Sumiko Nakai

Long terminal repeat-like elements flank a human immunoglobulin epsilon pseudogene that lacks introns.

There are at least three immunoglobulin epsilon genes (C epsilon 1, C epsilon 2, and C epsilon 3) in the human genome. The nucleotide sequences of the expressed epsilon gene (C epsilon 1) and one (C epsilon 3) of the two epsilon pseudogenes were compared. The results show that the C epsilon 3 gene lacks the three intervening sequences entirely and has a 31‐base A‐rich sequence 16 bases 3′ to the putative poly(A) addition signal, indicating that the C epsilon 3 gene is a processed gene. The C epsilon 3 gene sequence is homologous to the five separate DNA segments of the C epsilon 1 gene; namely, a segment in the 5′‐flanking region (100 bases) and four exons, which are interrupted by a spacer region or intervening sequences. Long terminal repeat (LTR)‐like sequences which contain TATAAA and AATAAA sequences as well as terminal inverted repeats are present in both 5′‐ and 3′‐flanking regions. The 5′ and 3′ LTR‐like sequences do not, however, constitute a direct repeat, unlike transposable elements of eukaryotes and retroviruses. The 3′ LTR‐like sequence is repetitive in the human genome, but is not homologous to the Alu family DNA. Models for the evolutionary origin of the processed gene flanked by the LTR‐like sequences are discussed. The C epsilon 3 gene has a new open frame which codes potentially for an unknown protein of 292 amino acid residues.

The Bacillus subtilis dnaC gene encodes a protein homologous to the DnaB helicase of Escherichia coli

Within the region of the Bacillus subtilis chromosome assigned to us in the genome sequencing project, we found a gene, the product of which is similar to the DnaB protein (replicative DNA helicase) of Escherichia coli. Three B. subtilis dna gene mutations, dnaC30 and ts56 causing defects in elongation and ts199 causing a defect in the initiation of replication, were mapped in the gene by transformation and DNA sequencing. Both dnaC30 and ts56 have been located near the amino-terminal end of the B. subtilis DnaC protein. In contrast, ts199 has been located near the carboxy-terminal of the protein. Our results indicate that the B. subtilis dnaC gene encodes a counterpart of the E. coli dnaB helicase.

Human immunoglobulin D segments: isolation of a new D segment and polymorphic deletion of the D1 segment

We have isolated and identified a new human germline D segment which is not physically linked to the known D cluster. The nucleotide sequence of the new D segment was highly homologous with the known D segments. Frequent polymorphic deletion of the D1 segment was found in the Japanese population. Nucleotide sequences surrounding the deletion indicate that homologous recombination is likely to be responsible for the deletion of the D1 segment.

Organization and Reorganization of Constant Region Genes of Immunoglobulin Heavy Chains: Genetic Basis for Class Switching

We have determined the complete organization of the mouse CH gene family, which is comprised of the 8 CH genes in the order 5’-JH-6.5kb-Cμ-4.5kb-Cδ-55kb-Cγ3-34kb-Cγ1-21kb-Cγ2b-15kb-Cγ2a-14kb-Ce-12kb-Cα-3’. The S regions, which contain characteristic tandemly repeated unit sequences, are located 5’ to each CH gene except for the Cδ gene. There are at least two types of repetitive sequences dispersed in this 200 kb region. No pseudogenes are present. The arrangements of the CH genes in BALB/c and C57BL mice are similar, but the lengths of the S regions vary. The basic structures of all the CH genes are similar in that coding sequences are interrupted at the junctions of the domains and the hinge regions. Comparison of the nucleotide sequences of the CH genes revealed that sequence segments have been exchanged among members of the CH gene family. Cloning and characterization of human Cγ genes, i.e. Cγ1, Cγ2, Cγ3, Cγ4 and φCγ, indicate that the human Cγ gene family evolved by dynamic DNA rearrangements, including gene duplication, exon duplication, and exon reassortment by unequal crossing-over. A human pseudo-epsilon gene (Ce3) is a processed gene that has completely spliced out introns. The presence of movable genetic elements surrounding the Ce3 gene suggests that the Ce gene evolved by a translocation mechanism. Although S-S recombination has been shown to take place in myelomas and hybridomas secreting a large amount of immunoglobulin, analyses of the CH gene organization in normal spleen B cells bearing immunoglobulin on their surface suggest that RNA splicing may be responsible for the first step in class switching, followed by S-S recombination. The nucleotide sequences of S regions contain short common sequences, TGGG(G) and (G)AGCT. Comparison of nucleotide sequences surrounding recombination sites revealed common sequences TGAG and TGGG. A sister chromatid exchange model was proposed to explain deletion of CH genes accompanying S-S recombination. We have found that the S region serves as a preferred recombination site in E.coli extracts.