Alternate splicing pathways of the immunoglobulin heavy chain transcript of a teleost fish,Ictalurus punctatus

Previously we sequenced a partial cDNA clone encoding the 3' region of the message for the membrane receptor form of the heavy (mu) chain of the channel catfish which indicated that the first transmembrane (TM1) exon is spliced directly to the C mu 3 exon and not into a cryptic site within the CH4 exon, as occurs in other vertebrates. Studies utilizing polymerase chain reaction analysis of mRNA and further analysis of cDNA clones now confirm that the only detectable splicing pattern used in micron production by the channel catfish utilizes this C mu 3----TM1 pathway of pre-mRNA splicing.     

Complete structure and organization of immunoglobulin heavy chain constant region genes in a phylogenetically primitive vertebrate

Immunoglobulin (Ig) gene organization in Heterodontus francisci (horned shark), a phylogenetically primitive vertebrate, is unique. Homologous Ig heavy chain variable (VH) and constant region (CH) specific probes were used to screen a spleen cDNA library constructed in lambda gt11. Both secretory (SEC) and transmembrane (TM) cDNA clones were recovered; the latter were identified by a negative selection strategy. The complete sequence of the CH portion of a Heterodontus genomic DNA-lambda clone also was determined. The sequences of the individual CH genes differ from each other in all exons. When compared to mammalian prototypes, similarities in exon and intron organization as well as conservation of sequences involved with differential splicing of SEC and TM mRNA indicate that Heterodontus heavy chain genes are of the mu type, although intron lengths are uniformly longer in Heterodontus. Heterodontus genes are not associated, however, with the family of DNA sequences that have been implicated in heavy chain class switching in mammals. Spleen cDNA library screening and RNA blot analyses indicate that mRNAs encoding TM Ig are exceedingly rare. The relationship between this quantitative difference and the distribution of polyadenylation signal sequences suggests that regulation of Ig gene expression in Heterodontus may be highly dependent on position effects.     

Gene segments encoding membrane domains of the human immunoglobulin gamma 3 and alpha chains

The carboxyterminal region of the heavy chains, according to its hydrophilic or hydrophobic properties, determines whether the immunoglobulin will be secreted or membrane-bound. We have determined the nucleotide sequences of the human IGHG3, IGHA1, and IGHA2 membrane exons isolated from genomic DNA libraries. The IGHG3 M1 and M2 exons are separated by a long intron of 2.1 kilobases (kb) containing an highly repeated motif of 34 base pairs (bp). The IGHA1 and IGHA2 genes, like the mouse Igh-A gene, have a single exon encoding the extracellular, transmembrane, and cytoplasmic regions. For each class of immunoglobulins, the sequences of membrane exons are highly conserved between human and mouse, but no alignment is possible for the flanking regions. In contrast, for a same species, the sequences of the heavy chain membrane exons differ from one class to another. While the hydrophobic profile of the membrane core is well conserved, the cytoplasmic region differs in length and in composition. None of the intracellular domains presents the sequence implied in signal transduction, implying that membrane immunoglobulins need other proteins, which probably interact with the constant or membrane domain, to transmit signals leading to B-cell activation.The nucleotide sequence data reported in this paper have been submitted to the EMBL nucleotide sequence database and have been assigned the accession numbers M35288-91. Address correspondence and offprint requests to: M.-P. Lefranc.     

The nucleotide sequence of the mouse immunoglobulin epsilon gene: comparison with the human epsilon gene sequence

We have determined the nucleotide sequence of the immunoglobulin epsilon gene cloned from newborn mouse DNA. The epsilon gene sequence allows prediction of the amino acid sequence of the constant region of the epsilon chain and comparison of it with sequences of the human epsilon and other mouse immunoglobulin genes. The epsilon gene was shown to be under the weakest selection pressure at the protein level among the immunoglobulin genes although the divergence at the synonymous position is similar. Our results suggest that the epsilon gene may be dispensable, which is in accord with the fact that IgE has only obscure roles in the immune defense system but has an undesirable role as a mediator of hypersensitivity. The sequence data suggest that the human and murine epsilon genes were derived from different ancestors duplicated a long time ago. The amino acid sequence of the epsilon chain is more homologous to those of the gamma chains than the other mouse heavy chains. Two membrane exons, separated by an 80-base intron, were identified 1.7 kb 3' to the CH4 domain of the epsilon gene and shown to conserve a hydrophobic portion similar to those of other heavy chain genes. RNA blot hybridization showed that the epsilon membrane exons are transcribed into two species of mRNA in an IgE hybridoma.     

用基因组DNA剪接技术克隆SIgA相关基因

目的：克隆分泌型IgA（SIgA）相关基因--J链基因(IgJ)、多聚免疫球蛋白受体基因（pIgR）和IgA重链恒定区基因（IGHA）,为进一步构建SIgA真核表达质粒奠定基础。方法：采用本室建立的"基因组DNA剪接"技术,根据已发表的IgJ、pIgR和IGHA的核苷酸序列,通过计算机软件分别设计各个基因片段外显子的优化引物,从人外周血基因组DNA中直接扩增各基因的外显子序列;然后人工设计融合相邻外显子的融合引物,采用重叠PCR技术,把各基因片段的外显子串联起来形成全长编码序列,完成基因组DNA的体外剪接。扩增的PCR产物纯化后克隆到pGEM-T Easy Vector中,通过DNA测序对阳性克隆进行分析鉴定。结果：PCR扩增的IgJ、pIgR和IGHA基因与预期大小一致;测序结果表明本实验获得的上述基因与GenBank中的目标基因序列完全一致。结论：本文通过基因组DNA剪接技术成功克隆人类SIgA三个相关基因,提示此技术是合成多外显子cDNA的有效手段。     

Mechanisms of divergence and convergence of the human immunoglobulin alpha 1 and alpha 2 constant region gene sequences

Nucleotide sequences of the human alpha 1 and two allelic alpha 2 immunoglobulin heavy chain constant region genes are presented. The genes contain three exons, each encoding a single constant region protein domain. The protein hinge region is encoded at the 5' end of the second exon, and the rapid evolutionary changes in length of the hinge correspond to duplications or deletions within the hinge-coding region, probably facilitated by repeats in the DNA sequence. Alignment of the alpha 1 and alpha 2 gene sequences reveals an unusual coupled deletion-duplication in the 5'-flanking region, which can be explained in terms of a slipped-strand mispairing model. Comparison of nucleotide sequences of the alpha 1 gene and two alleles of the alpha 2 gene indicates a localized transfer of genetic information from the 3' end of the alpha 1 gene to one of the alpha 2 alleles, probably by a gene conversion. At one end of the region within which conversion apparently occurred, there is a 40 bp sequence of the type that can form Z-DNA.     

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.     

Cloning and characterization of the non-catalytic heavy chain of mouse complement factor I gene: structure comparison with the human homologue

The gene sequence encoding the non-catalytic heavy chain of mouse complement factor I (mCFI) was cloned and its exon-intron organization and domain structure characterized. The genomic organization of mCFI differs in several aspects from its human homologue (hCFI). The intron sizes are remarkably different. Exons 2 and 4 in mCFI are larger than their counterparts in hCFI by 9 bp and 6 bp respectively. Whereas the diversity (D) region of hCFI is encoded by two exons (exon 7 or hD2 and exon 8 or hD4), this region in mCFI is encoded by three exons; exon 6A or mD1 (located at the 3'-end of the LDLr A2 domain), exon 7 or mD2 and exon 8, an extended exon (56 bp) composed of mD3, fused upstream of mD4. In contrast, hCFI lacks D1 and D3 subregions and exon 8 in hCFI consists of only hD4, 36 bp in length. Thus the heavy chain of mCFI is organized into 10 exons compared to 9 exons in hCFI.     

Immunoglobulin heavy chain constant region of five Acipenseridae: cDNA sequence and evolutionary relationship

The immunoglobulin M (IgM) heavy chain constant region genes of Russian sturgeon (Acipenser gueldenstaedtii), Sterlte sturgeon (Acipenser ruthenus), Amur sturgeon (Acipenser schrenckii), Chinese sturgeon (Acipenser sinensis) and Great sturgeon (Huso huso) were cloned and analyzed with molecular biology and bioinformatics methods. We cloned IGH nucleic acid sequences by RT-PCR using the specific primer, then determined the characteristics and functions of the amino acid sequences. The gene contains four constant region domain-encoding exons (CH1-4), of which CH4 sub-regions were the most conserved in IgM heavy chain constant region domain and had the highest identity within all the experimental species. According to the analysis of the phylogenetic tree, the variation expectation value (K(aa)), and species differentiation time (T) in the CH4 sub-region, we found that Chinese sturgeon and the other five sturgeon form one whole bifurcation of the tree, while, among the five left, Amur sturgeon and Huso sturgeon, Russian sturgeon and Siberian sturgeon (data from GenBank), Sterlte itself forms three other bifurcations. This result can clearly explain the relations of taxonomic status, geographical distribution and evolution among the species studied.     

Immunoglobulin heavy chain gene organization and complexity in the skate, Raja erinacea

Immunoglobulin heavy chain genes from Raja erinacea have been isolated by cross hybridization with probes derived from the immunoglobulin genes of Heterodontus francisci (horned shark), a representative of a different elasmobranch order. Heavy chain variable (VH), diversity (DH) and joining (JH) segments are linked closely to constant region (CH) exons, as has been described in another elasmobranch. The nucleotide sequence homology of VH gene segments within Raja and between different elasmobranch species is high, suggesting that members of this phylogenetic subclass may share one VH family. The organization of immunoglobulin genes segments is diverse; both VD-J and VD-DJ joined genes have been detected in the genome of non-lymphoid cells. JH segment sequence diversity is high, in contrast to that seen in a related elasmobranch. These data suggest that the clustered V-D-J-C form of immunoglobulin heavy chain organization, including germline joined components, may occur in all subclasses of elasmobranchs. While variation in VH gene structure is limited, gene organization appears to be diverse.     

Secretion of a homodimeric V alpha C kappa T-cell receptor-immunoglobulin chimeric protein

Transfection into lymphoid cells of a chimeric T-cell receptor-immunoglobulin gene has been used to generate a secreted water-soluble form of the variable (V) domain of a human T-cell receptor alpha chain for use in structural (i.e. x-ray crystallographic) studies. The chimeric protein consists of the V alpha region of the T-cell receptor of a diphtheria toxoid-specific human T-cell clone fused to a human immunoglobulin kappa light chain constant (C) region. It is efficiently secreted by myeloma cells as a noncovalent homodimer of 65-kDa molecular mass in the absence of either immunoglobulin heavy or light chain. The V alpha C kappa protein is extensively glycosylated, and its secretion is glycosylation-dependent. Chimeric genes containing the V beta region of this particular T-cell receptor linked to immunoglobulin C kappa or C gamma 2 regions are expressed intracellularly, but the products, although glycosylated, are not secreted, nor do they assemble with the V alpha C kappa protein. This suggests that the chimeric beta chain-immunoglobulin proteins are incorrectly folded and/or processed due either to the design of the gene fusions themselves or to the absence of vital T-cell-specific accessory molecules in the myeloma host.     

The expression and characterization of rat IgE produced by construction of the epsilon-heavy chain gene from exon modules.

A system of exon "modules" was produced from the functionally rearranged epsilon-heavy gene isolated from the rat IgE-secreting immunocytoma IR162. The five individual exons, encoding the variable and constant region domains, were isolated and subcloned into the multiple cloning site of a pair of plasmid vectors with opposed orientation multiple cloning sites. The use of opposed orientation multiple cloning sites and the flanking restriction enzyme sites contained therein allows for the modular manipulation of the gene. These exon modules were initially used to reconstruct the epsilon-heavy chain gene into the native configuration to demonstrate the efficacy of the modular system for synthesis of IgE. Upon transfection into the rat myeloma cell line Y3, the reconstructed gene produced a polypeptide that associated with the endogenous light chain polypeptide and was secreted from the cell as tetrameric IgE. All physical and functional characterizations indicate that the IgE molecule produced is indistinguishable from native IR162 IgE. This modular system of exons will facilitate the manipulation of IgE structure through the systematic assembly of different epsilon-heavy chain mutant constructions. The resulting novel IgE proteins will be very useful to study the molecular nature of the interaction of IgE with its Fc receptor.     

The nucleotide sequence of a human immunoglobulin C gamma1 gene

We report the nucleotide sequence of a gene encoding the constant region of a human immunoglobulin gamma 1 heavy chain (C gamma 1). A comparison of this sequence with those of the C gamma 2 and C gamma 4 genes reveals that these three human C gamma genes share considerable homology in both coding and noncoding regions. The nucleotide sequence differences indicate that these genes diverged from one another approximately 608 million years ago. An examination of hinge exons shows that these coding regions have evolved more rapidly than any other areas of the C gamma genes in terms of both base substitution and deletion/insertion events. Coding sequence diversity also is observed in areas of CH domains which border the hinge.     

Evolution of the human killer cell inhibitory receptor family

Phylogenetic analysis of different domains of human natural killer cell inhibitory receptors (KIR) implicated both intragenic duplication and deletion of exons and interlocus recombination in the evolution of these receptors. In phylogenies of the extracellular immunoglobulin (Ig) superfamily C2-set domains and of the pre-membrane (PM) domain, KIR receptors having two C2-set domains and those having three such domains tended to form separate clusters. However, the phylogenies of the transmembrane (TM) and cytoplasmic (CYT) domains showed quite different topologies, suggesting that major sites of interlocus recombination have been between exon 6 (encoding PM) and exon 7 (encoding TM) and between exon 7 and exons 8-9 (encoding CYT). Examination of the pattern of nucleotide substitution in the exons encoding Ig C2-set domains supported the hypothesis that positive Darwinian selection has acted to diversify the residues within these domains that are involved in contact with class I MHC molecules.     

Expression of a recombinant murine IgE in transfected myeloma cells

We constructed a recombinant gene encoding an immunoglobulin (Ig) heavy chain consisting of the variable region from the phosphorylcholine (PC)-specific secreting myeloma MOPC167 and the epsilon constant region from SJL mice. This gene, cloned into the shuttle vector pSV2gpt, was transfected into J558L myeloma cells, and stable transformants that expressed the epsilon gene were cloned. The IgE heavy chain in these transformants is associated with the endogenous lambda light chain and is secreted as an intact IgE molecule. However, the secreted IgE does not bind to PC conjugated to bovine serum albumin (PC-BSA). The MOPC167 kappa chain gene was cloned into the shuttle vector pSV2neo and was transfected into the epsilon heavy-chain transformant. Stable transformants were cloned that expressed both the epsilon heavy chain and the kappa light chain. IgE secreted from such a transformant was shown to bind to PC-BSA. Both types of secreted recombinant IgE bound to rat basophilic leukemia (RBL) cells, but only the IgE produced by the cell line transformed with the MOPC167 kappa gene could be cross-linked with PC-BSA to cause serotonin release.     

A second gene, VpreB in the lambda 5 locus of the mouse, which appears to be selectively expressed in pre-B lymphocytes.

The murine gene lambda 5 is selectively expressed in pre-B lymphocytes. Of the three exons encoding lambda 5, exons II and III show strong homologies to immunoglobulin lambda light (L) chain gene segments, i.e. to J lambda intron and exon, and C lambda exon sequences respectively. We have now found, 4.6 kb upstream of lambda 5, another gene composed of two exons which is selectively expressed in pre-B cell lines as a 0.85 kb mRNA potentially coding for a protein of 142 amino acids including a 19 amino acid-long signal peptide. The 5' sequences of this gene show homologies to sequences encoding the variable regions of kappa and lambda L chains and of heavy (H) chains. The deduced amino acid sequence contains the consensus cysteine residues as well as other consensus amino acids at positions which characterize immunoglobulin (Ig) domains. We call the second gene VpreB. The 3' end of VpreB encoding the 26 carboxyl terminal amino acids shows no homology to any known nucleotide sequence. The putative protein encoded by VpreB is a potential candidate for association with the putative protein encoded by lambda 5, and thereby a candidate for association with H chains in pre-B cells. Southern blot analysis of DNA from liver (germ line) and 70Z/3 pre-B cell lines reveals two genes which hybridize to the VpreB gene. We call VpreB1 the gene which is found 5' of lambda 5. The other gene, called VpreB2, which has not yet been located within the genome, shows 97% nucleotide sequence homology to VpreB1 in an area of 1 kb which covers the coding region of the gene.(ABSTRACT TRUNCATED AT 250 WORDS)