Somatic mutation in genes for the variable portion of the immunoglobulin heavy chain

The size of the gene pool potentially encoding antibodies to p-azophenyl arsonate has been examined. A heavy chain-specific full-length complementary DNA clone has been constructed with the use of messenger RNA from a hybridoma that produces antibodies to the arsonate hapten and bears nearly a full complement of the determinants comprising the cross-reactive idiotype (CRI). The sequences of both the complementary DNA clone and the corresponding immunoglobulin heavy chain have been independently determined. A probe for the variable region gene was prepared from the original heavy chain complementary DNA clone and used to analyze, by Southern filter hybridization, genomic DNA from both A/J (CRI positive) and BALB/c (CRI negative) mice. Approximately 20 to 25 restriction fragments containing "germline" variable region gene segments were detected in both strains, and many are shared by both, Since 35 CRI-positive heavy chains have been partially sequenced thus far and 31 are different, the results of the hybridization analysis suggest that somatic mutation events involving the variable region gene segments of the heavy chain play a role in the origin of the amino acid sequence diversity seen in this system.

Mouse IgA heavy chain gene sequence: implications for evolution of immunoglobulin hinge axons

The complete nucleotide sequence of the gene and mRNA coding for the constant (C) region of the secreted form of the BALB/c mouse IgA immunoglobulin alpha heavy (H) chain has been determined. As in other immunoglobulins, the three C region domains of the alpha protein, C alpha 1, C alpha 2, and C alpha 3 are coded in separate exons. However, the hinge region of C alpha is not coded on a separate exon as it is in other hinge-containing immunoglobulins. Instead, the alpha hinge is coded as a 5' extension of the C alpha 2 exon, and we suggest that it may have evolved by duplication leading to incorporation of an acceptor RNA splice site into the coding portion of the C alpha 2 exon. Extensions of this concept could provide an explanation for duplications in the human alpha 1 chain.

Molecular cloning of equine herpesvirus type 1 DNA: analysis of standard and defective viral genomes and viral sequences in oncogenically transformed cells

Genomic DNA sequences of equine herpesvirus type 1 (EHV-1) have been cloned as BamHI and EcoRI restriction fragments into the plasmid pBR322 and propagated in Escherichia coli. With the exception of two EcoRI restriction fragments that reside in the S region of the viral genome, all of the cloned fragments demonstrated the same electrophoretic mobilities, restriction cleavage sites, and blot-hybridization patterns as did the parent fragments produced by BamHI or EcoRI digestion of virion DNA. The EcoRI J fragment and the BamHI E fragment of the L-region terminus were cloned after the addition of appropriate linker oligonucleotides. Fragments originating from each of the two isomeric forms of EHV-1 DNA were contained in this library of clones. Supramolar DNA fragments present only in the DNA of defective interfering (DI) particles of EHV-1 were generated from Bgl II digestion of DNA preparations enriched for EHV-1 DI particles and were cloned as Bgl II and EcoRI fragments into the plasmid vector. The cloned viral sequences represented in this defective genome mapped to the S region of EHV-1 DNA. Blot-hybridization analysis of EHV-1 transformed and tumor cell DNAs with the cloned BamHI B fragment confirmed that subgenomic viral sequences are present and indicated that those sequences map to the viral genome between 0.32 and 0.43 map unit.

Mouse immunoglobulin D: construction and characterization of a cloned delta chain cDNA

TEPC 1017 is a BALB/c plasmacytoma that synthesizes IgD in large enough amounts to permit the isolation of mRNA for mouse delta chains. cDNA has been prepared from this mRNA, and an 880-base-pair fragment of it has been cloned by recombinant DNA techniques. The hybridization selection technique has been used to show that this cDNA clone specifically binds only mRNA that can be translated into immunoprecipitable delta chains. the sequence of a portion of this clone has been determined and, when translated, shows homology with the C delta 3 of a human myeloma protein. Using this cDNA clone as a probe, we have found that several different-sized delta RNAs are present in TEPC 1017 and in another IgD-secreting plasmacytoma, TEPC 1033.

Mapping of heavy chain genes for mouse immunoglobulins M and D

A single DNA fragment containing both mu and delta immunoglobulin heavy chain genes has been cloned from normal BALB/c mouse liver DNA with a new lambda phage vector Charon 28. The physical distance between the membrane terminal exon of mu and the first domain of delta is 2466 base pairs, with delta on the 3' side of mu. A single transcript could contain a variable region and both mu and delta constant regions. The dual expression of immunoglobulins M and D on spleen B cells may be due to alternate splicing of this transcript.

Mouse immunoglobulin D: messenger RNA and genomic DNA sequences

The molecular structure of a mouse immunoglobulin D from a plasmacytoma tumor and that of the normal mouse gene coding for immunoglobulin D are presented. The DNA sequence results indicate an unusual structure for the tumor delta chain in two respects: (i) Only two constant (C) region domains, termed C delta 1 and C delta 3 by homology considerations, are found; the two domains are separated by an unusual hinge region C delta H that lacks cysteine residues and thus cannot provide the covalent cross-links between heavy chains typically seen in immunoglobulins. The two domains and hinge are all coded on separate exons. (ii) At the carboxyl end of the delta chain there is a stretch of 26 amino acids that is coded from an exon located 2750 to 4600 base pairs downstream from the rest of the gene. Analogy with immunoglobulin M suggests that this distally coded segment C delta DC may have a membrane-binding function; however, it is only moderately hydrophobic. A fifth potential exon (C delta AC), located adjacent to the 3' (carboxyl) end of C delta 3, could code for a stretch of 49 amino acids. The tumor's expression of the delta gene may be aberrant, but the simplest interpretation would be that this tumor expresses one of the several biologically significant forms of the delta chain.

J genes for heavy chain immunoglobulins of mouse

A 15,8-kilobase pair fragment of BALB/c mouse liver DNA, cloned in the Charon 4A lambda phage vector system, was shown to contain the mu heavy chain constant region (CHmu) gene for the mouse immunoglobulin M. In addition, this fragment of DNA contains at least two J genes, used to code for the carboxyl terminal portion of heavy chain variable regions. These genes are located in genomic DNA about eight kilobase pairs to the 5' side of the CHmu gene. The complete nucleotide sequence of a 1120-base pair stretch of DNA that includes the two J genes has been determined.

A mouse alpha-globin-related pseudogene lacking intervening sequences

A mouse alpha-globin-related pseudogene (psi alpha 30.5) completely lacks intervening sequences, and could not code for a functional globin poypeptide because of frameshifts. The widespread occurrence of globin pseudogenes in other species suggests that they are not 'dead' genes but may be important in controlling globin expression.

Structure of the constant and 3' untranslated regions of the murine gamma 2b heavy chain messenger RNA

The complete coding sequence for the constant region of the mouse gamma 2b immunoglobulin heavy chain and the 3' untranslated region has been determined. The coding portion of the sequence is 1008 nucleotides long (amino acid residues 114 to 449), and the 3' noncoding region contains 102 nucleotides preceeding the polyadenylate. An extra carboxyl-terminal lysine residue which had not been observed in the gamma 2b or other gamma subclass protein sequences occurs in the nucleotide sequence and is probably processed posttranslationally. A 17-nucleotide sequence occurs with slight variation twice in CH1 and once in CH2 domains in the same relative location but with different translational phase. This sequence may be the site of crossover in a gamma 2b . gamma 2a heavy chain variant, an indication of possible recombinational activity of some kind.

Sequence of the cloned gene for the constant region of murine gamma 2b immunoglobulin heavy chain

The complete nucleotide sequence of the gamma 2b constant region gene cloned from BALB/c liver DNA is reported. The sequence of approximately 1870 base pairs includes the 5' flanking, 3' untranslated, and 3' flanking regions and three introns. The C gamma 2b coding region is divided by these introns into four segments corresponding to the homology domains and hinge region of the protein. The introns separating the hinge from the CH2 domain and the CH2 from the CH3 domain are small (106 and 119 base pairs). A larger intervening sequence of 314 base pairs separates the CH1 and hinge regions. The stretch of DNA comprising this large intron plus the hinge shows a strong homology with the other CH domains.

Staphylococcal nuclease reviewed: a prototypic study in contemporary enzymology. IV. The nuclease as a model for protein folding

This is the last in a series of four articles in which the chemical, enzymological and crystallographic work on Ribonucleate (deoxyribonucleate)-3'-nucleotidohydrolase, EC 3.1.4.4 (staphylococcal nuclease, micrococcal nuclease) will be reviewed and correlated. This article discusses the use of the nuclease as a model system for the study of the mechanisms and energetics of the folding-unfolding reaction in proteins and for the study of the interrelationships between amino acid sequence and three-dimensional structure.

Staphylococcal nuclease reviewed: a prototypic study in contemporary enzymology. III. Correlation of the three-dimensional structure with the mechanisms of enzymatic action

This is the third in a series of four articles in which the chemical, enzymological and crystallographic work on Ribonucleate (deoxribonucleate)-3'-nucleotidohydrolase, EC 3.1.4.4 (staphylococcal nuclease, micrococcal nuclease) will be reviewed and correlated. This article describes the structure of the nuclease and of a nuclease-inhibitor complex as determined by x-ray crystallography. The crystal structures are correlated with some of the known chemical and enzymological properties of the enzyme, and the three areas combined to propose a mechanism of action.

Staphylococcal nuclease reviewed: a prototypic study in contemporary enzymology. II. Solution studies of the nucleotide binding site and the effects of nucleotide binding

This is the second of a series of four articles in which the chemical, enzymological and crystallographic work on Ribonucleate (deoxyribonucleate)-3'-nucleotidohydrolase, EC 3.1.4.4. (staphylococcal nuclease, micrococcal nuclease) will be reviewed and correlated. This article discusses studies in solution delineating the extent of the binding site of the enzyme and identifying some of the particular amino acid residues that form this site. In addition, the effects of the very potent inhibitory combination of thymidine-3',5'-diphosphate and Ca2+ on the conformation of the enzyme and its physical, chemical and enzymological properties will be reviewed.

Cloning human fetal gamma globin and mouse alpha-type globin DNA: characterization and partial sequencing

Two globin-related clones isolated from collections of bacteriophages containing unfractionated Eco RI fragments of human and mouse DNA were characterized. Charon3AHs51.1Hbgamma includes 2.7 kilobase pairs of human DNA containing a large part of a fetal gamma globin chain structural gene; Charon 3AMm30.5 includes 4.7 kilobase pairs of mouse DNA related to alpha globin. The human fetal gamma globin gene has within its coding region two intervening sequences of noncoding DNA, IVS 1 and IVS 2, of approximately 1-0 and 900 base pairs. Sequence IVS 1 is located at the position of one of the two intervening sequences occurring in adult globin genes; IVS 2 is located at the position of the other.

Cloning human fetal gamma globin and mouse alpha-type globin DNA: preparation and screening of shotgun collections

Shotgun collections of Charon 3A bacteriophages containing Eco RI fragments of human and mouse DNA were constructed with the use of in vitro packaging. Plaques were screened by hybridization, and globin-specific clones were isolated from both human (Charon 3AHs51.1) and mouse (Charon 3AMm30.5). The fragments cloned were detected in unfractionated genomic DNA by the Southern method of hybridization.

Staphylococcal nuclease reviewed: a prototypic study in contemporary enzymology. I. Isolation; physical and enzymatic properties

This is the first of a series of four articles in which the chemical, enzymological, and crystallographic work on Ribonucleate (deoxyribonucleate)-3'-nucleotidohydrolase, EC 3.1.4.7, (Staphylococcal nuclease, Micrococcal nuclease) will be reviewed and correlated. This article discusses the purification of the enzyme and its general physical and enzymological properties. Subsequent articles will deal with specific studies of the nucleotide binding site, crystallographic studies of a nuclease-inhibitor complex, use of the nuclease as a model for protein folding and possible mechanisms for the action of the enzyme.

Structure of hemoglobins Zürich [His E7(63)beta replaced by Arg] and Sydney [Val E11(67)beta replaced by Ala] and role of the distal residues in ligand binding

In hemoglobin Zürich the side chain of the distal arginine attaches itself to the propionate of the heme, leaving the heme pocket wide open, allowing sulfanilamides easy access to the iron, and doubling the partition coefficient between CO and O2. The replacement of the distal valine by alanine in hemoglobin Sydney leaves a large gap inside the heme pocket, which is partly filled by a water molecule bonded to the distal histidine. Hemoglobin Sydney has the same partition coefficient between CO and O2 as hemoglobin A. Replacement of the distal histidine increases the stretching frequency of CO linked to the beta heme by 6 cm-1, but replacement of the distal valine increases it by only 3 cm-1, but replacement of the distal histidine leaves the O-O stretching frequency unchanged.

Tumor-inhibiting properties of the neutral P-O-ethyl ester of adenosine 3':5'-monophosphate in correlation with its crystal and molecular structure

The P-O-ethyl ester of cAMP has been synthesized, its inhibition of solid and ascites tumors studied, and its pattern of urinary excretion followed. Et-cAMP is more effective than cAMP against solid sarcoma 180 in mice and against Ehrlich ascites carcinoma cells in tissue culture. The urinary excretion pattern of injected E-t-cAMP suggests that about two-thirds of the injected dose (13 mumol per animal) is retained in the rat rather than being promptly excreted. Liver slice studies of the effect on glycogenolysis suggest that the Et-cAMP is converted to cAMP intracellularly. The compound crystallizes in space group P21 with one molecule per asymmetric unit. The base ring has the anti conformation. The ethyl group is endo to the base ring and is axial in the flattened chair-conformer six-membered ring formed by the 3'-5' O-P-O cyclization. In most other respects the structure of the compound is closely similar to the known structures of other cyclic nucleotides.