The organization and diversity of immunoglobulin genes

A comparison of immunoglobulin IGHV, IGHD and IGHJ genes in wild-derived and classical inbred mouse strains

The genomes of classical inbred mouse strains include genes derived from all three major subspecies of the house mouse, Mus musculus. We recently posited that genetic diversity in the immunoglobulin heavy chain (IGH) gene loci of C57BL/6 and BALB/c mice reflects differences in subspecies origin. To investigate this hypothesis, we conducted high-throughput sequencing of IGH gene rearrangements to document IGH variable (IGHV), joining (IGHJ) and diversity (IGHD) genes in four inbred wild-derived mouse strains (CAST/EiJ, LEWES/EiJ, MSM/MsJ and PWD/PhJ) and a single disease model strain (NOD/ShiLtJ), collectively representing genetic backgrounds of several major mouse subspecies. A total of 341 germline IGHV sequences were inferred in the wild-derived strains, including 247 not curated in the international ImMunoGeneTics information system. By contrast, 83/84 inferred NOD IGHV genes had previously been observed in C57BL/6 mice. Variability among the strains examined was observed for only a single IGHJ gene, involving a description of a novel allele. By contrast, unexpected variation was found in the IGHD gene loci, with four previously unreported IGHD gene sequences being documented. Very few IGHV sequences of C57BL/6 and BALB/c mice were shared with strains representing major subspecies, suggesting that their IGH loci may be complex mosaics of genes of disparate origins. This suggests a similar level of diversity is likely present in the IGH loci of other classical inbred strains. This must now be documented if we are to properly understand interstrain variation in models of antibody-mediated disease.

Splitting the difference: the germline-somatic mutation debate on generating antibody diversity

In the debate about the mechanism for the generation of immunological diversity, the initial positions of both 'somaticists' and 'germliners' were diametrically opposed. Then, as data developed favoring first one and then the other side, concessions were made, until the final solution showed that each had been at least partially correct.

Immunity in plants and animals: common ends through different means using similar tools

A comparative approach is potentially useful for understanding the role of mammal innate immunity role in stimulating adaptive immunity as well as the relationship between these two types of immune strategies. Considerable progress has been made in the elucidation of the co-ordinated events involved in plant perception of infection and their mobilisation of defence responses. Although lacking immunoglobulin molecules, circulating cells, and phagocytic processes, plants successfully use pre-formed physical and chemical innate defences, as well as inducible adaptive immune strategies. In the present paper, we review some shared and divergent immune aspects present in both animals and plants.

A high production rate of translatable IgG mRNA accounts for the amplified synthesis of IgG in myeloma cells

The aim of the present work was to determine whether the accumulation of Ig mRNA in myeloma cells is due to a high rate of production or to a high stability of these molecules. Specific mRNAs for the light and heavy polypeptide chains of IgG were isolated from the murine MPC-11 myeloma tumor cells by immune precipitation of polysomes which synthesize these chains. It was found that the immune-precipitated polysomes were enriched 10--30-fold in the gamma and chi mRNA sequences respectively. In the wheat germ cell-free system the chi mRNA preparation was translated mainly into three polypeptides of Mr 25 000, 18 000, and 15 000. The method of immune precipitation of polysomes was also used to characterize three variant clones of MPC-11 myeloma. It was found that little if any gamma-chain polysomes are present in the L-chain producer and non-producer clones, while a substantial amount of chi-chain polysomes was present in the non-producer clone. This may be due to the presence in the non-producer cells of the constant region chi-chain fragment. In order to determine the relative synthesis rate of chi and gamma mRNAs, pulse-labelled polysomes were immune precipitated using antibodies to chi and gamma chains. It was found that chi and gamma mRNA molecules are produced at a very high relative rate each accounting for 10--15% of the total labeled mRNA after 1 h of labeling. These values are higher than the steady-state pool size of chi and gamma mRNA, which was 5--6%, and indicates that the half-life of these molecules is not unusually high. It is concluded that the amplified synthesis of immunoglobulin chains in myeloma cells is mainly due to a high rate of production of translatable chi and gamma mRNAs.

Subcytoplasmic distribution of thyroglobulin mRNA in normal sheep thyroid

The thyroglobulin 33-S mRNA was isolated from sheep thyroid total polysomes. The 33-S RNA, twice purified on a 1% sodium dodecylsulfate/sucrose gradient, was 30-fold enriched in thyroglobulin messenger activity and was estimated as 50% pure by its messenger activity and 80% pure by the electrophoretic profile. It was used as template for complementary DNA synthesis and hybridized up to 85% of the DNA copy with pseudo-first-order kinetics. Back-hybridization kinetics showed that the purified mRNA corresponds to a major kinetic component with a base sequence complexity of 10000 nucleotides as determined by comparison to globin mRNA. Cross-reactivity of [3H]cDNA with liver RNA is less than 10%. Restriction endonuclease digestion of [3H]cDNA yielded a discrete band pattern. The distribution of thyroglobulin mRNA among free polysomes, membrane-bound polysomes and extrapolysomal pools was analyzed using hybridization to the specific [3H]cDNA probe. Free particles were recovered in the supernatant and membrane-bound particles in the pellet after a brief centrifugation of detergent-free homogenate (5 min at 27000 x g: procedure A; 12 min at 130000 x g: procedure B) with precautions taken to avoid cross-contamination. Using procedure A, 80% of thyroglobulin mRNA sequences were found in the membrane-bound fraction. Using procedure B, where contamination of free particles by membrane-bound particles was avoided by high-speed initial centrifugation and further isolation through a discontinuous sucrose gradient, 95-98% of thyroglobulin mRNA sequences were recovered in membrane-bound polysomes. In total polysomes, 89% of thyroglobulin mRNA sequences were in the polysomal area and shifted to ribosomal subunits after EDTA treatment.

Organization of kappa light chain genes in germ-line and somatic tissue

We studied the organization of the kappa light chain genes in germ-line (sperm) and somatic (embryo) tissues. We constructed a plasmid containing a DNA insert coding for the kappa chain MOPC 167 and used the Southern blotting technique to determine the organization of kappa variable and constant region genes. In the haploid genome of the mouse there is only one constant region gene detectable and it has the same organization in sperm and embryo DNAs. There are several variable region genes in sperm and embryo that are related to the Vk167 gene. The organization of the V genes in sperm and embryo DNAs is identical. These results show that there is no rearrangement of variable region genes (or "minigenes") during early embryogenesis.

Antibody diversity

Three important aspects of immunoglobulin gene organization and structure have emerged from studies of cloned immunoglobulin kappa chain genes. (i) Multiple variable genes are encoded separately in the genome of both immunoglobulin-producing and uncommitted (embryonic) cells, thereby establishing the evolutionary base for generating immunoglobulin diversity. (ii) These genes exist as many small, closely related families (subgroups) that share close sequence homology largely within their own subgroup. (iii) Comparison of two cloned variable gene segments derived from a single subgroup reveals a feature of their structure that distinguishes them from fixed genes (that is, globin genes) and provides, through extensive surrounding sequence homology, a large target for intergenic recombination. This last observation suggests that a simple recombination mechanism may account for their genetic instability in both germ line and somatic cells.

Multiple related immunoglobulin variable-region genes identified by cloning and sequence analysis

We have identified at least six EcoRI fragments of mouse DNA that encode variable-region gene sequences closely related to the mouse kappa light chain, MOPC-149. Two of these fragments have been cloned, and the entire nucleotide sequence of the variable-region genes encoded on each has been determined. Both genes encode closely related variable-region sequences extending from codon position 1 through position 97. Neither fragment encodes a constant-region sequence. Although both genes are closely related, they differ from one another and from the sequence expressed in the MOPC-149 cell from which they were cloned. These few differences cluster within the complementarity-determining regions although several occur in framework sequences as well. We therefore conclude that an antibody-producing cell contains genetic information corresponding to its expressed sequence and several other closely related but silent sequences. These initial results raise the possibility that similar sets of genes might exist corresponding to each of the many subgroups already identified among mouse kappa light chains. If true, this would further suggest that the mouse genome might be rich enough in variable-region genes so as to encode a major portion of the variable-region repertoire.

Synthesis of histone messenger RNAs by RNA polymerase II in nuclei from S phase HeLa S3 cells

Nuclei were isolated from synchronized HeLa S3 cells and transcribed utilizing their endogenous RNA polymerases. Our data suggest that S phase nuclei are capable of synthesizing histone mRNA sequences while nuclei from G1 phase cells are not. Transcription of histone mRNA sequences by S phase nuclei can be abolished completely by low levels of alpha-amanitin (1.0 microgram/ml, a concentration which completely inhibits RNA polymerase II). From these results it appears that transcription of the histone mRNA sequences occurs during the S phase but not during the G1 phase of the cell cycle and that RNA polymerase II is responsible for histone gene readout.

Glutamine as a precursor to N-terminal pyrrolid-2-one-5-carboxylic acid in mouse immunoglobulin lambda-type light chains. Amino acid-sequence variability at the N-terminal extra piece of lambda-type light-chain precursors

The mRNA molecules coding for three mouse immunoglobulin lambda-type light (L) chains (MOPC-104E lambda(1), RPC-20 lambda(1), MOPC-315 lambda(2)) programme the cell-free synthesis of precursors larger than the mature proteins. Radioactive amino acid-sequence analyses of each of the three precursors labelled with [(3)H]alanine, [(3)H]serine, [(3)H]glutamine, [(3)H]glutamic acid and [(3)H]threonine showed that an extra piece, at least 18 residues long, is linked to the N-terminus of the mature L-chains. The N-terminal extra-peptide segment may be 19 residues long, since analyses of precursors labelled with [(35)S]methionine indicated an additional N-terminal methionine residue which was recovered in low yields. Presumably this is the initiator methionine, which is known to be short lived in eukaryotes. The mature forms of MOPC-104E, RPC-20 and MOPC-315 lambda L-chains are blocked at the N-termini by pyrrolid-2-one-5-carboxylic acid (pyroglutamic acid). Sequence analyses of precursors labelled with [(3)H]glutamine and [(3)H]glutamic acid showed incorporation only of glutamine in a position that matches with the position of pyrrolid-2-one-5-carboxylic acid in the mature forms of all three precursors, and incorporation of glutamic acid in other positions. The data showed the absence of glutamine-glutamic acid interconversion, since the radioactive peaks obtained from either (3)H-labelled amino acid were discrete, and free from cross-contamination. These results prove that glutamine is the precursor amino acid of pyrrolid-2-one-5-carboxylic acid at the N-termini of the mature MOPC-104E lambda(1), RPC-20 lambda(1) and MOPC-315 lambda(2) L-chains. Thus the formation of pyrrolid-2-one-5-carboxylic acid by cyclization of glutamine is a post-translational event which occurs after, or concomitant with, cleavage of the extra piece from the precursor to yield the mature L-chain. The variable (V) regions (110 amino acid residues) of mouse lambda L-chains are quite similar: when compared with that of MOPC-104E lambda(1) chain, the V-region of RPC-20 lambda(1) chain differs in one residue, and the V-region of MOPC-315 lambda(2) chain differs in 11 residues. The partial sequence data show that the N-terminal extra pieces of the two lambda(1) L-chain precursors have, so far, identical partial sequences; the extra piece of the lambda(2) L-chain precursor differs from these in at least three out of 19 positions.

Immunochemical isolation of gamma-globulin mRNA and estimation of immunoglobulin gene reiteration

The polyribosomes synthesizing gamma-globulin have been isolated by the achievement of specific precipitation using bentonite-treated anti-IgG antibody. The RNA extracted from the immunochemically precipitated polysomes was tested for its ability to direct the synthesis of proteins in a cell-free system. The specific gamma-globulin-synthesizing activity (cpm of gamma-globulin synthesized/microgram RNA) of this RNA was 10-fold greater than that from total polysomes. gamma-globulin mRNA (messenger RNA) isolated by immunoprecipitation was more than 89% pure with respect to contamination by other species of mRNA. The products synthesized by the cell-free system were also analyzed by sodium dodecyl sulphate(SDS)-polyacrylamide gel electrophoresis. This RNA has been hybridized with mouse myeloma DNA. The estimation of immunoglobulin gene reiteration was carried out using hybridization kinetics with consideration given to the DNA/RNA ratio since the estimation from the "half Cot value" is not accurate. The results suggest that in the mouse there are about 20 copies per subgroup of genes coding for the variable region of the H and L chains.

Synthesis of the brain-specific S-100 protein in a cell-free system from wheat embryo programmed with poly(A)-containing RNA from rabbit brain

Polyadenylated polysomal RNA was prepared from rabbit cerebral hemispheres using phenol extraction and chromatography on oligo(dT)-cellulose. This RNA directed the synthesis of the brain-specific S-100 protein in cell-free extracts from wheat embryo. S-100 protein was absent from the products of endogenous incorporation and from a reaction programmed with kidney mRNA. These results suggest that S-100 protein mRNA contains a poly(adenylic acid) sequence and rule out the necessity of a brain-specific factor for translation of -S100 protein mRNA.

Sequences related to immunoglobulin kappa chain messenger RNA in T cells

We investigated by molecular hybridization whether T cells contain RNA sequences homologous to RNA which codes for immunoglobulin kappa-chain (k-chain). A radioactive probe of complementary DNA (cDNA) was prepared by transcription of purified k-chain mRNA from mouse myeloma MOPC-41 with reverse transcriptase (RNA-dependent-DNA nucleotidyltransferase) from avian myeloblastosis virus. The cDNA probably corresponded only to the constant region and 3'-terminus of k-chain mRNA. Kappa-chain cDNA was found to hybridize efficiently with RNA from both thymus cells and an established culture of thymoma cells. The thymus and thymoma cells contained 99.8% and 100% theta-positive cells, respectively. Quantitatively the average thymus T cell (thymus derived lymphocyte) contained about one half as much k-chain mRNA as the average spleen B cell ("bursa" dependent lymphocyte), whereas the thymoma cells contained only 1/33 as much. Control hybridizations of k-chain cDNA with myeloma and liver RNA support the conclusion that T cells in the thymus and in the thymoma cell line synthesize k-chain mRNA-like molecules. The thermal stability of hybrids of k-chain cDNA with RNA from spleen, thymus, thymoma, and another k-chain producing myeloma tumor was lower than that with MOPC-41 RNA. This finding may be due to the existence of several slightly different ck genes in the mouse as suggested by various control experiments.

Purification and translation of an immunoglobulin lambda chain messenger RNA from mouse myeloma

Here we describe the 500-fold purification of an mRNA encoding an immunoglobulin lambda light chain derived from the mouse myeloma tumor, RPC-20. Purification involves the isolation of membrane-bound polysomes, oligo(dT)-cellulose chromatography, and sucrose gradient centrifugation under conditions favoring denaturation of polynucleotide complexes. The mRNA purified in this way directs the cell-free synthesis of a polypeptide which is five or six amino acids longer than the mature form of RPC-20 light chain. In addition to directing the synthesis of a precursor-like polypeptide, the mRNA migrates on electrophoresis as a band containing approximately 1150 nucleotides, about 500 more than required to encode the mature form of the light chain.

Quantitation of constant and variable region genes for mouse immunoglobulin lambda chains

We have synthesized and characterized cDNA complementary to purified mRNA derived from the lambda chain producing myeloma tumor, RPC-20. This cDNA is of sufficinet length to encode the constant region and a major portion of the variable region sequence of the lambda gene. In addition, the expected range of cross-hybridization of this lambda probe has been shown to extend to several different members of the closely related lambda subgroup, as well as to a member of the lambda subgroup represented by MOPC-315. Since there are a minimum of seven known members of the common lambda subgroup in addition to MOPC-315, these sequences, in accordance with the germ line hypothesis, must be represented by a minimum of eight variable region genes. Using the RPC-20 cDNA probe and hybridization kinetic analysis, this sequence was found to be represented as approximately two copies per haploid genome in DNA derived from a variety of k-and lambda-producing tumors and normal tissue. Inasmuch as the cross-hybridization range of the probe has been assessed and a minimum size of the lambda subgroup determined, this observation tends to rule out separate germ line genes corresponding to each individual lambda light chain variant. Certain reservations about these conclusions are discussed.

No detectable reiteration of genes coding for mouse MOPC 41 immunoglobulin light-chain mRNA

RNA fractions rich in immunoglobulin light (L)-chain mRNA were isolated from mouse myeloma MOPC 41 by procedures previously described, and chemically labeled with 125I. These RNA fractions were hybridized with MOPC 41 DNA under conditions of DNA excess. Hybridization conditions were chosen under which the entire sequence of the L-chain mRNA probe, thus including the variable region, remains available for hybridization throughout the reaction. The hybridization (C0t) curve showed double transition kinetics, with one component corresponding to about 250 gene copies and the other to about two to four copies. In contrast, when MOPC 41 L-chain mRNA was further purified as a single band by gel elecptrophoresis in 99% formamide, the hybridization curve showed only a single transition, corresponding to about two to four genes, with the disappearance of the "reiterated" component. That component resulted therefore from contaminating RNA species. The data indicate that no reiteration can be detected by RNase or by hydroxylapatite for the genes corresponding to the entire sequence of MOPC 41 L-chain mRNA, including the untranslated segments, within the limits of detectability of short reiterated segments. It thus appears that there is only one or very few genes corresponding to the 41 L-chain variable region "subgroup" in MOPC 41 DNA. The possibility that the variable genes of plasmocytes might result frm a combination of several nonreiterated germline genes is discussed.

Reiteration frequency of immunoglobulin light chain genes: further evidence for somatic generation of antibody diversity

Methods have been developed for preparing mouse immunoglobulin light chain mRNA of better than 90% purity. Hybridization of both lambda and kappa mRNAs to excess liver DNA yielded results compatible with gene reiteration frequencies of two to three. There was no evidence of hybridization of these highly purified mRNAs to reiterated DNA, and, in fact, the kinetics of hybridization were very similar to that of purified globin mRNA. Purified lambda mRNA from tumors producing structurally different lambda chains were used in competition hybridization experiments. An unlabeled lambda mRNA competed with another, labeled lambda mRNA to the same extent as homologous unlabeled lambda mRNA. That is, base sequence homology among lambda mRNAs is so high that any lambda mRNA should cross-hybridize with all germ line variable (Vlambda) genes at least for those V-regions which are represented among myelomas. From amino-acid sequence data, it is argued that there are probably more than 25 different lambda V regions. Hence it is concluded that the number of germ line genes is too small to account for the diversity of lambda chains. A similar conclusion is drawn for kappa chains.

Characterization of cytoplasmic DNA of mouse-myeloma cells

Cytoplasmic DNA from mouse myeloma cells comprised between 1% and 2% of the total cellular DNA. Detergent-prepared cytoplasmic lysate consisted mainly of 8-S and 22-S species. While these DNA species were present in the 13000 times g pellet of the detergent-prepared cytoplasmic lysate, only the light DNA species was present in the 13000 times g supernatant fraction. In neutral CsCl gradients the DNA of both cytoplasmic fractions had a buoyant density of 1700 g/cm3, which is identical to that of nuclear DNA. The similarity between the cytoplasmic and nuclear DNA was also demonstrated by analysis on alkaline CsCl gradients. A small proportion of closed-circular DNA, presumably of mitochondrial origin, was demonstrated only in cytoplasmic fraction obtained from mechanically disrupted cells and not in detergent-prepared cytoplasmic lysate. It was found that poly (A)-containing mRNA and 28-S ribosomal RNA hybridized to about the same extent to the cytoplasmic DNA as compared to nuclear DNA. The results indicate that most of the cytoplasmic DNA in myeloma cells is similar to nuclear DNA and does not consist of mitochondrial DNA.

Effect of estrogen on gene expression: purification of vitellogenin messenger RNA

We report initial studies on estrogen-mediated regulation of egg yolk protein synthesis in the rooster. Egg yolk proteins are normally synthesized as a large precursor, vitellogenin, in the liver of the laying hen; roosters synthesize vitellogenin only when treated with estrogen. Polysomal RNA from the liver of estrogen-treated roosters was translated in a reticulocyte cell-free system, and the newly synthesized proteins were identified by a highly specific and sensitive indirect immunoprecipitation reaction. The messenger RNA that specifies vitellogenin has been purified more than 800-fold from rooster liver polysomal RNA by a combination of methods, including immunoprecipitation of polysomes and chromatography of RNA on poly(U)-Sepharose.