Structure of C-terminal half of two H-2 antigens from cloned mRNA

Self peptides and the peptidic self

Twenty years ago, antigenic and self peptides presented by MHC molecules were absent from the immunological scene. While foreign peptides could be assayed by immune reactions, self peptides, as elusive and invisible as they were at the time, were bound to have an immunological role. How self peptides are selected and presented by MHC molecules, and how self MHC-peptide complexes are seen or not seen by T cells raised multiple questions particularly related to MHC restriction, alloreactivity, positive and negative selection, the nature of tumor antigens and tolerance. These issues were addressed in the "peptiditic self model" (1986) and subsequent hypothesis. They are retrospectively and critically reviewed here in the context of our current understanding of these major immunological phenomena.

Transforming growth factor beta 1 (TGF-beta 1) controls expression of major histocompatibility genes in the postnatal mouse: aberrant histocompatibility antigen expression in the pathogenesis of the TGF-beta 1 null mouse phenotype

The phenotype of the transforming growth factor beta 1 (TGF-beta 1) null mouse has been previously described and is characterized by inflammatory infiltrates in multiple organs leading to a wasting syndrome and death as early as 3 weeks after birth. Since this phenotype occurs in the absence of any detectable pathogen, potential autoimmune disease mechanisms were investigated. We examined major histocompatibility complex (MHC) mRNA expression in tissues of the TGF-beta 1 null mouse and found levels of both the class I and class II MHC mRNA elevated compared to normal or TGF-beta 1 heterozygous littermates. This elevated expression was seen prior to any evidence of inflammatory infiltrates, suggesting a causal relationship between increased MHC expression and activation of immune cell populations. Cell surface expression of MHC molecules was detected by immunohistochemistry and correlated well with mRNA levels. Expression of mRNA for interferon gamma and its receptor was unchanged at the ages when increased MHC expression became apparent. Down-regulation of class I MHC expression by TGF-beta 1 was also demonstrated in vitro in fibroblasts isolated from TGF-beta 1 null mice. These findings suggest that one natural function of TGF-beta 1 is to control expression of both MHC classes. Altered regulation of MHC expression may be a critical step leading to the multifocal inflammation and wasting syndrome seen in the TGF-beta 1 null mouse. These results suggest potential applications for TGF-beta in the management of autoimmune disease, allograft rejection, and other problems associated with altered MHC expression.

c-myc, c-fos, and c-jun regulation in the regenerating livers of normal and H-2K/c-myc transgenic mice

We investigated the mechanisms of regulation of c-myc, c-fos, and c-jun at the early stages of liver regeneration in mice. We show that the transient increase in steady-state levels of c-myc mRNA at the start of liver regeneration is most probably regulated by posttranscriptional mechanisms. Although there was a marked increase in c-myc transcriptional initiation shortly after partial hepatectomy, a block in elongation prevented the completion of most transcripts. To gain further information on the mechanism of regulation of c-myc expression during liver regeneration, we used transgenic mice harboring the human c-myc gene driven by the H-2K promoter. In these animals, the murine c-myc responded to the growth stimulus generated by partial hepatectomy, whereas the expression of the transgene was constitutive and did not change in the regenerating liver. However, the mRNA from both genes increased markedly after cycloheximide injection, suggesting that the regulation of c-myc mRNA abundance in the regenerating liver differs from that occurring after protein synthesis inhibition. Furthermore, we show that in normal mice c-fos and c-jun mRNA levels and transcriptional rates increase within 30 min after partial hepatectomy. c-fos transcriptional elongation was restricted in nongrowing liver, but the block was partially relieved in the regenerating liver. Nevertheless, for both c-fos and c-jun, changes in steady-state mRNA detected after partial hepatectomy were much greater than the transcriptional increase. In the regenerating liver of H-2K/c-myc mice, c-fos and c-jun expression was diminished, whereas mouse c-myc expression was enhanced in comparison with that in nontransgenic animals.

c-myc, c-fos, and c-jun regulation in the regenerating livers of normal and H-2K/c-myc transgenic mice

We investigated the mechanisms of regulation of c-myc, c-fos, and c-jun at the early stages of liver regeneration in mice. We show that the transient increase in steady-state levels of c-myc mRNA at the start of liver regeneration is most probably regulated by posttranscriptional mechanisms. Although there was a marked increase in c-myc transcriptional initiation shortly after partial hepatectomy, a block in elongation prevented the completion of most transcripts. To gain further information on the mechanism of regulation of c-myc expression during liver regeneration, we used transgenic mice harboring the human c-myc gene driven by the H-2K promoter. In these animals, the murine c-myc responded to the growth stimulus generated by partial hepatectomy, whereas the expression of the transgene was constitutive and did not change in the regenerating liver. However, the mRNA from both genes increased markedly after cycloheximide injection, suggesting that the regulation of c-myc mRNA abundance in the regenerating liver differs from that occurring after protein synthesis inhibition. Furthermore, we show that in normal mice c-fos and c-jun mRNA levels and transcriptional rates increase within 30 min after partial hepatectomy. c-fos transcriptional elongation was restricted in nongrowing liver, but the block was partially relieved in the regenerating liver. Nevertheless, for both c-fos and c-jun, changes in steady-state mRNA detected after partial hepatectomy were much greater than the transcriptional increase. In the regenerating liver of H-2K/c-myc mice, c-fos and c-jun expression was diminished, whereas mouse c-myc expression was enhanced in comparison with that in nontransgenic animals.

Conformations of proline residues in membrane environments

Although noted as hydrophilic residues with helix-breaking potential, proline residues are observed in putatively alpha-helical transmembrane (TM) segments of many channel-forming integral membrane proteins. In addition to the recognized property of X-Pro peptide bonds (where X = any amino acid) to occur in cis as well as trans isomeric states, the tertiary amide character of the X-Pro bond confers increased propensity for involvement of its carbonyl group in specific H-bonded structures (e.g., beta- and gamma-turns) and/or liganding interactions with positively charged species. To examine this latter situation in further detail, we identified Leu-Pro-Phe as a consensus sequence triad based on actual occurrences of intramembranous Pro residues in transport protein TM segments. Accordingly, we have undertaken the synthesis of hydrophobic peptides with potential membrane affinity, of which t-butyloxycarbonyl-L-Ala-L-Ala-L-Ala-L-Leu-L-Pro-L-Phe-OH (t-Boc-AAALPF-OH) is an initial compound. Partitioning of this peptide into model membrane environments composed of lipid micelles induces specific conformation(s) for the membrane-bound hexapeptide, as monitored by 75-MHz 13C-nmr spectral behavior of 13C-enriched Leu and Pro carbonyl carbons, and by 300-MHz 1H-nmr spectra of peptide alpha, beta, and aromatic protons. Data are interpreted in terms of an intramolecularly H-bonded inverse gamma-turn conformation in the membrane environment involving the Leu-Pro-Phe triad. The inherent structural instability of a Pro-containing segment in a TM helix due to the multiplicity of possible local conformations is discussed as a functional aspect of membrane-buried prolines in transport proteins.

Structural requirements for membrane assembly of proteins spanning the membrane several times

We have investigated the structural requirements for the biogenesis of proteins spanning the membrane several times. Proteins containing various combinations of topological signals (signal anchor and stop transfer sequences) were synthesized in a cell-free translation system and their membrane topology was determined. Proteins spanning the membrane twice were obtained when a signal anchor sequence was followed by either a stop transfer sequence or a second signal anchor sequence. Thus, a signal anchor sequence in the second position can function as a stop transfer sequence, spanning the membrane in the opposite orientation to that of the first signal anchor sequence. A signal anchor sequence in the third position was able to insert amino acid sequences located COOH terminal to it. We conclude that proteins spanning the membrane several times can be generated by stringing together signal anchor and stop transfer sequences. However, not all proteins with three topological signals were found to span the membrane three times. A certain segment located between the first and second topological signal could prevent stable membrane integration of a third signal anchor segment.

Limited polymorphism of both classes of MHC genes in four different species of the Balkan mole rat

We analyzed the restriction fragment length polymorphism of class I and class II MHC genes in DNA from 20 individuals belonging to the four different species of the complex of species of Balkan mole rats Spalax leucodon captured at four different localities in Yugoslavia. All populations were tested with four restriction enzymes and one conserved mouse probe for each of the two classes of MHC genes. The probes employed detect either limited polymorphism of class I genes or lack of polymorphic bands containing class II genes. Of the two other subterranean rodents that have been studied, four karyotype forms of the Israeli mole rat show polymorphism in both classes of MHC genes similar to the one found in all other mammals (Nizetić et al. 1985), and the Syrian hamster shows limited polymorphism of class I genes and high polymorphism of class II genes (McGuire et al. 1985). Balkan mole rats belong to a new group in this respect, different from all mammals studied so far, since they apparently show limited polymorphism of both classes of MHC genes.

Kinetics of cellular oncogene expression in mouse lymphocytes. II. Regulation of c-fos and c-myc gene expression

Newly isolated lymphocytes from mouse spleens express the c-fos oncogene even in the absence of mitogen with maximal mRNA levels 60 min post preparation of single cell suspension, whereas c-myc mRNA levels increase only after mitogenic stimulation with maximal mRNA levels 6 h post stimulation. The half-lives of c-fos mRNA are generally very short; they increase from 14 min (after 30 min of culture) to 70 min (after 2 h of culture). The half-lives of c-myc mRNA decrease from 50 min (at 2 and 6 h post stimulation with concanavalin A) to 12 min (at 48 h post stimulation). The c-fos gene transcription is already turned on in time-0 lymphocytes 10 min after disruption of the organ structure of the spleens and is down-regulated after 2 h and later. In nuclear run-on experiments with nonstimulated lymphocytes there is already significant transcription of the first exon of c-myc, but almost no elongation of the transcript to exon 2 and 3. In concanavalin A-treated lymphocytes elongation is stimulated about 5-fold within 6 h and returns to background levels at 48 h post stimulation. The nuclear run-on analyses of nonactivated lymphocytes showed a signal for RNA complementary to c-myc mRNA detected with a probe specific for the exon 1/intron 1 boundary of c-myc, which disappeared with increasing time of concanavalin A stimulation. This anti-sense transcription may play a role in regulating the elongation of c-myc transcripts.

Transcriptional control of mu- and kappa-gene expression in resting and bacterial lipopolysaccharide-activated normal B cells

When murine resting B cells are polyclonally stimulated by bacterial lipopolysaccharide (LPS) in vitro for a short period of 4 days, they are activated to DNA synthesis and cell division, and they also differentiate to immunoglobulin (Ig)-secreting plasma cells. These two events are accompanied with several qualitative changes at the Ig mRNA level: the disappearance of delta mRNA after stimulation, the switch from membrane to secretory form of mu-mRNA, and the late appearance of IgM joining chain (J-chain) mRNA. There is also a quantitative increase of Ig-gene expression at the level of: Ig gene transcription, mu-, kappa- and J-chain mRNA accumulation, and Ig translation and secretion. A comparison of Ig transcription rates before and in the course of LPS stimulation, as determined by in vitro transcriptional run-on assays, has shown that there is a large increase of the RNA polymerase density on both mu- and kappa-loci (30-60-fold), which is quantitatively comparable with the accumulation of both mu- and kappa-mRNAs at the steady state mRNA level. These data therefore suggest that former results obtained with tumor cells regarding post-transcriptional control of Ig gene expression do not reflect the physiological behavior of normal B cells with respect to the molecular events of B cell triggering. We also propose that additional molecular events such as RNA processing and the transcriptional activation of J-chain gene might be essential for controlling the maximal transcriptional rate across the Ig loci.

During B-cell differentiation enhancer activity and transcription rate of immunoglobulin heavy chain genes are high before mRNA accumulation

During differentiation of B lymphocytes, a low level of immunoglobulin heavy chain gene transcripts is apparent at the pre-B-cell stage, and a dramatic increase in immunoglobulin mRNA level is seen after stimulated B cells have matured into immunoglobulin-secreting plasma cells. We have measured the transcription rate of endogenous heavy chain genes using cell lines representative of various stages of murine B-lymphocyte differentiation. We observe a good correlation between RNA polymerase density, as determined by nuclear run-on transcription experiments, and the activity of the heavy chain gene enhancer, as assayed by transfection experiments. Both enhancer activity and heavy chain gene transcription are very high in pre-B-cell lines. Thus we conclude that the increased accumulation of immunoglobulin heavy chain mRNA in immunoglobulin-secreting plasma cells is regulated mainly by posttranscriptional processes.

Kinetics of cellular oncogene expression in mouse lymphocytes. I. Expression of c-myc and c-ras-Ha in T lymphocytes induced by various mitogens

Murine splenic T lymphocytes display maximal cellular myc gene (c-myc) expression already 3 h after concanavalin A stimulation and subsequent down-regulation before the onset of DNA synthesis. Stimulation by leucoagglutinin in the presence or absence of interleukin 2 leads to only low initial levels of c-myc-specific RNA which, however, increase later on. A similar pattern of c-myc expression is shown by the Lyt-2+ T cell subpopulation stimulated with either concanavalin A or leucoagglutinin in the presence of interleukin 2. Although [3H]thymidine incorporation was identical, the leucoagglutinin-stimulated Lyt-2+ T cells were void of any demonstrable c-myc-specific RNA at 3 h post-stimulation. Thus, the kinetics of c-myc expression in mouse T lymphocytes are not at all uniform, but depend on the mitogen and the subpopulation. In contrast, levels of c-ras-Ha-specific RNA were always low at early times, always increased towards the onset of DNA synthesis and down-regulation was not observed.

Hypothesis about the function of membrane-buried proline residues in transport proteins

In a survey of the bilayer-spanning regions of integral membrane proteins, membrane-buried proline residues were found in nearly all transport proteins examined, whereas membrane-buried regions of nontransport proteins were largely devoid of intramembranous proline residues. When amino acids from the complete sequences of representative sets of transport and nontransport membrane proteins were analyzed for the distribution of proline residues between aqueous vs. membranous domains, proline was shown to be selectively excluded from membranous domains of the nontransport proteins, in accord with expectation from energetic and structural considerations. In contrast, proline residues in transport proteins were evenly distributed between aqueous and membranous domains, consistent with the notion that functional membrane-buried proline residues are selectively included in transport proteins. As cis peptide bonds involving proline arise in proteins and have been implicated in protein dynamic processes, the cis-trans isomerization of an Xaa-Pro peptide bond (Xaa = unspecified amino acid) buried within the membrane--and the resulting redirection of the protein chain--is proposed to provide the reversible conformational change requisite for the regulation (opening/closing) of a transport channel. Parallel to this function, the relatively negative character of the carbonyl groups of Xaa-Pro peptide bonds may promote their participation as intramembranous liganding sites for positive species in proton/cation transport processes.

Sequences encoding two trypsin inhibitors occur in strikingly similar genomic environments

The nucleotide sequences of two approx. 4 kilobase pair segments of the bovine genome are presented. One segment contains a coding region for bovine pancreatic trypsin inhibitor (BPTI) and the other segment contains a coding region for a BPTI homologue. The two 4 kilobase pair sequences are strikingly similar over approx. 3.4 kilobase pairs of their sequence, including putative intron sequences, suggesting that they have evolved from a gene duplication event.

IgM RNA switch from membrane to secretory form is prevented by adding antireceptor antibody to bacterial lipopolysaccharide-stimulated murine primary B-cell cultures

Bacterial lipopolysaccharide (LPS) induces proliferation of resting primary murine B lymphocytes and their differentiation into Ig-secreting cells. This is accompanied by an increase in the rate of Ig gene transcription and the accumulation of mu heavy chain secretory mRNA. Specific antiantigen receptor antibody (anti-mu) induces resting B cells to proliferation but not differentiation. Upon addition of both LPS and anti-mu to cultures, resting B cells again proliferate but do not differentiate. RNA transfer blots of the Ig mRNA 2 days after induction with LPS/anti-mu show a specific deficiency of the 2.4-kilobase (kb) mu secretory mRNA, whereas the levels of the 2.7-kb mu membrane and 1.2-kb kappa light chain mRNAs are as high as in cells treated with LPS alone. Between days 3 and 4 after treatment with both reagents, reductions of mu membrane and, to a smaller extent, kappa mRNA become apparent. As measured by nuclear run-on transcription experiments at day 2, the transcription rates of Ig mu and the Ig kappa transcription units are equal in both induction experiments. Only at later stages do the LPS/anti-mu-treated cells transcribe Ig genes at a lower rate. Thus, the anti-mu treatment, drastically reducing the mu secretory mRNA production at early stages, represents a negative regulation occurring primarily at the posttranscriptional level.

Major histocompatibility complex of the mole-rat. II. Restriction fragment polymorphism

The major histocompatibility complex (Mhc) is a group of loci coding for lymphocyte membrane glycoproteins that provide the context for the recognition of foreign antigens in the initial phase of the immune response. The complex contains a large number of loci, some of which are highly polymorphic. The complexity and polymorphism pose a number of questions concerning the evolution of the Mhc. In an attempt to answer some of these questions, we have begun to study the Mhc of the mole-rat, Spalax ehrenbergi, a rodent representing a complex of sibling species occupying ecologically and geographically clearly delineated regions within the borders of Israel. In an earlier publication we identified the Spalax major histocompatibility (Smh) complex serologically and biochemically. Here, we analyze the Smh by Southern blotting of DNA fragments produced by restriction enzyme digestion. The fragments were hybridized to mouse probes specific for class I, class II, and C4 genes. The analysis has revealed that the Smh complex contains as many class I genes as the mouse does and that these genes are polymorphic. The number of class II genes could not be determined with certainty, but it is probably not greater than in the mouse. Polymorphism was also detected at the loci coding for the complement component 4 (C4), which are probably closely linked to the Smh complex. The polymorphism of mole-rat class I loci contrasts with the reported monomorphism of these loci in the Syrian hamster. Since the mole-rat leads a solitary, subterranean life, as the Syrian hamster does, ecology cannot be an explanation for the lack of class I polymorphism in the latter species.

DNA sequence of the mouse H-2Dd transplantation antigen gene

The inbred BALB/c mouse has three transplantation antigens, H2-Kd, H2-Ld, and H2-Dd. We present the complete nucleotide sequence of the H2-Dd gene as well as 777 residues of previously unpublished H-2Dd protein sequence. These data complete the sequences of all the BALB/c transplantation antigen genes and permit detailed comparison with each other and with their counterparts from the inbred C57BL/10 mouse. Transplantation antigens may differ from one another by as much as 5%-15% of their amino acid sequence for the external domains. These extensive differences may arise by gene conversion. The H-2D region of the BALB/c mouse encodes the H2-Dd and the H2-Ld genes. Serologic data suggest that at least two additional transplantation antigen molecules, H2-Rd and H2-Md, are encoded in the H-2D region of the major compatibility complex. Paradoxically, gene cloning studies have only identified the H2-Dd and the H2-Ld genes in the H-2D region. A complete DNA sequence of the H2-Dd gene shows that a variety of alternative splice sites exist throughout the gene, which may lead to additional gene products and may explain the multiplicity of H-2D-encoded polypeptides.

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

A cDNA clone that shares considerable homology with mRNA for class-I major-histocompatibility (MHC) antigens has been isolated from a cDNA library constructed from an insulin-secreting tumor of the NEDH rat (RIN). Although there is very strong homology between the third extracellular domain of this gene, and other class-I antigen genes, a stop codon was noticed at the junction between the external and transmembrane regions of its protein. Thus, this gene codes for a truncated class-I antigen that lacks both transmembrane and cytoplasmic domains but has hydrophilic amino acids towards its C-terminus and therefore resembles a soluble protein. This gene was found to be transcribed at significant levels in the rat testis and an insulin-secreting tumor, but transcription was negligible in liver and kidney. The partial nucleotide sequence of this gene in a Wistar rat genomic clone indicates that the cDNA clone is represented in the rat genome complete with premature termination codon, thus eliminating the possibility of artifactual origins for the clone.

Family organization of mouse H-2 class I genes

The H-2 complex of the mouse contains numerous class I genes of unknown function. These genes are here classified into families according to homology in the exons encoding the variable domains. There are one major and at least five minor families, whose members are partly clustered and partly interspersed on the mouse chromosome. DNA sequences show that not only Tla and Qa-2 but also other minor-family genes have intact coding domains. These may be expressible genes of novel types.

An H-2K gene of the tw32 mutant at the T/t complex is a close parent of an H-2Kq gene

Two recombinant mice have been recovered from the progeny of Ttf/tw32 + animals. They have lost the tw32 lethality factor(s) and gained tufted, presumably from the T chromosome. Southern blot analysis of class I genes of these two new partial tPA027 and tPA286 haplotypes indicates that they have retained at least part of the major histocompatibility complex of the tw32 chromosome (H-2 haplotype H-2w28). We have prepared a phage library of Eco RI-digested DNA from homozygous tPA027 animals. Upon screening the library with a cDNA probe specific for H-2K genes, we isolated a class I gene displaying all of the distinctive features of a genuine H-2K gene, and which could thus be defined as an H-2Kw28 gene. The H-2Kw28 gene is 92-95% homologous to H-2Kb and H-2Kd genes and differs significantly from the other class I genes sequenced so far. Homology with the H-2Kb sequence reaches nearly 100% in the 3' part of the H-2Kw28 gene. Moreover, the homology with an H-2Kq cDNA sequence reaches 99.8%. Several hypotheses can account for the near identity of H-2Kb, H-2Kq, and H-2Kw28 gene sequences: either recombination between H-2w28 and H-2b and H-2q sequences occurred before or at the time the strain was established, or the class I genes of the tw32 chromosome and the H-2b and H-2q genes found in inbred strains of mice have separated from each other rather recently.

Functional insertion of an Alu type 2 (B2 SINE) repetitive sequence in murine class I genes

The regulation of expression of the family of MHC (major histocompatibility complex) class I genes is complex. Sequence analysis has revealed that class I genes from the H-2D subregion of the MHC (which includes the D and L genes) differ from the class I gene from the H-2K subregion (the K gene) by the insertion of a type 2 Alu-like repetitive element (the murine B2 sequence) within the 3' noncoding region of the D and L genes. The consequence of this insertion in the D and L genes is the introduction of a novel polyadenylation signal, which is preferentially used over the more distal signal, the analog of that found in the K gene. The insertion of the type 2 Alu-like sequence results in a change in the preferred site for endonucleolytic cleavage which is necessary for generating a correct 3' terminus for polyadenylation. The data demonstrate that the type 2 Alu-like sequence has a function; the data also suggest a possible regulatory role of this sequence in the expression of class I genes.

Analysis of membrane and surface protein sequences with the hydrophobic moment plot

An algorithm has been developed which identifies alpha-helices involved in the interactions of membrane proteins with lipid bilayers and which distinguishes them from helices in soluble proteins. The membrane-associated helices are then classified with the aid of the hydrophobic moment plot, on which the hydrophobic moment of each helix is plotted as a function of its hydrophobicity. The magnitude of hydrophobic moment measures the amphiphilicity of the helix (and hence its tendency to seek a surface between hydrophobic and hydrophilic phases), and the hydrophobicity measures its affinity for the membrane interior. Segments of membrane proteins in alpha-helices tend to fall in one of three regions of a hydrophobic moment plot: (1) monomeric transmembrane anchors (class I HLA transmembrane sequences) lie in the region of highest hydrophobicity and smallest hydrophobic moment; (2) helices presumed to be paired (such as the transmembrane M segments of surface immunoglobulins) and helices which are bundled together in membranes (such as bacteriorhodopsin) fall in the adjacent region with higher hydrophobic moment and smaller hydrophobicity; and (3) helices from surface-seeking proteins (such as melittin) fall in the region with still higher hydrophobic moment. alpha-Helices from globular proteins mainly fall in a region of lower mean hydrophobicity and hydrophobic moment. Application of these methods to the sequence of diphtheria toxin suggests four transmembrane helices and a surface-seeking helix in fragment B, the moiety known to have transmembrane function.

A human T cell-specific cDNA clone encodes a protein having extensive homology to immunoglobulin chains

We have cloned and sequenced a human mRNA specific for mammalian T-lymphoid cells. The message was found to be expressed in human and murine T lymphoblasts, thymocytes and phytohaemagglutinin-stimulated T lymphocytes. The protein deduced from the cDNA sequence has a molecular weight of 34,938 and shows extensive similarity to the entire length of the variable, joining and constant regions of mammalian immunoglobulin light chains. In addition, the relative positions of the cysteine residues are similar to those of the light chains of murine and human immunoglobulin molecules. These properties suggest that the cDNA clone may correspond to a message that specifies part of the human T-cell receptor.

Evolution of the genes for the beta subunits of human chorionic gonadotropin and luteinizing hormone

Nucleotide sequence comparisons of the single gene for the human luteinizing hormone gene beta subunit with two of the seven genes for the human chorionic gonadotropin beta subunit suggest that the beta human chorionic gonadotropin genes have evolved from an ancestral beta luteinizing hormone gene by a series of selected changes with very little neutral drift. Moreover, the 24 amino acid carboxy-terminal extension of the human chorionic gonadotropin beta subunit appears to have arisen by a single base deletion that incorporated the 3'-untranslated region of the ancestral beta luteinizing hormone gene into the coding region.

Correction of complex heteroduplexes made of mouse H-2 gene sequences in Escherichia coli K-12

We have prepared heteroduplexes between two plasmids that carry, in the same orientation, two H-2 cDNA inserts, 1.15 and 1.0 kilobase long, respectively. Their sequences encode two distinct class I transplantation antigens of the mouse and differ by 8% of their nucleotides. Molecules with a rearranged array of restriction sites were found after transformation and cloning in an Escherichia coli recA- host. Nucleotide sequences showed that the rearranged molecules derived their nucleotides from the two parental strands. Thus, correction of these complex heteroduplexes takes place in E. coli and probably involves repair mechanisms. It provides the basis for a mutational process in which several nucleotides (amino acids) can be altered in a single event. It also offers a practical means of making genetic variants. Several other implications are discussed.

Different exon-intron organization at the 5' part of a mouse class I gene is used to generate a novel H-2Kd-related mRNA

A cDNA library constructed from liver mRNA of DBA/2 (H-2d) mice has been screened with H-2-specific probes. The nucleotide sequence of one clone (pH-2d-24) indicates that it derives from an H-2 gene with an unexpected exon-intron organization. Nucleotide sequence comparisons suggest that two distinct mRNAs are produced from a single H-2Kd gene by a mechanism involving the use of alternative splicing sites in its 5' region. pH-2d-24 carries an open reading frame encoding a thus-far-undescribed polypeptide product identical to an H-2Kd-molecule, except for the NH2-terminal half of the first domain.

The structure of the mouse immunoglobulin in gamma 3 membrane gene segment

The genomic region containing the mouse immunoglobulin gamma 3 heavy chain membrane (M) exons has been located and sequenced. The exon structure is highly similar to that of the other mouse gamma chains, with strong sequence conservation in the coding regions and the intron 5' to the M1 exon. The intron between M1 and M2 shows moderate sequence homology but very strong conservation of size. RNA blots suggest that gamma 3 membrane exon usage is similar to that seen in other immunoglobulin membrane heavy chain mRNAs. The transmembrane region contains the invariant residues which have been noted in all other heavy chain sequences and which were previously proposed to be interactive in a two-chain model for insertion through the lymphocyte membrane. Conserved residues with similar spacing have been seen in class II histocompatibility antigens, which are also two-chain transmembrane molecules, but not in class I antigens, which span cell membranes with a single chain.

HLA class I genes integrated into murine cells are inducible by interferon

In human cells treated with interferon, there is an increase in the amount of HLA-A, B, C mRNA and, to a lower extent, membrane-bound antigen. However, the mechanism of this mRNA enhancement is still unknown. Using mouse L cells transfected with a unique class I HLA gene, we were able to show that both the related HLA mRNA and protein are increased after murine but not human interferon treatment. Moreover, the discrepancy between interferon-directed HLA mRNA and protein enhancement is also observed. The mouse transfected cells allowed us to study more precisely the origin of this discrepancy.

On the insertion of proteins into membranes

Recent data concerning the primary structure and the interactions of proteins with membranes suggest the existence of two classes of integral membrane proteins. In the first class, the polypeptide chain crosses the membrane only once. The membrane penetrating fragment is markedly hydrophobic and contains several positive charges on its C-terminal border. In the second class, the protein is folded in a complex fashion within the membrane and the knowledge of its amino acid sequence is not sufficient to predict the manner in which the protein interacts with the membrane.

Unusual evolutionary conservation and frequent DNA segment exchange in class I genes of the major histocompatibility complex

From comparisons of homologous DNA sequences for many different genes, it was shown that the silent positions of protein-encoding regions and introns evolve at high and remarkably similar rates for different genes. In addition, both silent positions and introns behave like clocks; they accumulated base substitutions at approximately constant rates with respect to geological time. The rates of evolution were estimated to be 5.5 X 10(-9), 3.7 X 10(-9), and 5.3 X 10(-9) per site per year for silent positions, short introns (less than approximately equal to 300 base pairs), and long introns (more than approximately equal to 500 base pairs), respectively. Contrary to expectation from the evolutionary clocks, DNA sequence comparison between pHLA 12.4 (a cloned HLA sequence) of man and Ld together with other H-2 genes of mouse, the class I genes of the major histocompatibility complex, revealed a surprisingly small amount of base substitution for both the introns and the silent positions; the degree of divergence is only about 60% of that of standard genes in the same species comparison. Furthermore, several segmental homologies have been observed between the class I genes of mouse, suggesting the frequent occurrence of gene conversion or double unequal crossing-over in evolution. Interrelations between the extreme polymorphism of the class I genes, the low evolutionary drift of the introns and the silent positions, and the frequent gene conversion or unequal crossing-over within the mouse genes are discussed.

HLA-A2 and HLA-B7 antigens are phosphorylated in vitro by rous sarcoma virus kinase (pp60v-src) at a tyrosine residue encoded in a highly conserved exon of the intracellular domain

HLA-A2 and -B7 antigens are phosphorylated by Rous sarcoma kinase (pp60v-src) in vitro. The phosphate group is attached to the heavy chains as determined by NaDodSO4/polyacrylamide gel electrophoresis. The site of phosphorylation was localized to the COOH-terminal intracellular domain by its susceptibility to limited trypsin proteolysis. Furthermore, the 32P-labeled amino acid is a single tyrosine residue located in the COOH terminus of the heavy chain. The protein sequences of known class I human and murine intracellular domains contain a highly conserved sequence -K-G-G-X-Y- located NH2-terminally to the single tyrosine residue of this domain. The DNA sequences that encode class I antigen intracellular domains were compared by computer with a homology matrix program. Exon 6 which encodes the conserved tyrosine-containing protein sequence in both human and mouse is 75% homologous across species and 90-100% homologous within species. The significance of the high degree of conservation within exon 6 is discussed.

Allospecific and virus-specific cytolytic T lymphocytes are restricted to the N or C1 domain of H-2 antigens expressed on L cells after DNA-mediated gene transfer

In order to identify the site(s) on major histocompatibility molecules recognized by cytolytic T lymphocytes (CTLs), the recognition of H-2 antigens expressed when cloned genes are introduced into mouse L cells by DNA-mediated gene transfer has come under investigation. Recently, recombinant H-2 genes have been constructed in vitro from restriction endonuclease fragments of cloned H-2Dd and H-2Ld genes which exchange the N and C1 external domains (exon shuffling). These hybrid H-2 genes direct the synthesis of hybrid H-2 antigens when introduced into L cells by DNA-mediated gene transfer. These transformed L cells have been used as target cells to achieve a more precise localization of the sites recognized by allospecific and virus-specific CTLs. CTL systems were chosen that allow one to probe allospecific Ld or Dd recognition or virus-restricted Ld or Dd recognition. Using this approach we were able to map essential CTL recognition sites to the N and C1 domains of class 1 molecules.

The distribution of interspersed repeats is nonuniform and conserved in the mouse and human genomes

We investigated the genomic distribution of mouse and human repeated sequences by assessing their relative amounts in the four major components into which these genomes can be resolved by density gradient centrifugation techniques. These components are families of fragments that account for most or all of main-band DNAs, range in dG + dC content from 37% to 49%, and are derived by preparative breakage from long DNA segments (greater than 300 kb) of fairly homogeneous composition, the isochores. The results indicate that the short repeats of the B1 family of mouse and of the Alu I family of man are most frequent in the heavy components, whereas the long repeats of the BamHI family of mouse and of the Kpn I family of man are mainly present in the two light components. These results show that the genomic distribution of repeated sequences is nonuniform and conserved in two mammalian species. In addition, we observed that the base composition of two classes of repeats (60% dG + dC for short repeats; 39% dG + dC for long repeats) is correlated with the composition of the major components in which they are embedded. Finally, we obtained evidence that not only the short repeats but also the long repeats are transcribed, these transcripts having been found in mouse poly(A)+ mRNA.

A directional process of gene conversion is expected to yield dynamic polymorphism associated with stability of alternative alleles in class I histocompatibility antigens gene family

This work is a contribution to the discussion of the polymorphism of class I histocompatibility antigens (H-2 antigens in the mouse). Specially, the involvement of gene conversion in H-2 polymorphism has been explored through the use of a simplified computer model. It thus appears that in a population of limited size, gene conversion can promote allelic polymorphism while homogenizing the DNA sequences in a multigene family, only if it acts as a directional process. The DNA sequences of the preferential targets are then polymorphic and evolutionary versatile, while other genes of the family mostly behave as sequence donors, have more stable DNA sequences and are much less polymorphic. The characteristics of such a polymorphism generator are discussed with respect to their functional and evolutionary implications.

A cDNA clone containing the entire coding sequence of a mouse H-2Kd histocompatibility antigen

We have isolated a cDNA clone carrying a 1560 bp long insert which contains the entire coding and 3' untranslated regions of an H-2K(d) mouse histocompatibility antigen. Its sequence and overal features are described. They point to the existence of unique properties of DNA sequences associated with the H-2K(d) antigen.

The murine Ia alpha chains, E alpha and A alpha, show a surprising degree of sequence homology

The I region of the murine major histocompatibility complex codes for a group of glycoproteins, the Ia antigens, thought to be involved in the control of immune responsiveness. Each Ia antigen complex contains a "heavy chain," a "light chain," and the "invariant chain." We describe here the isolation and characterization of genomic and cDNA clones for one of the heavy chains, Ak alpha. The complete nucleotide sequence of the cDNA clone is presented, and the predicted amino acid sequence is compared with that of another alpha chain, Ek alpha. About 50% of the amino acids are identical, a finding somewhat unexpected on the basis of preliminary protein sequence data.

Structure and biosynthesis of histocompatibility antigens (H-2, HLA)

Histocompatibility antigens (H-2K, D and L, and HLA-A, B and C) are highly polymorphic cell surface proteins. Their primary structure has been determined by sequencing the protein, complementary DNAs (cDNAs) or genes in several laboratories. H-2Ld and Kd antigens are encoded by eight separate exons: one encodes the signal sequence, three encode the external domains, one encodes the membrane spanning segment and three encode the cytoplasmic domain. A similar structural organization has been found for an HLA gene. H-2 and HLA antigens are synthesized on membrane-bound ribosomes and are co-translationally inserted into the membrane of the endoplasmic reticulum. Here they assemble with beta 2-microglobulin, a small secretory protein. We describe the structure, the membrane insertion in vitro and in vivo, the intracellular transport and the surface expression of these antigens.

Complete amino acid sequence of an HLA-DR antigen-like beta chain as predicted from the nucleotide sequence: similarities with immunoglobulins and HLA-A, -B, and -C antigens

The complete nucleotide sequence of an HLA-DR antigen-like beta-chain cDNA clone was determined. The 1,080 base pairs include the complete coding region and most of the untranslated portion. The predicted amino acid sequence has 229 residues. The beta chain contains two immunoglobulin-like disulfide loops and a 21-amino acid residue membrane-integrated segment. Ten amino acid residues reside on the cytoplasmic side of the plasma membrane. The single asparagine-linked carbohydrate moiety is attached to asparagine-19. The NH2-terminal 91 residues of the beta chain are homologous to the corresponding region of HLA-A, -B, and -C antigen heavy chains. Residues 92-192 of the beta chain display statistically significant homology to members of the immunoglobulin family, beta 2-microglobulin, and the immunoglobulin-like domain of HLA-A, -B, and -C antigen heavy chains. These data establish that the major histocompatibility antigens of class I and class II type and the constant regions of immunoglobulins are evolutionarily related.

Structure and expression of a mouse major histocompatibility antigen gene, H-2Ld

A genomic clone encoding H-2Ld, a mouse major transplantation antigen, has been identified and the structure of the H-2Ld gene has been partially determined. We isolated 35 genomic clones from a BALB/c (H-2d) genomic library by hybridization to mouse or human probes. One of these clones encodes H-2Ld as determined by two criteria. First, the gene encodes a protein that is identical at the 76 known amino acid positions for H-2Ld. Second, when introduced into L cells by DNA-mediated gene transfer, a new H-2 antigen is expressed that is recognized by anti-H-2Ld monoclonal antibodies. The sequence of the H-2Ld protein predicted by the DNA sequences shows more than 80% homology to known H-2 antigens. H-2L-like sequences are found in mutant H-2Kb molecules, suggesting that gene conversion or reciprocal recombination may play a role in the development of H-2 polymorphism.

Identification of the 48-base-long primordial building block sequence of mouse immunoglobulin variable region genes

Mouse immunoglobulin heavy-chain variable region (Ig VH) genes apparently arose from the approximately 600-base-pair-long (approximately 12 tandem repeats of the 48-base-pair-long primordial building block sequence TTC-AGC-AGC-CTG-ACT-GGA-TAT-GAC-CTG-GAG-TGG-ACT-TAC-TGC-GCA-AGA) that in the original reading frame specified the amino acid sequence Phe-Ser-Ser-Leu-Thr-Gly-Tyr-Asp-Leu-Glu-Trp-Thr-Tyr-Cys-Ala-Arg. The previously identified, shorter prototype building blocks merely represented particular portions of the above primordial sequence. Even today, the direct descendant in toto of this primordial sequence specifies the last one-sixth of each VH coding sequence: the 83rd to 98th amino acid residues. Furthermore, its four truncated derivatives specify the 4th to 14th, 17th to 23rd, 29th to 37th, and 38th to 48th amino acid residues. Accordingly, all three relatively invariant--therefore, conserved--framework regions (FW-1, FW-2, and FW-3) of VHs are specified by recognizable--therefore, conserved--descendants of the primordial sequence.

DNA sequence of a gene encoding a BALB/c mouse Ld transplantation antigen

The sequence of a gene, denoted 27.5, encoding a transplantation antigen for the BALB/c mouse has been determined. Gene transfer studies and comparison of the translated sequence with the partial amino acid sequence of the Ld transplantation antigen establish that gene 27.5 encodes an Ld polypeptide. A comparison of the gene 27.5 sequence with several complementary DNA sequences suggests that the BALB/c mouse may contain a number of closely related L-like genes. Gene 27.5 has eight exons that correlate with the structural domains of the transplantation antigen.