region including the promotor region, and the amino acid sequence of its product are compared to mammalian class II B genes and to the previously described B-LBIII gene, which probably is a pseudogene since no B-LBIII transcript could be identified. The 5' flanking region of B-LBII exhibits homologs of transcription-controlling sequence motifs, namely S, X, X2, and Y boxes, of class II A and B genes of rodents and man. However, the promotor region of B-LBIII lacks an equivalent of the S box, displays two nucleic acid substitutions in the core sequence of the Y box, and exhibits a 16 base pair (bp) deletion upstream of the site of initiation of transcription. Therefore, an aberrant promotor region is likely to account for the pseudogene-like nature of B-LBIII, which displays open-reading frames in all exons. The data obtained with the functional B-LBII gene are in line with our previous interpretation that both genomic organization and tertiary structure of class II beta molecules are remarkably conserved between birds and mammals.

Translation in Xenopus laevis oocytes of hybrid selected LEW rat RT1.B alpha- and beta-chain transcripts results in serologically discrete class II polypeptide chain complexes

Using the non-crossreactive mAb MRC-OX3 and MRC-OX6, two serologically distinct RT1.B-specific (I-A equivalent) alpha, beta heterodimers have previously been described by us as residing at the cell surface of LEW rat spleen cells. The two-chain elements were suggested to represent stable conformation isomers, diverged by dissociation of the mature gamma-chain from a mAb MRC-OX6 reactive biosynthetic intermediate, composed of terminally glycosylated alpha-, beta- and gamma-chains. In this study we addressed the question of whether or not the presence of terminally glycosylated invariant gamma-chain was obligatory for the formation of the two MRC-OX3 and MRC-OX6 reactive two-chain complexes. The synthesis of RT1.B-specific alpha, beta heterodimers was therefore initiated, in the absence of accompanying invariant gamma-chains, by microinjecting hybrid-selected RT1.B alpha- and beta-specific mRNA into oocytes of Xenopus laevis for translation. Class II molecules produced were analyzed by affinity chromatography of radioactive-labeled oocyte detergent lysates using the appropriate monoclonal immunoadsorbents for identification. Although rat gamma-chain mRNA was excluded in this assay system, distinct MRC-OX3 and MRC-OX6 reactive two-chain complexes were detected by two-dimensional gel electrophoresis. These findings clearly indicate that the formation of the two RT1.B-specific alpha, beta heterodimers is independent of the presence of the rat invariant gamma-chain.

Identification of Leishmania genes encoding proteins containing tandemly repeating peptides

A genomic Leishmania major DNA expression library was screened using antibodies raised against L. major membranes. Two different clones were identified that encoded proteins containing regions of tandemly repeated peptides. Clone 20 encodes a repetitive peptide of 14 amino acids, while clone 39 encodes a repetitive peptide of 10 amino acids. DNA from clone 20 hybridized with two RNA species of 9,500 and 5,200 nucleotides in length, while DNA from clone 39 hybridized to a single RNA species of 7,500 nucleotides. Antibodies against clone 20 fusion protein recognized a series of L. major proteins of apparent mol wt 250,000. Regions of repetitive peptides is a characteristic shared by many malarial protein antigens and this feature has been implicated in immune evasion. Intracellular parasites such as Leishmania and Plasmodia, therefore, may have evolved similar mechanisms consisting of the expression of proteins containing tandemly repeating peptides that are involved in immune evasion.

Polymorphism and mapping of the class II genes in the rat: RT1.B, RT1.D, and RT1.H, a new DP-like region

The major histocompatibility complex of the rat (RT1) encodes the class II molecules involved with antigen presentation and cell to cell communication. The organization of these class II genes has been studied by Southern blot hybridization using genomic DNA from inbred and recombinant rat strains digested with various restriction endonuclease and hybridized under stringent conditions with probes for mouse class II and human class II genes. Analysis of the restriction fragment length polymorphisms has mapped the class II genes relative to each other. We have confirmed the order of the alpha- and beta-chain genes in the RT1.B region, mapped the RT1.D region relative to RT1.B and showed that it has alpha- and beta-chain loci, and identified a new HLA-DP-like locus, RT1.H, to the RT1.A side of RT1.B. The RT1.H alpha and RT1.H beta genes map to the region around the recombination point in R22, and there appears to be a hot spot of recombination in RT1.H. The H beta and D beta genes have high levels of polymorphism; B beta, B alpha, and H alpha have intermediate levels of polymorphism, and D alpha has a low level of polymorphism.

DNA sequence analysis of the rat RT1.B alpha gene

The major histocompatibility complex (MHC) of the rat (RT1 complex) encodes two sets of class II molecules referred to as RT1.B and RT1.D. The RT1.B alpha gene was isolated for a Sprague-Dawley (RT1b) rat genomic library using a rat RT1.B alpha chain cDNA as a hybridization probe. The coding and the majority of the intron DNA sequence was determined. The structure of the RT1.B alpha gene is equivalent to that of H-2 and HLA alpha chain genes. Comparison of the nucleotide and predicted amino acid sequences of the RT1.B alpha gene with those of the H-2 and HLA genes revealed a high degree of overall sequence conservation. However, two regions of the first external domain (alpha 1), residues 19-23 and 45-78, exhibit marked sequence variation. Two blocks of conserved nucleotide sequence were identified in the 5' promoter region of the RT1.B alpha gene that have been described in all MHC class II genes sequenced to date. These conserved sequences may be involved in the coordinate regulation of expression of class II genes. The cloned RT1.B alpha gene was efficiently transcribed when transfected to mouse L cells.