Structure of human immunoglobulin gamma genes: implications for evolution of a gene family

We have cloned five human immunoglobulin gamma genes from a fetal liver gene library. Four of them encode the known human immunoglobulin gamma chains gamma 1, gamma 2, gamma 3 and gamma 4. A fifth gamma gene seems to be a pseudogene. Nucleotide sequence determination demonstrates that the gamma 3 gene contains four separate hinge exons. Comparison of these hinge exons with those of the other gamma genes indicates that the first hinge exon is homologous to that of the pseudogene, and that the other three hinge exons are homologous to that of the gamma 1 gene, suggesting that the gamma 3 gene ancestor is a hybrid gene created by unequal crossing-over between the ancestral gamma 1 and psi gamma genes. Amplification of the gamma 1-type hinge exon probably followed to complete the gamma 3 gene. This hypothesis inevitably postulates the gene order 5'-gamma 1-gamma 3-psi gamma-3'. Cloning of overlapping chromosomal segments demonstrates that the gamma 2 gene is located 19 kb 5' to the gamma 4 gene. These analyses indicate that the human gamma-gene family has evolved by several types of DNA rearrangemet, including duplication of a complete gene; duplication of a hinge exon; and reassortment of exons by unequal cross-over between two adjacent genes.

Nucleotide sequences of gene segments encoding membrane domains of immunoglobulin gamma chains

The nucleotide sequences of the exons encoding membrane-bound IgG1, IgG2a, and IgG2b of mouse were determined and compared with the sequence of membrane-bound IgM. The sequences indicate that membrane-bound gamma chains bear an additional 71 residues at the COOH termini, including 17-residue acidic, 26-residue hydrophobic, and 28 residue hydrophilic portions. The hydrophobic portion, which seems to be anchored in the lipid bilayer of the membrane, is highly conserved among membrane-bound mu and gamma chains. We propose the presence of a membrane protein that recognizes the conserved hydrophobic segment and anchors the membrane-bound immunoglobulin. Comparison of the nucleotide sequences revealed another example of intervening sequence-mediated domain exchange around one of the membrane exons.

Organization of the constant-region gene family of the mouse immunoglobulin heavy chain

We cloned overlapping DNA segments that encompass the region from the immunoglobulin JH segments to the C gamma 3 gene of BALB/c mouse. We have now cloned the entire region (about 200 kilobases) of the constant-region gene family of the immunoglobulin heavy chain, the organization of which is 5'-JH-6.5 kb-C mu-4.5 kb-C delta-55 kb-C gamma 3-34 kb-C gamma 1-21 kb-C gamma 2b-15 kb-C gamma 2a-14 kb-C epsilon-12 kb-C alpha-3'. Using these cloned DNAs, we have characterized several structural features of the constant-region gene loci. There are no other J region segments except for those at the 5' side of the C mu gene. The S region is 5' to each CH gene except for the C delta gene, and the nucleotide sequences of the S region share some homology. There is no reasonably conserved pseudogene. There are at least two species of reiterated sequences scattered in these loci. Cloning and Southern blot hybridization analyses indicate that the general organizations of the heavy-chain gene loci of BALB/c and C57BL/6 mice, which have many different serological markers, are fundamentally similar but different in the lengths of S regions. Restriction enzyme cleavage maps of the whole constant-region gene loci were constructed with respect to eight restriction endonucleases.

Rearrangements of immunoglobulin genes during differentiation and evolution

Immunoglobulin genes are shown to undergo dynamic rearrangements during differentiation as well as evolution. We have demonstrated that a complete immunoglobulin heavy chain gene is formed by at least two types of DNA rearrangement during B cell differentiation. The first type of rearrangement is V-D-J recombination to complete a variable region sequence and the second type is S-S recombination to switch a constant region sequence. Both types of recombination are accompanied by deletion of the intervening DNA segment. Structure and organization of CH genes are elucidated by molecular cloning and nucleotide sequence determination. Organization of H chain genes is summarized as VH-(unknown distance)-JH-(6.5 kb)-C mu-(4.5 kb)-C delta-(unknown distance)-C gamma 3-(34 kb)-C gamma 1-(21 kb)-C gamma 2b-(15 kb)-C gamma 2a-(14.5 kb)-C epsilon-(12.5 kb)-C alpha. The S-S recombination takes place at the S region which is located at the 5' side of each CH gene. Nucleotide sequence of the S region comprises tandem repetition of closely related sequences. The S-S recombination seems to be mediated by short common sequences shared among S regions. A sister chromatid exchange model was proposed as a mechanism for S-S recombination. Comparison of nucleotide sequences of CH genes indicates that immunoglobulin genes have scrambled by intervening sequence-mediated domain transfer during their evolution.

Structure of a rearranged gamma 1 chain gene and its implication to immunoglobulin class-switch mechanism

An expressed gene for gamma 1 chain of MC 101 myeloma was cloned from a phage library containing partial EcoRI digests of MC 101 DNA. The cloned DNA was analyzed by restriction enzyme cleavage, Southern blot hybridization, R-loop formation, and nucleotide sequence determination. The results indicate that the expressed gamma 1 chain gene comprises at least four germline DNA segments, namely a variable-region gene, a segment of the 5' flanking region of the mu chain gene (containing J regions), a segment of the 5' flanking region of the alpha chain gene, and the gamma 1 chain gene with its flanking regions. The presence of the alpha chain gene-flanking switch (S) region (S alpha region) at the 5' side of the gamma 1 chain gene-flanking region (S gamma 1 region) indicates that the heavy chain class switch may not be mediated by stepwise linear deletion along the order of the heavy chain constant-region genes (5'-mu-gamma 3-gamma 1-gamma 2b-gamma 2a-alpha-3'). We propose a siter-chromatid exchange model that explains class switch-associated deletion of heavy chain genes by unequal crossing-over events between sister chromatids.

The complete nucleotide sequence of mouse immunoglobin gamma 2a gene and evolution of heavy chain genes: further evidence for intervening sequence-mediated domain transfer

We have determined the complete nucleotide sequence (1990 base pairs) of mouse immunoglobulin gamma 2a gene, and compared it with the sequences of other gamma subclass genes so far sequenced, i.e. gamma 1 and gamma 2b genes. Divergence of the nucleotide sequence between a compared pair of the gamma genes varies extensively among different segments of the gene. For example, comparison of the gamma 2a and gamma 2b genes has revealed a remarkable homology in a long continuous segment (about 900 bases) that covers from the 3' portion of the first intervening sequence to the third intervening sequence. However, there is no particular segment of the gamma gene that is conserved universally among the three gamma genes. These findings suggest that, during their evolution, segments of the gamma genes had been scrambled between different subclass genes through recombinations within intervening sequences, thus providing further evidence for the intervening sequence-mediated domain transfer hypothesis. We have discussed several possible phylogenic trees which can explain the difference of divergence in various segments of the gamma genes.

Cloning of mouse immunoglobulin epsilon gene and its location within the heavy chain gene cluster

Mouse immunoglobulin epsilon chain gene was cloned from DNA of a hybridoma producing anti-dinitrophenyl IgE, which was constructed by fusing a spleen cell of a BALB/c mouse with a variant clone of MOPC21 myeloma (IgG1 producer). Because a given active heavy chain constant region (CH) gene is linked to a heavy chain joining segment (JH) gene at its 5' side, the expressed C epsilon gene of the hybridoma was cloned from a phage library containing partial Sau3A digests of IgE hybridoma DNA by using a J gene fragment as a probe. Among 6 X 10(5) phages screened, five positive clones were obtained and three of them were identified as C epsilon gene clones by restriction mapping, Southern blot hybridization, R-loop formation, and partial nucleotide sequence determination. The determined nucleotide sequence predicted the amino acid sequence which resembles a part of the CH3 domain of human epsilon chain. The deletion profile of the C epsilon gene in various myelomas expressing different CH genes indicates that the C epsilon gene is located between the C gamma 2a and C alpha genes. The linkage (5'-epsilon-alpha-3') was directly confirmed by molecular cloning of the overlapping chromosomal segments from newborn mouse DNA.

Repetitive sequences in class-switch recombination regions of immunoglobulin heavy chain genes

Immunoglobulin class switch involves a unique recombination event that takes place at the region 5' to each heavy chain constant region gene during B lymphocyte differentiation. Such regions that are responsible for the class-switch recombination are defined as S regions (Kataoka et al., Proc. Natl. Acad. Sci. USA 77, 919, 1980). We have cloned a rearranged gamma 2b gene from a mouse myeloma (MPC11) and compared its structure with the germ line counterparts. The rearranged gamma 2b gene contained the 5' flanking region of the gamma 3 gene (S gamma 3 region) which are linked to the 5' flanking region of the gamma 2b gene (S gamma 2b region). We have determined nucleotide sequences surrounding the recombination site of the rearranged and germ line gamma 2b genes, which include the S gamma 2b and S gamma 3 regions. Both gamma 2b and S gamma 3 regions comprise tandem repetition of conserved units of 49 bp. Similar 49 bp repeating units are also found in the previously determined sequence of the S gamma 1 region in which class-switch recombination took place in MC101 myeloma. The nucleotide sequences of the S gamma 1, S gamma 2b and S gamma 3 repeating units share significant homology with each other. The S mu region, partial nucleotide sequence of which was previously determined, contains abundant short sequences such as AGCT, TGGG and AGCTGGGG which are shared in common by repeating sequences in S gamma regions. These results suggest that the recombination responsible for class switch from mu to gamma or from a gamma to another gamma, may be facilitated directly or indirectly by homology of repeating sequences in S regions.

Ordering of mouse immunoglobulin heavy chain genes by molecular cloning

We have determined the order of the mouse immunoglobulin gamma 1, gamma 2 b, gamma 2 a and epsilon genes by molecular cloning of overlapping chromosomal segments. The results clearly demonstrate that the order is 5'-gamma 1-(21 kilobases)-gamma 2b-(15 kilobases)-gamma 2a-(15 kilobases)-epsilon-3'. There seem to be no J regions at the 5' side of each constant region gene so far obtained except for the mu gene and these constant region genes seem to have repetitive sequences characteristic of switch (S) regions at their 5' side.

Cloning of human immunoglobulin mu gene and comparison with mouse mu gene

We have cloned a 12 kb DNA segment containing human mu gene and its flanking sequence from human fetal liver DNA library using mouse mu gene as a probe. Partial nucleotide sequence determination shows that the cloned DNA contains the sequence encoding human mu chain. This is the first constant region gene of the human heavy chain that is cloned. We have compared human and mouse mu genes by heteroduplex analysis and Southern blot hybridization. The results clearly show that not only the sequence encoding the CH4 domain but also the 5'-flanking (S mu) sequence is conserved between human and mouse mu genes, suggesting that the nucleotide sequence in the S mu region has an important biological function, presumably a recognition signal for the class switch recombinant as proposed previously.

Induction and regulation of immunoglobulin expression in a murine pre-B cell line, 70Z/3. I. Cell cycle-associated induction of sIgM expression and kappa-chain synthesis in 70Z/3 cells by LPS stimulation

Stimulation of a murine pre-B cell line, 70Z/3, with LPS induced sIgM expression and an increase of L kappa-chain mRNA within 12 hr. In synchronized 70Z/3 cells, the cell division cycle was 10 to 11 hr and LSP-stimulation did not affect the cell division cycle. LPS-signals given at G1/S boundary induced sIgM expression in the G2 to M-phase. On the other hand, LPS-signals given after M-phase did not induce sIgM expression. Inhibition of cell division with demecorcin did not affect sIgM expression in the M-phase. Induction of intracellular kappa-chain synthesis was also observed in the G2 to M-phase when the LPS-stimulation was provided at G1/S boundary, but LPS-signals given after the M-phase did not induce de novo synthesis of kappa-chain. These results showed that LPS-induced sIgM expression and synthesis of kappa-chain were cell cycle-related events and sIgM expression was associated wih de novo synthesis of kappa-chain.

Induction and regulation of immunoglobulin expression in a murine pre-B cell line, 70Z/3. I. Cell cycle-associated induction of sIgM expression and kappa-chain synthesis in 70Z/3 cells by LPS stimulation

Stimulation of a murine pre-B cell line, 70Z/3, with LPS induced sIgM expression and an increase of L kappa-chain mRNA within 12 hr. In synchronized 70Z/3 cells, the cell division cycle was 10 to 11 hr and LSP-stimulation did not affect the cell division cycle. LPS-signals given at G1/S boundary induced sIgM expression in the G2 to M-phase. On the other hand, LPS-signals given after M-phase did not induce sIgM expression. Inhibition of cell division with demecorcin did not affect sIgM expression in the M-phase. Induction of intracellular kappa-chain synthesis was also observed in the G2 to M-phase when the LPS-stimulation was provided at G1/S boundary, but LPS-signals given after the M-phase did not induce de novo synthesis of kappa-chain. These results showed that LPS-induced sIgM expression and synthesis of kappa-chain were cell cycle-related events and sIgM expression was associated wih de novo synthesis of kappa-chain.

Nucleotide sequences of class-switch recombination region of the mouse immunoglobulin gamma 2b-chain gene

We have cloned a rearranged gamma 2b-chain gene from mouse myeloma MOPC141. Nucleotide-sequence determination demonstrated that the rearranged gamma 2b-chain gene was formed by a recombination between the region flanking the 5'-ends of the embryonic mu-chain gene and that of the gamma 2b-chain genes. Nucleotide sequences similar to the one located adjacent to the recombination site were found in other parts of the region flanking the 5'-end of the mu-chain-gene, as well as in the region flanking the 5'-end of the gamma 1-chain gene. The common sequence (GGTANNAAAGNAC) shares extensive homology with the sequence proximal to the insertion site of the bacterial insertion element IS2.

Complete nucleotide sequence of mouse immunoglobulin mu gene and comparison with other immunoglobulin heavy chain genes

We have determined the complete nucleotides sequence (2168 bases) of the immunoglobulin mu gene cloned from newborn mouse DNA. The cloned 13kb fragment contained the entire constant region gene sequence that is interrupted by three intervening sequences at the junction of domains as previously shown in the gamma 1, gamma 2 b and alpha genes. The amino acid sequence predicted by the nucleotide sequence agrees with that of the mu chain secreted by a myeloma MOPC104E except for 8 residues out of 448 residues. The homologous domains of the mu, gamma 1 and gamma 2b genes are more similar to each other than the different domains of the mu genes are. The result implicates that the class of the immunoglobulin heavy chain genes diverged after the heavy chain genes established the multi-domain structure. The short intervening sequences of the mu and gamma genes are more conserved than the coding sequences except for the COOH-terminal domains. The results implicate that the nucleotide sequence of the intervening sequence is under selective pressure, possibly to maintain a secondary structure of the nuclear RNA to be spliced.

Deletion of immunoglobulin heavy chain genes from expressed allelic chromosome

We have studied the organization of immunoglobulin heavy-chain genes in a gamma 2b-chain (BALB/c allotype)-producing myeloma BKC F1 # 15 induced in a F1 mouse between C57BL and BALB/c. Southern blot hybridization studies using cloned mu, gamma 1 and gamma 2b-chain genes as probes demonstrate that the mu- and gamma 1-chain genes of the expressed chromosome are deleted while these genes of the unexpressed chromosome are retained. The gamma 2b-chain gene of the expressed allele is rearranged while that gene of the unexpressed allele seems unchanged, as do the gamma 2a-chain genes. These results support the allelic deletion mechanism in heavy-chain class switch and the order of H chain genes.

Cloning and determination of a putative promoter region of a mouse ribosomal deoxyribonucleic acid fragment

An endonuclease EcoRI digest of mouse DNA was subjected to molecular cloning, after partial purification with respect to the ribosomal RNA sequence, using lambda gtWES x lambda B with an in vitro packaging technique. Twelve positive clones were obtained from approximately 2 X 10(4) plaques. One of the clones transferred to the plasmid pBR322 (PMrEL-1) was about 14.9 kb long, hybridizing only with 18S rRNA but not with 28S rRNA. Hybridization of restriction fragments and electron microscopic studies of the R-loop confirmed that this fragment carried about half of the 18S rRNA sequences at one end, suggesting that it contained the initiation site for the 45S preribosomal RNA (pre-rRNA). S1-nuclease protection mapping with hybrids between restriction fragments of the cloned DNA and the 45S pre-rRNA indicated that at least major transcription of the 45S RNA started at a site approximately 4.0 kb upstream from the 5' end of the 18S rRNA. This was confirmed by electron microscopic observations of these hybrids.

Untranslated immunoglobulin kappa light chain mRNA in a lambda light chain-producing mouse myeloma, MOPC104E

Fourteen clones were isolated in culture from a mouse myeloma, MOPC104E. All clones had kappa and lambda types of light chain mRNAs in approximately equimolar quantity as assayed by hybridization with specific complementary DNA (cDNA). However, the myeloma produces and secretes only lambda-type light chain protein. Both kappa- and lambda-type mRNAs in these clones were indistinguishable from kappa- and lambda-type mRNAs of other myelomas with respect to (a) adsorption to oligo-(dT) cellulose, (b) molecular size (12.6 S), and (c) thermal stability of the hybrids formed with corresponding cDNA. The kappa chain mRNA of MOPC104E cells, however, was translated very inefficiently both in vivo and in vitro, whereas the lambda chain mRNA was translated efficiently. These results indicate that each cell of MOPC104E myeloma synthesizes a crippled kappa chain mRNA in addition to a normal lambda chain mRNA.

Nucleotide sequence divergence of mouse immunoglobulin gamma 1 and gamma 2b chain genes and the hypothesis of intervening sequence-mediated domain transfer

The nucleotide sequences of the constant portions of mouse immunoglobulin gamma 1 and gamma 2b genes were compared. A remarkable homology was found in a long (about 500 nucleotides) continuous segment including the entire CH1 coding region and about the first half of the first intervening sequence. Furthermore, comparison of amino acid sequences of four gamma-class chains revealed that the CH1 domain shows limited divergence among gamma 1, gamma 2a, and gamma 2b. Interestingly, the homology region extends to the CH2 domain in gamma 2a and gamma 2b. These findings suggest that, during their evolution, a double unequal crossing-over event has taken place at different intervening sequences, resulting in the transfer of the DNA segment coding for the CH1 domain or CH1-CH2 domains. A possible evolutionary implication for such an "intervening sequence-mediated domain transfer" event is discussed.

Immunoglobulin gamma 1 heavy chain gene: structural gene sequences cloned in a bacterial plasmid

Immunoglobulin gamma 1 heavy chain cDNA was cloned into an Escherichia coli plasmid pCR1 and its nucleotide sequence was determined. The hybrid plasmid contained approx. 900-bases-long gamma 1 chain cDNA sequence, including the complete sequence of the CH2 and CH3 domains and the 3' untranslated region, and partial sequence of the CH1 domain. The nucleotide sequence predicts an extra lysine at the carboxyl-terminus of the gamma 1 chain. Comparison of the nucleotide sequence of 3' untranslated regions of the immunoglobulin gamma 1 chain and kappa light chain showed a significant homology although lengths are quite divergent.