Characterization of two class I major histocompatibility rat cDNA clones, one of which contains a premature termination codon

Differentially expressed DNA sequences following recovery from unilateral testicular torsion in rat

The molecular response during recovery from torsion-induced stress in the testis is diverse with a variety of mechanisms. In this study, using unilateral testicular torsion in rat as a model, we used subtractive hybridisation to identify differentially expressed DNA sequences in the torsioned and control testes. Three genes were identified as being down regulated in the torsioned testis compared with controls: Control Testis genes 1, 2 and 3 (CT1, CT2 and CT3). Two genes were up regulated in the torsioned testes: Torsioned Testes genes 1 and 2 (TT1 and TT2). Differential expression was confirmed by Reverse Northern blot analysis. An homology search revealed that CT1 had 88% homology with rat metallothionein cDNA; CT2 had 81% homology with rat cell surface antigen in MHC class I, but no homology could be found for CT3. TT1 had 92% identity with rat Rieske iron-sulphur protein mRNA whereas TT2 had 73% identity with a human clone of unknown function (RP 11-252D22). These results indicate that changes in gene expression occur following torsion induced stress, and that identification of differentially expressed genes may provide insights into the mechanisms of cellular tissue damage in this model.

RT1-U: Identification of a Novel, Active, Class Ib Alloantigen of the Rat MHC

In common with other mammalian species, the laboratory rat (Rattus norvegicus) expresses MHC class I molecules that have been categorized as either classical (class Ia) or nonclassical (class Ib). This distinction separates the class Ia molecules that play a conventional role in peptide Ag presentation to CD8 T cells from the others, whose function is unconventional or undefined. The class Ia molecules are encoded by the RT1-A region of the rat MHC, while the RT1-C/E/M region encodes up to 60 other class I genes or gene fragments, a number of which are known to be expressed (or to be expressible). Here we report upon novel MHC class Ib genes of the rat that we have expression cloned using new monoclonal alloantibodies and which we term RT1-U. The products detected by these Abs were readily identifiable by two-dimensional analysis of immunoprecipitates and were shown to be distinct from the class Ia products. Cellular studies of these molecules indicate that they function efficiently as targets for cytotoxic killing by appropriately raised polyclonal alloreactive CTL populations. The sequences of these class Ib genes group together in phylogenetic analysis, suggesting a unique locus or family. The combined serological, CTL, and sequence data all indicate that these products are genetically polymorphic.

Two distinct forms of soluble MHC class I molecules synthesized by different mechanisms in normal rat cells in vitro

Rat soluble MHC class I synthesis was studied at both RNA and protein levels to determine whether multiple forms of soluble MHC class I molecules are produced by different mechanisms. RT-PCR and sequencing of MHC class I transcripts identified an alternatively spliced nonclassical MHC class I gene product, lacking both exon 5 and 6, in both spleen and liver. Immunoprecipitation and SDS-PAGE identified two distinct soluble MHC class I proteins in both splenocyte- and hepatocyte-culture supernatants. The 36Kd classical soluble MHC class I protein (RT1.Aa) was precipitated by both allele-specific (MN4.91.6, R3/13, R2/15S) and pan-reactive (OX18) mAbs. The 39Kd non-RT1.A soluble MHC class I protein was precipitated only by OX18. The production of soluble RT1.Aa was inhibited by a metalloproteinase inhibitor, but not by serine/thiol protease inhibitors. None of these protease inhibitors interfered with the soluble non-RT1.A production, suggesting that it might be derived from an alternatively spliced MHC class I transcript. The soluble non-RT1.A was always associated with beta2m. However, soluble RT1.Aa molecule was cleaved in beta2m-free form and was reassociated with beta2m in culture supernatants. Thus two soluble MHC class I molecules, classical (36Kd RT1.Aa) and nonclassical (the alternatively spliced transcript), were produced from rat cells. Alternative splicing led to the nonclassical soluble MHC class I synthesis. Proteolytic cleavage by metalloproteinase led to the classical soluble MHC class I synthesis.

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.

Structural and functional analysis of three D/L-like class I molecules from H-2v: indications of an ancestral family of D/L genes

Three cDNA with D region gene features have been identified from the H- 2v haplotype. Provisionally, the sequences have been designated as D/Lv1, D/Lv2, and D/Lv3. The coding segments for the antigen binding domain (ABD) of all three D/Lv genes were engineered into a class I genomic expression vector and expressed in L cells. FACS analysis of the three D/Lv-Ld gene transfectants revealed that the D/Lv1 molecules were recognized by both monoclonal antibodies (mAbs) 141 and 142, and the D/Lv2 molecules were recognized by mAb 143. In addition to the D/Lv1 molecules, the mAb 141 also recognized the D/Lv3 molecules. Both the D/Lv1-Ld and D/Lv2-Ld transfectants were killed efficiently by H- 2Dv region-specific alloreactive CTL. The D/Lv3 gene is the first identified D region gene other than D and L that is transcribed abundantly in spleen and the D/Lv3 RNA is present as two alternatively spliced forms. Structural analysis of the D/Lv3 hybrid molecules showed that it was susceptible to proteolysis and thermolabile at 37 degrees C, suggesting D/Lv3 is a transcribed pseudogene. A parsimony tree analysis of three D/Lv sequences with a set of class I gene sequences revealed that the H-2v sequences clustered with D region genes. The presence of a third gene with D/L-like features in H-2v, yet structurally different from the known D/L alleles, raises the possibility that the current D/L genes evolved from a family of D/L- like genes, some of which are no longer represented among many of the mouse major histocompatibility complex haplotypes. The observation that D region alleles cluster into subgroups suggests that the alleles are not all related to each other by linear descent through a single locus. We propose that current alleles are derived from more than one ancestral locus in a manner similar to the origin of the gamma 2 a immunoglobulin constant region alleles.

Transmembrane domain length variation in the evolution of major histocompatibility complex class I genes

The fifth exons of major histocompatibility complex (MHC) class I genes encode a transmembrane domain (TM) that is largely responsible for class I antigen cell-surface expression usually through conventional hydrophobic amino acid-membrane interactions or, less often, through phosphatidylinositol linkage. In this report we show that Peromyscus leucopus, a Cricetidae rodent, has MHC class I genes (Pele-A genes) encoding three distinct sizes of TMs. Increases in TM lengths were due to tandem duplications of sequences similar to human hypervariable minisatellite repeats and the lambda chi site. We discerned remnants of a similar duplication event in comparable rodent and primate MHC class I genes. Furthermore, several duplications and deletions appear to have occurred independently in H-2, RT1, Pele-A, and ChLA genes in near-identical positions. Accumulated data suggests that sequences in the fifth exon of MHC class I genes may, therefore, constitute a mutational or recombinational hot spot that is mediated by minisatellite- and chi-like sequences imbedded within the coding region. The MHC class I genes may thus have recruited "selfish" DNA in their evolution to encode cell surface proteins. Expression of Pele-A genes was examined by the polymerase chain reaction (PCR) using oligonucleotide primers specific for exon 4 and 5 sequences. The PCR product sizes indicated that genes encoding each TM domain length are ubiquitously transcribed.

Class I major histocompatibility complex cDNA clones from sheep thymus: alternative splicing could make a long cytoplasmic tail

To investigate the class I major histocompatibility complex (MHC) genes expressed in the young sheep thymus, a cDNA library was screened with a human HLA-B7 cDNA probe under conditions of relaxed stringency. Thirteen clones were isolated and found by partial sequences to fall into five classes, requiring the expression of at least three loci. One sequence was found six times, almost half of the total, and may thus represent the major message expressed in the young sheep thymus. One of the clones was found to have failed to excise the intron between cytoplasmic exons 7 and 8, leading to the predicted synthesis of a cytoplasmic domain 23 amino acids longer than the other sheep sequences, and 15 amino acids longer than any cytoplasmic domain previously described. The sequences of all the clones were found to be most similar to bovine, and least similar to mouse class I MHC sequences.

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.

Changes in the expression of class I major histocompatibility complex antigen RNA induced by interferon in rat hepatoma cells

The rat hepatoma cell line 17X was studied to determine if it expressed major histocompatibility complex (MHC) class I antigen RNA and to see if interferon treatment would affect its expression. Under normal cell culture conditions, MHC class I RNA in 17X hepatoma cells is virtually undetectable. Administration of rat interferon at a concentration of 1000 units/ml for 48 h to 17X cells in culture resulted in the appearance of detectable levels of RNA for MHC class I antigens. The interferon-induced increase in class I RNA was accompanied by de novo synthesis of immunoprecipitable, metabolically radiolabeled class I antigens in the 17X hepatoma cells.

Comparison of exon 5 sequences from 35 class I genes of the BALB/c mouse

DNA sequences of the fifth exon, which encodes the transmembrane domain, were determined for the BALB/c mouse class I MHC genes and used to study the relationships between them. Based on nucleotide sequence similarity, the exon 5 sequences can be divided into seven groups. Although most members within each group are at least 80% similar to each other, comparison between groups reveals that the groups share little similarity. However, in spite of the extensive variation of the fifth exon sequences, analysis of their predicted amino acid translations reveals that only four class I gene fifth exons have frameshifts or stop codons that terminate their translation and prevent them from encoding a domain that is both hydrophobic and long enough to span a lipid bilayer. Exactly 27 of the remaining fifth exons could encode a domain that is similar to those of the transplantation antigens in that it consists of a proline-rich connecting peptide, a transmembrane segment, and a cytoplasmic portion with membrane-anchoring basic residues. The conservation of this motif in the majority of the fifth exon translations in spite of extensive variation suggests that selective pressure exists for these exons to maintain their ability to encode a functional transmembrane domain, raising the possibility that many of the nonclassical class I genes encode functionally important products.

Primary structure of a C-hordein gene from barley

The nucleotide sequence of a 2065 base pair HindIII fragment, containing a gene (lambda hor1-14) belonging to the Hor1 locus in barley, has been determined. The fragment consists of 1044 bp of coding region interrupted by an amber codon at base 481, a 5' non-coding region of 428 bp and a 3' non-coding region with 593 bp. The deduced amino acid sequence of the mature protein (327 amino acids) is characterized by an octapeptide motif PQQPFPQQ which is repeated throughout the peptide chain between a unique 12 amino acid long NH2-terminal and an equally unique 10 amino acid long COOH-terminal end. The proline + glutamine content is 62% and the next three most abundant amino acids are leucine (9%), phenylalanine (8%) and isoleucine (3%). In the 5' non-coding region there is a TATA box at -98 bp from the start methionine. The 3' non-coding region has a polyadenylation signal 76 bp downstream from the TAA stop codon. The deduced amino acid sequences of the NH2- and COOH-terminals of lambda hor1-14 are very similar but not identical to those known from the Edman degradation and carboxypeptidase Y analysis of C-hordein polypeptides. The 3' coding and non-coding region of lambda hor1-14 is closely similar but different in detail to the known C-hordein cDNA clones. One polyadenylation signal is found in lambda hor1-14 whereas two are present in each of the three known C-hordein cDNAs. These differences and the amber codon interrupting the open reading frame indicate that this gene is silent.

Identification in rat liver and serum of water-soluble class I MHC molecules possibly homologous to the murine Q10 gene product

We have identified large quantities of a water-soluble, non-RT1.A class I MHC molecule in the serum of the DA rat strain, with a similar molecule being found in aqueous extracts of DA liver. The non-RT1.A class I molecules have heavy chains of 41 kD, which is smaller than RT1.A class I molecules isolated from liver membranes (45 kD) but larger than water-soluble RT1.A class I molecules previously identified in serum and aqueous extracts of liver and kidney (40 kD). NH3-terminal amino acid sequencing of bulk-purified RT1.A class I molecules and of this novel non-RT1.A class I molecule revealed two substitutions, in the first 25 amino acids, Tyr----His at position 9, and Ala----Ser at position 24. The non-RT1.A class I molecule did not react with any of the well-characterized polymorphic and monomorphic antibodies directed against RT1.Aa class I molecules, but did react with the MRC OX18 antibody. A similar class I molecule could not be identified on liver membranes. The non-RT1.A class I molecule was found in large quantities (approximately 20 micrograms/ml) in the serum of the DA rat strain, and similarly large quantities appeared to be present in the sera of BN, PVG, and LEW.RT1a rats. WAG and LEW.RT1u rats had readily detectable but lower amounts of this molecule in their serum, while LEW and SHR rats had little if any present. This molecule probably represents the rat homologue of the murine Q10 gene product, and is the major class I product in the serum of the DA rat strain.

A deletion in a rat major histocompatibility complex class I gene is linked to the absence of beta 2-microglobulin-containing serum molecules

Class I major histocompatibility antigens are composed of a heavy chain that is noncovalently associated with beta 2-microglobulin (beta 2m). Most class I molecules are membrane bound, but mouse and rat cDNA clones and genes without a functional code for the transmembrane amino acids have been identified. The membrane-associated class I molecules are important in the control of cell-mediated cytotoxicity, while the function of the soluble molecules remains unclear. Previous studies have shown that beta 2m circulates in rat serum in three different molecular weight classes. The first is free beta 2m (Mr, 12,000), the second is about Mr 70,000, and the third is roughly Mr 200,000. In an inbred subline of immunodeficient, diabetes-prone BioBreeding rats (BioBreeding/Hagedorn), previous work detected two restriction fragment polymorphisms in class I major histocompatibility complex genes, one of them a gene deletion on a 7-kilobase BamHI fragment and the other on a 2-kilobase BamHI fragment. In these rats we have found that the third serum beta 2m-binding size class is absent. Analysis of F1 and F2 individuals following cross-breeding between BioBreeding/Hagedorn rats and genetically related (nondiabetic) control BioBreeding w-subline rats demonstrated that the large-size serum peak of beta 2m was associated with the presence of the class I restriction fragments.

The nucleotide sequence of a HMW glutenin subunit gene located on chromosome 1A of wheat (Triticum aestivum L.)

A cloned 8.2 kb EcoRI fragment has been isolated from a genomic library of DNA derived from Triticum aestivum L. cv. Cheyenne. This fragment contains sequences related to the high molecular weight (HMW) subunits of glutenin, proteins considered to be important in determining the elastic properties of gluten. The cloned HMW subunit gene appears to be derived from chromosome 1A. The nucleotide sequence of this gene has provided new information on the structure and evolution of the HMW subunits. However, hybrid-selection translation experiments suggest that this gene is silent.