Structural relationship between alpha 1-microglobulin from man, guinea-pig, rat and rabbit

Rabbit alpha 1-microglobulin was purified from the urine of sodium-chromate-treated animals by the use of gel chromatography on Sephadex G-100, affinity chromatography on concanavalin-A--Sepharose and ion-exchange chromatography on DEAE-Sephadex. Rabbit alpha 1-microglobulin had a molecular mass of 25.6 kDa on SDS/polyacrylamide gel electrophoresis. Alpha 1-microglobulin has previously been purified from the urine of humans, guinea-pigs and rats by similar methods, and the molecular masses of the four homologues were compared by SDS/polyacrylamide gel electrophoresis and gel chromatography in a denaturing medium. By these two methods the human homologue was 6 kDa and 3 kDa larger, respectively, than the other three proteins. Endoglycosidase F digestion of alpha 1-microglobulin, followed by SDS/polyacrylamide gel electrophoresis, revealed three protein bands in the human alpha 1-microglobulin sample, and only two bands in guinea-pig, rat and rabbit alpha 1-microglobulin, with a gap between each band of 2.6--2.9 kDa. The amino-terminal amino acid sequences of the four homologues were determined and between 72% and 81% homology was seen. The five amino-terminal amino acids present in the other species were missing in guinea-pig alpha 1-microglobulin. Our results indicate that human alpha 1-microglobulin is substituted with two N-linked oligosaccharides, while only one is attached to each of the other alpha 1-microglobulins, and that the extra glycosylamine-linked oligosaccharide in the human protein is attached to asparagine in position 17. Finally it is shown that all four homologues inhibit antigen stimulation of human lymphocytes, a finding which is consistent with our previous suggestion that the N-linked oligosaccharides carry the immunosuppressive activity of alpha 1-microglobulin.

Structure of a gene encoding the 1.7 S storage protein, napin, from Brassica napus

A rapeseed chromosomal region containing a gene (napA), which encodes the 1.7 S seed storage protein (napin), was isolated in several overlapping recombinant clones from a phage lambda genomic library. Following restriction enzyme mapping of the genomic region, a subclone containing the napA coding region as well as some 1.1 and 1.4 kilobases of DNA from the 5' and 3' regions, respectively, was mapped and sequenced. The gene turned out to lack introns. Southern blotting analyses utilizing a napin cDNA clone as a probe revealed the presence of on the order of 10 napin genes in the rapeseed genome. The major polyadenylated transcript encoded by these genes was shown to be an 850-nucleotide species, the initiation site of which was mapped onto the napA gene. The major initiation site for transcription is located some 33 nucleotides downstream from a sequence perfectly conforming to the consensus sequence of a TATA box. Further analyses of the sequence revealed several features that may be of relevance for the expression of the napin genes.

The extracellular portion of HLA-DR alpha chain is composed of two compactly folded domains

A truncated form of the class II antigen DR alpha chain of the human major histocompatibility complex was produced in bacteria. A cDNA clone encoding the intact chain was modified so that the segment encoding the signal sequence was replaced by an ATG codon and the 3' region downstream to the part corresponding to the third exon was replaced by a stop codon. The new construct was put under the control of the Tac promoter in a bacterial expression vector. The distance between the Shine-Delgarno sequence and the initiation codon was randomized so that clones with optimal expression of the truncated DR alpha chain could be obtained after induced expression and immunoscreening. The truncated DR alpha chain was subjected to limited proteolysis with chymotrypsin, and the resulting cleavage products were analysed by sodium dodecyl sulphate-polyacrylamide gel electrophoresis. Two fragments were visualized by western blotting. Electrophoresis in the absence and presence of reducing agents suggested that one of the proteolytic fragments contained a disulphide bridge. It is concluded that the extracellular portion of the DR alpha chain is composed of two compactly folded domains connected by an extended stretch of the polypeptide chain.

Matching of host genotype and serotypes of Coxsackie B virus in the development of juvenile diabetes

Thirty-six consecutive paediatric patients (0-16 years old) with recently contracted juvenile diabetes (IDDM) during 1982-84 were included in the study. Sera were assayed for recent or current Coxsackie B virus (CBV) infection using a specific and sensitive IgM RIA. Eighteen patients (50%) had IgM against CBV 1-5. The patients were also assayed for restriction fragment length polymorphism (RFLP) patterns with DNA probes coding for HLA-DR and DQ beta chains. The CBV-positive patients (n = 18) had either RFLP patterns associated with HLA-DR 3 or 4 or HLA-DQ patterns III or IV beta. Two of the CBV negative patients had neither HLA-DR 3 nor DR 4 and four of them had neither DQ patterns III nor IV. Eleven out of 18 CBV-positive patients had HLA-DQ III and DR 3 (61%) versus 5 out of 18 (28%) of the CBV-negative patients. All 11 patients with serology positive for CBV 2, 3, and 5 had HLA-DR 4 and DQ IV patterns. This was significantly (P less than 0.01) different from all five CBV 4-positive patients, who in contrast all had HLA-DR 3 or HLA-DQ III patterns. CBV 1-positive patients (n = 2) all had HLA-DR 3, 4, and HLA-DQ III, IV patterns. Thus CBV 4 seems to be significantly associated with a different host genetic constitution from at any rate CBV 2, 3, and 5, and possibly CBV 1.

Class II genes of the human major histocompatibility complex. Evolution of the DP region as deduced from nucleotide sequences of the four genes

The DP region of the human major histocompatibility complex contains two alpha genes and two beta genes. The DP alpha 1 and beta 1 genes encode the expressed DP histocompatibility antigen molecule, while the DP alpha 2 and beta 2 genes are inactive in the haplotypes examined. Here we present the sequence of the two DP beta genes and of the expressed DP alpha 1 gene. Nucleotide sequence comparisons reveal a considerably greater degree of similarity between the two beta genes than between the two alpha genes. We propose that a duplication giving rise to the DP alpha gene pair evolutionarily preceded the corresponding DP beta gene duplication. We also propose, based on the orientation of other class II gene pairs, that the original DP molecule was encoded by the DP beta 1 and DP alpha 2 genes. At some stage during the evolution of the DP region both of the two pseudogenes appear to have been expressed.

Class II genes of the human major histocompatibility complex. Comparisons of the DQ and DX alpha and beta genes

The human major histocompatibility complex, HLA, contains the genes of several class II molecules. We present here the molecular maps of the DQ and DX subregions and analyze the sequences of the polymorphic DQ alpha and DQ beta genes as well as the DX alpha and DX beta genes. The DQ alpha and DQ beta genes are oriented in opposite directions, approximately 12 kilobases apart. The DX alpha and DX beta genes are similarly oriented about 8 kilobases. The exon-intron organizations of the DQ alpha and DX alpha genes are analogous to those of other class II alpha genes. Comparison of the DQ alpha gene sequence to three DQ alpha cDNA clones shows that amino acid replacements are predominantly located between residues 45 and 80 in the amino-terminal domain. Analysis of the frequency of silent and replacement substitutions indicates that there is little selection against replacements in DQ alpha first domains. The exons encoding the second domains of DQ alpha and DX alpha are virtually identical, suggesting that a gene conversion event has occurred between these genes. The DX beta gene is very similar to the DQ beta gene but differs in the cytoplasmic portion. The DX beta gene contains a separate exon of 24 nucleotides encoding the core of the cytoplasmic tail. This exon is not expressed in the DQ beta genes due to a nonfunctional splice junction. Comparison of the number of nucleotide substitutions in the DQ beta first and second domain exons suggests that little or no phenotypic selection acts on the first domain whereas the second domain is under strong selection.

Class II genes of the human major histocompatibility complex. Organization and evolutionary relationship of the DR beta genes

The genes of the polymorphic HLA-DR molecules are located within the human major histocompatibility complex. We have studied the HLA-DR genes of an HLA homozygous individual typed to be DR4, Dw4, and DRw53. Fourteen cosmid and phage clones from genomic libraries were isolated and grouped into three clusters comprising a total of 165 kilobases. These clusters contain four DR beta genes. Nucleotide sequence determination showed that two of the genes encode beta chains that carry the DR4 and DRw53 specificities, respectively, while the other two genes are presumably pseudogenes. Comparisons of the nucleotide sequences of all four DR beta genes of the DR4 haplotype show that the genes are extensively similar, approximately 90% in both exons and introns. All four genes are equally similar to each other. These observations are consistent with the notion that the genes arose by duplications that were followed by homogenization through gene conversion. The existence of more than one DR beta gene homologue but only a single DR alpha gene homologue in mouse, rabbit, and cattle suggests that the DR beta gene duplications occurred at or early during mammalian speciation.

Class II genes of the human major histocompatibility complex. The DO beta gene is a divergent member of the class II beta gene family

A novel class II beta chain gene is described. This gene, tentatively called DO beta, displays considerably less polymorphism than beta genes of the DP, DQ, and DR loci. The nucleotide sequence of the DO beta gene is strikingly similar to that of the previously identified murine A beta 2 gene. The DO beta gene displays the same exon/intron organization as other beta genes although the fifth exon and the translated portion of the sixth exon are longer than in other genes. A striking feature of the amino acid sequence deduced from the DO beta gene sequence is the pronounced hydrophobicity of the NH2-terminal region. This feature distinguishes the putative DO beta chain from other class II beta chains and raises the possibility that DO beta chains may interact with an alpha chain that is structurally different from those of the DP, DQ, and DR loci. It further suggests that the putative DO molecule may have a function different from those of other class II antigens.

The complete amino acid sequence of human serum retinol-binding protein

The complete amino acid sequence of human serum Retinol-binding protein (RBP) including the distribution of its three disulfide bridges, has been determined. The protein consists of 182 amino acid residues, the order of which was determined following the isolation of five CNBr-fragments. Direct amino acid sequence analysis in an automatic liquid phase sequencer provided almost the entire sequences of the five CNBr-fragments. Several sets of enzymatically derived peptides of RBP were also used to elucidate the primary structure. RBP displays significant homology to bovine beta-lactoglobulin, human alpha 1-microglobulin and rat alpha 1-microglobulin. RBP contains an internal homology. Thus, residues 36 to 83 display statistically significant homology with residues 96 to 141.

Analysis of class II genes of the chicken MHC (B) by use of human DNA probes

Class II genes of the major histocompatibility complex (MHC) in the chicken have been investigated by Southern blot analysis using human cDNA probes for DQ alpha, DQ beta, DR alpha, and DR beta. Both beta probes but not the alpha probes cross-hybridized well with chicken DNA. The results indicated that the beta probes hybridized with at least two beta genes in the chicken MHC and there was no clear indication of a DQ-DR subdivision of chicken class II beta genes. The possibility of using human beta probes for MHC typing in the chicken was tested by using two homozygous individuals for each of 20 different, serologically defined, MHC (B) haplotypes originating from the domestic breeds of White Leghorn and Rhode Island Red, or from Red Jungle Fowl (the wild ancestral form). Genomic DNA samples from these individuals were digested with any one of the Eco RI and Pvu II restriction enzymes and hybridized with the DR beta probe. Restriction fragment length polymorphism (RFLP) was obtained with Pvu II only, which resolved seven different RFLP types. There was an excellent correlation between these RFLP types and the serological B typing since the RFLP type was identical within each pair of homozygotes. In addition to this broad survey of many haplotypes, a more detailed comparison was carried out on B21-like haplotypes originating from different breeds. No differences in restriction fragment patterns among these haplotypes could be resolved using any of the restriction enzymes Bg1 II, Eco RI, Hind III, Pst I, Pvu II, and Taq I.

Structure of the rapeseed 1.7 S storage protein, napin, and its precursor

Napin (1.7 S protein) is a basic, low molecular weight storage protein synthesized in rapeseed (Brassica napus) embryos during seed development. Napin is composed of two polypeptide chains with molecular weights of 9000 and 4000 that are held together by disulfide bonds. Comparison of the deduced amino acid sequence of a napin cDNA clone with that of napin peptide fragments established that napin is initially synthesized as a precursor of 178 residues. This polypeptide is subsequently processed through several proteolytic events, which ultimately generate the two mature napin chains, of 86 and 29 residues, respectively. Protein biosynthesis in vitro showed that the initial translation product (Mr 20,000) contains a signal sequence which is removed during transfer of the protein into the endoplasmic reticulum. Two additional peptides, of 22 and 19 residues, as well as the COOH-terminal residue, are also removed during maturation of napin, as deduced from the sequence comparison. Comparisons of the napin sequence with other known protein sequences established that there is a significant homology between napin and two other small seed proteins, the castor bean storage protein and a trypsin inhibitor from barley.

Only one DQ-beta restriction fragment pattern of each DR specificity is associated with insulin-dependent diabetes

Insulin-dependent diabetes is generally associated with the serologic HLA-DR specificities 3 and 4, in particular with DR-3,4 heterozygosity. The disease is negatively associated with DR-2. To investigate these associations further at the genomic level, DNA from 13 families with a proband having insulin-dependent diabetes, from 11 other individuals with the same disease, and from HLA-DR-matched control individuals was subjected to restriction fragment analysis. Three different enzymes (Bam HI, Eco RI, and Pvu II) and cDNA clones for three HLA-D region class II antigen alpha- and beta-chains (DR-beta, DQ-beta, and DQ-alpha) were used. In six families, a total of 11 siblings HLA-DR-identical to the proband were examined. There was no discrepancy between the hybridization patterns of the proband and those of the DR-identical siblings. Two different DQ-B fragment patterns were detected with each one of the serologic specificities DR-2 and DR-4. In both cases, only one of the patterns correlated significantly with diabetes. Thus, DQ-beta genomic hybridization may be used in conjunction with HLA-DR typing to identify individuals with higher relative risk to acquire insulin-dependent diabetes. These results may suggest that insulin-dependent diabetes is associated with the DQ rather than with the DR locus.

Only one DQ-beta restriction fragment pattern of each DR specificity is associated with insulin-dependent diabetes

Insulin-dependent diabetes is generally associated with the serologic HLA-DR specificities 3 and 4, in particular with DR-3,4 heterozygosity. The disease is negatively associated with DR-2. To investigate these associations further at the genomic level, DNA from 13 families with a proband having insulin-dependent diabetes, from 11 other individuals with the same disease, and from HLA-DR-matched control individuals was subjected to restriction fragment analysis. Three different enzymes (Bam HI, Eco RI, and Pvu II) and cDNA clones for three HLA-D region class II antigen alpha- and beta-chains (DR-beta, DQ-beta, and DQ-alpha) were used. In six families, a total of 11 siblings HLA-DR-identical to the proband were examined. There was no discrepancy between the hybridization patterns of the proband and those of the DR-identical siblings. Two different DQ-B fragment patterns were detected with each one of the serologic specificities DR-2 and DR-4. In both cases, only one of the patterns correlated significantly with diabetes. Thus, DQ-beta genomic hybridization may be used in conjunction with HLA-DR typing to identify individuals with higher relative risk to acquire insulin-dependent diabetes. These results may suggest that insulin-dependent diabetes is associated with the DQ rather than with the DR locus.

Spontaneous insertions into cosmid vector: a warning

During the course of characterization of a human genomic library we found that some of the selected pNNL cosmid clones carried only very short inserts. In addition, several clones that did contain full-length inserts were found to be unstable and generated repeated deletions of various portions of their inserts. Moreover, all the clones examined displayed rearrangements in the vector portions. The rearranged clones that were characterized by restriction mapping were found to have deletions starting between ClaI and HindIII in the region of the cos segment of the pNNL vector used in the construction of the library. We determined the nucleotide sequence of the 1300-bp EcoRI-PvuII segment located in the cos region, and by the computer search we found that it contains Escherichia coli insertion elements IS1.

Sequence of gene and cDNA encoding murine major histocompatibility complex class II gene A beta 2

The murine major histocompatibility complex is known to express two class II molecules, A and E. They are composed of one alpha- and one beta-polypeptide chain. Recently, we reported the finding of an additional beta-chain second domain exon tentatively designated A beta 2. We describe here the nucleotide sequence of the A beta 2 gene and an A beta 2 cDNA clone. A beta 2 displays the same exon organization as the known expressed beta-chain genes, and the predicted A beta 2 polypeptide shows all the characteristic features of the expressed beta-chains. The predicted A beta 2 polypeptide shows 49-56% amino acid sequence identity to A beta and E beta chains and to the human DP, DQ, and DR beta-chains. These are 63-79% homologous to each other, indicating that A beta 2 is the most divergent member of the beta-chain family. The A beta 2 gene seems to be transcribed in the same types of cells as other class II genes. Detection of incompletely spliced A beta 2 mRNA and the finding of a cDNA clone containing an intron segment suggest that A beta 2 transcripts are processed slowly. Hybridizations with A beta 2 probes to restriction enzyme-digested genomic DNA indicate that the A beta 2 gene displays lower allelic polymorphism than the A beta gene.

Intron sequences reveal evolutionary relationships among major histocompatibility complex class I genes

The multigene family of the class I histocompatibility antigens is unusual in that allelic and intergenic differences often are of equal magnitude. It has been suggested that this is due to gene conversion events, which would produce allelic variation but at the same time reduce intergenic differences. We compared the sequences of 11 class I genes in an attempt to elucidate the evolutionary history of this gene family. Our analysis shows that the intron sequences can be used to establish the order of divergence of various class I genes from each other. The results obtained agree with the order of divergence deduced from major insertion and deletion events. It appears that certain genes in the murine TL antigen-encoding region diverged very early from the H-2 and Qa-2,3 genes. The latter can be subgrouped as H-2 and Qa-2,3 genes by both sequence homology and insertion patterns. In contrast to the introns, exon sequences provide less information on evolutionary relationships. Thus, these analyses are consistent with the view that concerted evolution due to gene conversion occurs preferentially in exons.

HLA-DR beta genes vary in number between different DR specificities, whereas the number of DQ beta genes is constant

Probes isolated from DR and DQ beta cDNA and genomic clones were used in hybridizations to restriction enzyme-digested DNA from human homozygous typing cells (HTC) as well as other DR homozygous cells in order to estimate the number of beta genes in the DR/DQ class II region. Varying numbers of DR beta genes were found in HTC of different DR specificities, from possibly one in DR 8 cells to three in cells of DR 2 to 7. The DR beta genes of different specificities seem to be related to one another in a distinct fashion. In contrast, all HTC contain two DQ beta genes per chromosome. The restriction site polymorphism of DQ beta genes is considerably more extensive than that of DQ serology, although one of the genes seems to be nonpolymorphic. In addition to the two DP beta genes identified previously, a minimum of three to five DQ and DR beta genes exist in the human haploid genome.

HLA-DR beta genes vary in number between different DR specificities, whereas the number of DQ beta genes is constant

Probes isolated from DR and DQ beta cDNA and genomic clones were used in hybridizations to restriction enzyme-digested DNA from human homozygous typing cells (HTC) as well as other DR homozygous cells in order to estimate the number of beta genes in the DR/DQ class II region. Varying numbers of DR beta genes were found in HTC of different DR specificities, from possibly one in DR 8 cells to three in cells of DR 2 to 7. The DR beta genes of different specificities seem to be related to one another in a distinct fashion. In contrast, all HTC contain two DQ beta genes per chromosome. The restriction site polymorphism of DQ beta genes is considerably more extensive than that of DQ serology, although one of the genes seems to be nonpolymorphic. In addition to the two DP beta genes identified previously, a minimum of three to five DQ and DR beta genes exist in the human haploid genome.