Complete sequence of constant and 3' noncoding regions of an immunoglobulin mRNA using the dideoxynucleotide method of RNA sequencing

Nucleotide sequence of the middle dsRNA segment of bacteriophage phi 6: placement of the genes of membrane-associated proteins

The genome of the lipid-containing bacteriophage phi 6 contains three segments of double-stranded RNA. We have determined the nucleotide sequence of cDNA derived from the middle-size RNA segment. The coding sequences of three proteins on this segment were identified on the basis of size and the correlation of predicted N-terminal amino acid sequences with those found through the analysis of isolated proteins. In contrast to our results with the small phi 6 dsRNA segment, the open reading frames are not tightly clustered. The homologous terminal noncoding regions between the middle and small dsRNA segments are found to be more extensive than RNA sequencing had previously indicated.

Autoantibody-associated kappa light chain variable region gene expressed in chronic lymphocytic leukemia with little or no somatic mutation. Implications for etiology and immunotherapy

Recently the minor B cell subpopulation that expresses the CD5 (Leu-1) antigen has been implicated as a source of IgM autoantibodies. Chronic lymphocytic leukemia (CLL), the most common leukemia in humans, represents a malignancy of small B lymphocytes that also express the CD5 antigen. However, little is known concerning the antibody variable region genes (V genes) that are used by these malignant CD5 B cells. We have found that a relatively high frequency of CLL patients have leukemic B cells with surface immunoglobulin (sIg) recognized by 17.109, a murine mAb specific for a kappa light chain associated crossreactive idiotype (CRI) associated with rheumatoid factor and other IgM autoantibodies. Flow cytometric analyses revealed that the relative expression of the 17.109-CRI by circulating leukemic B cells was directly proportional to the levels of sIg kappa light chain, indicating that there exists stable idiotype expression in the leukemic population. To examine this at the molecular level, the nucleic acid sequences encoding the Ig kappa light chains of two unrelated patients with CLL bearing sIg with the 17.109-CRI were determined. Analyses of multiple independent kappa light chain cDNA clones did not reveal any evidence for sequence heterogeneity in the CLL cell population. Furthermore, the nucleic acid sequences expressed by the leukemic cells of these two patients were identical or very homologous to a germline V kappa gene isolated from placental DNA, designated Humkv 325, or "V kappa RF" because of its association with IgM autoantibodies. This study suggests; (a) that the malignant CD5+ B lymphocytes in CLL use the same V kappa gene that has been highly associated with IgM autoantibodies and (b) that the expression of V genes is stable in CLL, in contrast to other B cell malignancies examined to date. We propose that many CLL cases represent malignancies of autoreactive CD5 B cells that use a restricted set of conserved V genes. This property may render CLL particularly amenable to immunotherapy with antiidiotypic antibodies.

Sequence of a rat immunoglobulin gamma 2c heavy chain constant region cDNA: extensive homology to mouse gamma 3

The complete sequence of the rat immunoglobulin gamma 2c heavy chain constant region has been determined by cDNA cloning and by mRNA sequencing. Comparison with other heavy chain genes reveals a high degree of homology (87%) to mouse gamma 3 and suggests that rat and mouse gamma genes separated from a common set of three ancestral genes.

Defined recombinants of poliovirus and coxsackievirus: sequence-specific deletions and functional substitutions in the 5'-noncoding regions of viral RNAs

We describe the isolation of a variant of a polio--coxsackie recombinant virus (PCV110) containing a genomic RNA with a chimeric 5'-noncoding region. The variant virus [designated PCV110(1)] has growth and biosynthetic properties that are quite different from the original, temperature-sensitive isolate of the recombinant virus [designated PCV110(4)]. Nucleotide sequencing of the 5'-noncoding region of RNA from PCV110(1) revealed a 4-base deletion within the substituted coxsackievirus region of the chimeric genome that may contribute to the loss of temperature sensitivity of this variant recombinant virus. In addition, we have generated new recombinant viruses that contain (1) coxsackievirus sequences within the N66-N627 region of the poliovirus genome and (2) coxsackievirus sequences substituted from N1-N627 in the poliovirus genome. These recombinant viruses are not temperature sensitive for growth at 37 degrees and have biosynthetic properties similar to those of wild-type poliovirus. Our results provide evidence that replicase recognition signals encoded in the 5' noncoding regions of enterovirus genomic RNAs are not strictly sequence specific.

Streptococcus pyogenes type 12 M protein gene regulation by upstream sequences

A partial nucleotide sequence that included 1,693 base pairs of the M12 (emm12) gene of group A streptococci (strain CS24) and adjacent upstream DNA was determined. Type 12 M protein-specific mRNA of strain CS24 is transcribed from two promoters (P1 and P3) separated by 30 bases. The transcription start sites of the emm12 gene were located more than 400 bases downstream of a deletion that causes decreased M-protein gene transcription in strain CS64. Deletion analysis of M protein-expressing plasmids indicated that an upstream region greater than 1 kilobase is required for M-protein gene expression. The M-protein gene transcriptional unit appears to be monocistronic. Analysis of the emm12 DNA sequence revealed three major repeat regions. Two copies of each repeat, A and B, existed within the variable 5' end of the gene; repeat C demarcated the 5' end of the constant region shared by emm12 and emm6.

Influence of the macromolecular form of a B cell epitope on the expression of antibody variable and constant region structure

We investigated the influence of the macromolecular form of an epitope on the structure of antibody variable and constant regions expressed by the B cell population participating in an immune response to that epitope. Hybridomas were constructed from strain A/J mice undergoing either primary or secondary immune responses to p-azophenylarsonate conjugated to Brucella abortus (Ars-Bruc). We determined the sequences of the V genes expressed by hybridomas selected on the basis of expression of a single VH gene segment known to encode a large family of anti-Ars antibodies. These sequences were compared with the sequences of V genes expressed by a previously characterized panel of hybridomas isolated in the same way during the primary and secondary responses of A/J mice to Ars-KLH. The repertoire of Ars-specific V domains expressed among primary and secondary hybridomas elicited with these two forms of Ars were similar, as were the differences between primary and secondary V region somatic mutational alteration and affinity for Ars. In contrast, predominant expression of IgG2 anti-Ars antibodies was elicited in the secondary Ars-Bruc response, whereas secondary anti-Ars antibodies elicited with Ars-KLH are predominantly IgG1. Thus, differences in the macromolecular form of Ars clearly influence the isotypic profile of the anti-Ars response, but the expression, diversification, and selection of V domains elicited with this hapten are not greatly affected by such differences. Our results suggest that while isotype regulation is highly perceptive of the macromolecular form of a B cell epitope, V region regulation is primarily influenced by the molecular structure of that epitope.

The structure and evolution of immunoglobulin kappa chain constant region genes in the genus Rattus

We have cloned and sequenced the C-kappa (Ck) genes from seven species and subspecies of rats which have diverged over the past few million years in Australia. Comparisons of these sequences with each other and the Ck genes of the laboratory rat, Rattus norvegicus, indicate noncoding regions have accumulated fewer mutations than adjacent coding sequences, and amino acid replacing nucleotide substitutions in the coding regions have accumulated at a rate at least as great as silent changes. Exactly the opposite of both of these findings is observed when comparisons are made between Ck or other genes from more distantly related species, indicating that these features may be characteristic of Ck short-term evolutionary gene divergence. Changes in the coding regions of these genes result in a non-random distribution of amino acid substitutions on the three-dimensional alpha-carbon backbone of the Ck domain in the most serologically distinct forms of Ck. While phylogenetic relationships inferred from the Ck nucleotide sequences are in general agreement with those derived from other data, considerable differences are seen in rates of accumulation of Ck gene nucleotide substitutions vs rates of accumulation of enzyme polymorphisms.

Activation of memory and virgin B cell clones in hyperimmune animals

To study the long-term memory response, BALB/c mice were allowed to rest for over a year after a secondary immunization with the hapten 2-phenyl-oxazol-5-one (phOx). For the tertiary immunization two different protocols were used. In one protocol mice were injected i.v. and 3 days later spleen cells were fused to a nonproducing hybridoma line. PhOx-specific hybridomas were established and the sequence of the heavy and light chain mRNA was determined. This tertiary response resembled the diversity pattern of the secondary response with a further increase both in somatic mutations and in the average dissociation constant. The high number of somatic mutations demonstrates the persistence of memory B cell clones over a long time period. In the second protocol mice were boosted with an i.p. injection of alumprecipitated antigen phOx and 7 or 14 days later spleen cells were fused. Sequence analysis of heavy and light chain mRNA showed that these tertiary response antibody molecules had surprisingly few somatic mutations, indicating an activation of virgin B cell clones in these hyperimmunized animals. The maturation of these newly stimulated B cell clones seems to follow somewhat similar rules to those found for the primary response. It appears therefore that the two immunization protocols reflect the response of memory and virgin B cells, respectively.

Nucleotide sequence of a chicken vitellogenin gene and derived amino acid sequence of the encoded yolk precursor protein

The gene encoding the major vitellogenin from chicken has been completely sequenced and its exon-intron organization has been established. The gene is 20,342 base-pairs long and contains 35 exons with a combined length of 5787 base-pairs. They encode the 1850-amino acid pre-peptide of vitellogenin, which is the precursor of the mature yolk proteins, the serine-rich and heavily phosphorylated phosvitin and the lipovitellin. The 217-amino acid phosvitin polypeptide occupies an internal position (residue 1112 through 1328) within the vitellogenin molecule. The 125,000 and 30,000 Mr lipovitellin polypeptides are encoded by the sequences at the N-terminal and the C-terminal sides of the phosvitin section, respectively. The main features of the gene and protein sequences, and the evolutionary implications, are discussed.

In vivo generation and function of B cells in the presence of a monoclonal anti-IgM antibody: implications for B cell tolerance

C57BL/6 mice were chronically treated with milligram doses of the noncytotoxic monoclonal anti-mu b antibody MB86 (IgG1, kappa) from birth or from fetal life. The spleens of the manipulated animals contained large numbers (25% as compared to control mice) of B lineage cells which expressed IgMb on the surface after overnight incubation in vitro. The spleens also contained B cells whose surface IgM was unreactive with antibody MB86. A few such cells were immortalized by cell fusion. They included cells secreting mu together with lambda 2 chains which apparently prevent recognition by antibody MB86, and a point mutant in the first constant domain of the mu chain, changing the b to the a allotype. Cells expressing MB86- surface IgM did not selectively expand under MB86 treatment over the first few months of life. Serum Ig levels in the manipulated mice were normal except for IgM which was undetectable in most instances. In some animals low levels of MB86- IgM molecules were produced. At 7 weeks of age, mice treated with MB86 from birth produced normal-size IgG anti-(4-hydroxy-3-nitrophenyl)acetyl (NP) responses with the usual predominance of lambda 1 chain-bearing IgG1 antibodies. At the age of 5-6 months, and also in young mice treated with MB86 from fetal life, the responses were variable and presumably oligoclonal, with a tendency towards the production of antibodies with gamma 3 heavy and lambda 2 or lambda 3 light chains. We interpret these results to mean that B cells hit by antibody MB86 from the time of their generation become unresponsive to T cell-dependent stimulation, but are still able to expand. Occasionally, they escape functional suppression through class switching (to IgG3) upon mitogenic stimulation. At birth, C57BL/6 mice contain a mature B cell population which mediates normal immune responses under MB86 treatment and eventually dies out. Taken as a model of tolerance induction in B cells, the data provide evidence for "tolerant" cells and support the concept of an early phase of sensitivity to tolerance induction in B cell differentiation. The anti-NP response under MB86 treatment differed profoundly from control responses in idiotypic terms, but became normal as the animals recovered from suppression. This may reflect blockade by MB86 of idiotypic selection within the B cell population.

Site-directed mutagenesis of proteinase 3C results in a poliovirus deficient in synthesis of viral RNA polymerase

We used a synthetic double-stranded oligonucleotide to introduce amino acid substitutions into the proteinase 3C region of a poliovirus type 1 cDNA clone. The six different mutant viruses recovered exhibited a small-plaque phenotype when assayed on HeLa cells. Further investigation revealed that all the mutations (with the exception of one) yielded P3 region proteins that displayed altered mobility in sodium dodecyl sulfate-polyacrylamide gel electrophoresis. A conservative Val----Ala change at amino acid 54 of the proteinase resulted in a virus that was deficient in the production of the mature viral RNA polymerase 3D. Although this mutant achieved less than one-half of the wild-type levels of RNA synthesis during the course of infection, it still grew to nearly wild-type titers.

Adult B-cell repertoire is biased toward two heavy-chain variable-region genes that rearrange frequently in fetal pre-B cells

Fetal pre-B cells rearrange a very restricted set of immunoglobulin variable genes for the heavy chain (VH). To determine whether the adult B-cell repertoire is similarly skewed, we first identified the genes that rearrange in pre-B cells from BALB/c mice and then determined their frequency of rearrangement in adult B cells. In fetal pre-B cell lines, two genes, VH81X from the 7183 subfamily and VHOx2 from the Q52 subfamily, comprise 75% of the rearranged alleles of an estimated 1000 genes (P less than 0.001). Sequencing analyses revealed that rearrangements involving the two genes were both productive and nonproductive. The biased rearrangement of these two VH genes persists in B-cell hybridomas from adult mice at a frequency of 22%, as determined by Southern gel analysis and RNA sequencing. The sequence of one VHOx2 rearrangement from a hybridoma shows that the rearrangement is productive, suggesting that the gene encodes an antibody that could participate in the immune response. The data indicate that the adult B-cell repertoire is not random concerning usage of individual VH genes, and it may be shaped by the unknown mechanisms that cause preferential rearrangement of certain genes early in ontogeny.

Analysis of somatic mutation and class switching in naive and memory B cells generating adoptive primary and secondary responses

Clonal progeny of naive B cells (producing a primary antibody response) and of memory B cells (producing a secondary response) were identified in a cell transfer system. Primary response clones are typically derived from IgM precursors and express unmutated V regions. Multiple isotype switches occur in these clones. Secondary response clones derive from IgG1 precursors and express highly mutated V regions. Additional switches do not occur. With one exception, there was no evidence for somatic mutation during clonal expansion. The generation of mutated memory cells may thus represent a distinct differentiation pathway. Evidence is presented that, in this pathway, mutants that have lost antigen binding specificity but that remain available for stimulation by a different antigen arise upon antigenic stimulation.

Monoclonal BALB/c anti-progesterone antibodies use family IX variable region heavy chain genes

Variable region nucleotide sequences and respective translated amino acid sequences for three heavy chains (DB3, 11/32 and 10/8) and two light chains (DB3 and 11/32) of monoclonal mouse IgG1 anti-progesterone antibodies have been determined by primer extension mRNA sequencing. The three VH regions exhibit the same rarely observed VH IX gene family and have greater than 88% homology between them. Two associated light chain sequences are 95% homologous and belong to the V kappa I group. The N-terminal twenty two amino acids of the kappa light chain of the third antibody 10/8 have been determined by automated protein sequencing and are identical to those of 11/32. Thus, these three monoclonal anti-progesterones derived from separate fusions all use VHIX-V kappa 1 gene combinations.

Comparison of the structural organizations in the 3'-terminal regions of five avian retrovirus strains: RAV 7, RAV 50, B77, PR-B, and SR-B

In order to obtain information on the phylogenies of viral strains which belong to RSV (Rous sarcoma virus) and ALV (avian leukosis virus), the nucleotide sequences of noncoding regions adjacent to the U3 region in two ALV strains, Rous-associated virus 7 (RAV 7) and RAV 50, and three RSV strains, Bratislava 77 (B77), Prague:subgroup B (PR-B), and Schmidt-Ruppin:subgroup B (SR-B) were determined by extension from a common primer. The sequences thus deduced were compared with known sequences of other RSV and ALV strains and the structural features of the newly determined viral genomes were discussed.

Conservation in rotaviruses of the protein region containing the two sites associated with trypsin enhancement of infectivity

The primary structure of the region in the outer layer protein VP3, containing the two sites associated with trypsin enhancement of infectivity of rotavirus was found to be greatly conserved in cultivable human rotavirus serotypes 1 (Wa), 2 (DS1), and 3 (P) and in four human rotaviruses directly purified from feces. Significant differences with this conserved sequence were found in human rotavirus serotype 4 (ST3), isolated from an asymptomatic neonate, and in seven animal rotaviruses. However, the two trypsin cleavage sites were conserved in every rotavirus VP3 sequence analyzed.

The galactan-binding immunoglobulin Fab J539: an X-ray diffraction study at 2.6-A resolution

The crystal structure of the Fab of the galactan-binding immunoglobulin J539 (a mouse IgA,kappa) has been determined at a resolution of approximately 2.6 A by X-ray diffraction. The starting model was that obtained from the real space search described previously (Navia, M.A., Segal, D.M., Padlan, E.A., Davies, D.R., Rao, D.N., Rudikoff, S. and Potter, M. "Crystal structure of galactan-binding mouse immunoglobulin J539 Fab at 4.5 A resolution." Proc. Nat. Acad. Sci. USA, 76:4071-4074, 1979). This Fab structure has now been refined by restrained least-squares procedures to an R-value of 19% for the 11,690 unique reflections between 8.0 A and 2.6 A. The rms deviation from ideal bond lengths is 0.025 A. The overall structure differs from McPC603 Fab, another mouse IgA,kappa antibody, in that the elbow bend, relating the variable and constant parts of the molecule, is 145 degrees vs. 133 degrees for McPC603. The region of the molecule expected to be the antigen binding site contains a large cavity with two clefts leading away from it. This has been fitted with a model of an oligo-galactan.

Primary structure of IgE monoclonal antibodies expressing an intrastrain crossreactive idiotype

We have obtained amino acid sequences (by mRNA and amino acid sequencing) for two IgE kappa mAb that have specificity for the Ars hapten group and are related to the major idiotypic family, CRIA (crossreactive idiotype A), in the A strain of mouse. One mAb, SE20.2, fully expresses CRIA; the other, SE1.3, possesses some but not all of the characteristic idiotopes. Both IgE proteins contain VH and V kappa segments that are closely related to those associated with CRIA. The D segment of SE20.2 is also typical of CRIA+ mAb, but that of SE1.3 is one amino acid residue longer. Chain recombination experiments indicated that the L chain of SE1.3 is fully capable of supporting CRIA expression. Its deficiency with respect to idiotopes of CRIA was attributed to the extra amino acid in the D region and/or substitutions in the VH segment. A major objective was to ascertain the frequency of somatic mutations in IgE. For the VH segment (amino acids 1-98) of SE20.2, there are only three nucleotide differences and one uncertainty with respect to the nucleotide sequence of the germline gene associated with CRIA. A somewhat higher frequency of substitutions is present in the VH segment of SE1.3. The VK amino acid sequences of the IgE proteins are nearly identical to those of a prototype of the CRIA family, mAb R16.7. The results are discussed with reference to the mechanism of the IgM to IgE switch.

Mitotic recombination in germ cells generated two major histocompatibility complex mutant genes shown to be identical by RNA sequence analysis: Kbm9 and Kbm6

RNA sequencing represents a major procedural simplification for nucleotide sequence analysis of a transcribed gene. Using newly adapted mRNA and cDNA sequencing procedures, we have sequenced 855 nucleotides of Kbm9 mRNA, corresponding to the codons for the aminoterminal 285 amino acids. The inferred DNA sequence of the Kbm9 gene differs from the parental Kb sequence by single nucleotide alterations in each of codons 116 and 121, resulting in Tyr----Phe and Cys----Arg substitutions, respectively. The Kbm9 sequence is identical to that of another independently arising MHC mutant gene, Kbm6. As both the Kbm9 and Kbm6 genes were generated by recombination between the Kb and Q4 genes, our data indicate that the identical genetic interactions have occurred at least twice. The relatively large extent of identity between Q4 and Kb may be responsible for frequent recombination between the two genes. The parents of the original bm9 mutant mice had five identical mutant offspring, which can be explained by mitotic recombination in the germ cells, producing gonadal mosaicism in the C57BL/6 mother. Thus, mitotic recombination, and not meiotic recombination, appears to be responsible for the formation of at least some of the Kb mutants. Such a mechanism probably plays a major role in the generation of diversity in the major histocompatibility complex.

Nucleotide sequence of the small double-stranded RNA segment of bacteriophage phi 6: novel mechanism of natural translational control

The lipid-containing bacteriophage phi 6 has a genome composed of three segments of double-stranded RNA. We determined the nucleotide sequence of a cDNA copy of the smallest RNA segment. The coding sequences of the four proteins on this segment were identified. These sequences were clustered. Three of the genes had overlapping initiation-termination codons. All noncoding sequences were at the ends of the molecule. The genes of the small double-stranded RNA segment comprised two translational polarity groups. We propose that the translational coupling is the result of an inability of ribosomes to bind independently to two of the four genes. Translation of these genes occurred when ribosomes were delivered to them by translation of an upstream gene.

Relationship of VH and VL genes encoding three idiotypic families of anti-p-azobenzenearsonate antibodies

We describe here an intrastrain, cross-reactive idiotype (CRI), CRID, associated with anti-p-azobenzenearsonate antibodies of the A/J strain of mouse and distinguishable, by some but not by all of its idiotopes, from the major anti-p-azobenzenearsonate idiotype (CRIA). Molecules carrying the CRID idiotype have heavy chain variable-segment sequences that are identical or nearly identical to that of the germ-line-encoded heavy chain variable sequence of CRIA. Their light chain variable sequences are very similar to those present in a third idiotypic family, CRIC, that is a minor CRI in the A/J strain but a major CRI in BALB/c. This appears to represent a form of combinational diversity, in which the heavy and light chain variable region genes of two unrelated idiotypic families interact to form a third family, all involving antibodies of the same antigen-binding (anti-p-azobenzenearsonate) specificity. The D region of CRID, in the six monoclonal representatives studied (three IgMs, three IgGs), is unusual in that it comprises a single amino acid--arginine or serine; there are eight amino acids in the D region of CRI+A antibodies. Three different heavy chain joining regions, JH1, JH2, and JH3, are utilized. A serological reagent was developed that identifies CRID; it was used to show that the idiotype is present in relatively high concentration, comparable to that of CRIA, in anti-p-azobenzenearsonate antibodies taken soon after primary immunization. In serum taken later CRIA greatly predominates, but CRID persists at low levels.

Several V genes participate in the early phenyloxazolone response in various combinations

Seventeen monoclonal anti-2-phenyloxazolone antibodies from the early (day 7) primary response were partially sequenced with an mRNA method. Ten antibodies expressed the VH-Ox1 gene. The remaining seven express at least four but probably six different germ-line VH genes belonging to Dildrop's groups 1, 5, 6 and 7 (Immunol. Today 1984. 5: 85). Two of them have been met before in other antibodies, one (group 6) in J606 and the other (group 7) in antibodies to the influenza virus hemagglutinin. Eleven kappa chains were partially sequenced and five of them (all VH-Ox1 antibodies) express the V kappa-Ox1 gene. One expresses another germ-line gene of the V kappa-Ox1 family, one the V kappa 89.4 gene, three the V kappa 45.1 gene and one a new V kappa gene. The V kappa 45.1 gene was found to form anti-phOx antibodies with two new VH genes. The frequency of somatic mutations in day 7 antibodies was estimated by comparing germ-line sequences and antibody sequences. It is low (one mutation per 2500 nucleotides sequenced), twenty times lower than in antibodies obtained a week later. Two anti-idiotype antisera (495 and 260) are useful in the typing of monoclonal antibodies. 260 bound only to antibodies coded by both VH-Ox1 and V kappa-Ox1 genes. 495 bound strongly to antibodies coded by the VH-Ox1 gene and weakly to antibodies coded by the (related) VH101 gene regardless of the light chain partner.

EcoK selection vectors for shotgun cloning into M13 and deletion mutagenesis

For shotgun cloning into M13 vectors, a double-stranded cassette of synthetic oligonucleotides containing a SmaI site within the two halves of an EcoK site, has been introduced into the vector M13mp8. Cloning of blunt end DNA into the SmaI site destroys the EcoK site, and recombinants are therefore preferentially selected on transfection into a K strain of E.coli. For deletion mutagenesis using synthetic oligonucleotides, an M13 vector with four copies of the EcoK cassette has been made to facilitate the joining of lacZ or a Factor Xa cleavage site to any protein reading frame.

The T-cell-independent immune response to the hapten NP uses a large repertoire of heavy chain genes

Hybridomas generated from C57BL/6 mice immunized with the hapten NP coupled to ficoll, a T-cell-independent carrier, produce monoclonal antibodies that use a large repertoire of VH regions and light chains. This contrasts with the homogeneity of the strain-specific response to NP observed with T-cell-dependent carriers, where most of the antibodies use a single VH region, V186.2, in combination with the lambda-1 light chain. There is no evidence for somatic mutation in any of the sequenced regions of the antibodies generated by NP-ficoll. Thus T cell participation is required for the homogeneity of the strain-specific hapten response, and probably for somatic mutation as well.

A structural basis for the internal image in the idiotypic network: antibodies against synthetic Ab2-D regions cross-react with the original antigen

In the idiotypic cascade initiated by the random terpolymer (Glu60Ala30Tyr10)n or "GAT", we have identified, in the D region of Ab2 antibodies, either Glu-Glu-Tyr or Tyr-Tyr-Glu sequences which mimic GAT immunodominant epitopes, thus suggesting a structural basis for the internal image. Peptides containing the two D-region characteristic sequences were then synthesized and coupled to BSA. In mice, they elicited antibodies, a fraction of which recognized GAT. These observations speak in favour of the localization of an internal image of the GAT antigen in the D region of Ab2 antibodies.

Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses

Although the applicability of small subunit ribosomal RNA (16S rRNA) sequences for bacterial classification is now well accepted, the general use of these molecules has been hindered by the technical difficulty of obtaining their sequences. A protocol is described for rapidly generating large blocks of 16S rRNA sequence data without isolation of the 16S rRNA or cloning of its gene. The 16S rRNA in bulk cellular RNA preparations is selectively targeted for dideoxynucleotide-terminated sequencing by using reverse transcriptase and synthetic oligodeoxynucleotide primers complementary to universally conserved 16S rRNA sequences. Three particularly useful priming sites, which provide access to the three major 16S rRNA structural domains, routinely yield 800-1000 nucleotides of 16S rRNA sequence. The method is evaluated with respect to accuracy, sensitivity to modified nucleotides in the template RNA, and phylogenetic usefulness, by examination of several 16S rRNAs whose gene sequences are known. The relative simplicity of this approach should facilitate a rapid expansion of the 16S rRNA sequence collection available for phylogenetic analyses.

Gene repertoire of the anti-poly(Glu60Ala30Tyr10) (GAT) immune response: comparison of VH, V kappa, and D regions used by anti-GAT antibodies and monoclonal antibodies produced after anti-idiotypic immunization

Eight monoclonal antibodies were selected from BALB/c mice immunized with two different monoclonal anti-idiotypic antibodies recognizing two discrete idiotopes characteristic of the anti-poly(Glu60Ala30Tyr10) (GAT) antibody response. These monoclonal antibodies were previously classified as Ab1 (anti-GAT-like) and Ab3 (anti-anti-idiotype) on the basis of expression of the public idiotypic specificity (p.GAT) studied with a xenogeneic serum, anti-GAT activity, and expression of various public idiotopes. All the heavy chain variable region (VH) sequences from Ab1 are nearly identical to the VH sequences of Ab1 anti-GAT monoclonal antibodies. The same type of results has been found with the Ab1 kappa light chain variable region (V kappa) sequences. Confirming our classification, Ab3 VH and V kappa sequences were found to be completely different from Ab1 VH and V kappa sequences. The Ab1 diversity (D) regions are different from one another and different from the D regions found on monoclonal anti-GAT antibodies but function similarly. These D regions are not simply derived from already described D genes. Finally, our results suggest that in the anti-GAT response VH and V kappa sequence are mainly responsible for idiotype expression.

Structure of primary anti-(4-hydroxy-3-nitrophenyl)acetyl (NP) antibodies in normal and idiotypically suppressed C57BL/6 mice

Eight monoclonal antibodies from the primary response of C57BL/6 mice against the hapten (4-hydroxy-3-nitrophenyl)acetyl (NP) were isolated. The antibodies carry lambda 1 light chains and have similar affinities for the immunizing hapten. Sequence analysis at the level of mRNA reveals that all antibodies express the VH gene 186.2 and all but one the DFl 16.1 gene segment. The J segment of the heavy chain is JH2 in six cases and JH4 in two. Somatic point mutations are scarcely detectable in the antibodies, but there is extensive sequence variability at the boundaries of the D gene segment, mainly at its 5' end. However, seven of eight antibodies express tyrosine in position 99 of the heavy chain, encoded either by the 5' codon of DFl 16.1 or by presumed N sequences. In the former case, the tyrosine is the first of a stretch of three (positions 99-101). In the latter, a similar stretch (positions 99, 101, 102) is interrupted by aspartic acid, asparagine or cysteine in position 100. These variations profoundly affect idiotypic specificity. Six of the eight monoclonal antibodies came from mice neonatally suppressed by an anti-idiotope antibody whose target idiotope is regularly expressed in primary anti-NP responses and depends upon a non-germ-line-encoded aspartic acid in position 100 of the heavy chain. The sequence data show that the mice circumvent suppression by expressing antibodies which lack this aspartic acid but are otherwise structurally very similar to anti-NP antibodies from normal animals. Since suppression in the animals is partly controlled by regulatory T cells, we conclude that these T cells are highly restricted in their specificity in that they preferentially see a determinant which also depends upon the aspartic acid in position 100. The data suggest that the VH to D boundary serves as a target of idiotypic selection.

A single VH-gene associated with a variety of D- and J-segments encodes for a large family of ABPC48-related antibodies induced by antiidiotypic immunization

Two series of monoclonal antibodies have been obtained from BALB/c mice immunized against two antiABPC48 antiidiotypic antibodies. They are divided into two serologically different classes. Class I antibodies bind only the immunizing antibody; class II antibodies display a broad binding capacity to various antiidiotypic antibodies, and some bind levan, as does ABPC48. Northern blot analyses and partial mRNA sequencing show that all class II antibodies express the VH-gene coding for ABPC48 and UPC10 antilevan antibodies associated with a variety of D- and J-segments. The third hypervariable region of the sequenced antibody with antilevan activity is structurally related to that of ABPC48 and UPC10 antibodies but has a different genetic origin. This study indicates that the identification of idiotype-related antibodies arising from antiidiotypic immunization may be misleading, if based on their antigen-binding properties; and it stresses the importance of structural approaches for the analysis of regulatory mechanisms ruling immune responses.

Somatic mutation and clonal expansion of B cells in an antigen-driven immune response

The variable (V) regions of three closely related monoclonal antibodies produced by hybridomas which had been isolated from a single mouse were sequenced at the level of the mRNA. The sequences and the restriction analysis of the immunoglobulin loci carried by the hybridoma cells indicate that the antibodies are derived from cells belonging to a single B cell clone. The sequence data imply a high frequency and stepwise occurrence of somatic point mutations in the expressed V region genes and substantial clonal expansion of B cells in the mouse. The mutations appear to be randomly introduced into heavy and light chain V region genes. Mutations are also seen in the complementarity determining regions which may thus have been involved in the selection of the cells producing the three antibodies.

The internal image and the structural idiotypic network (Ab1, Ab2, Ab3) in the GAT system

The GAT repertoire expressed at the different levels of the classical idiotypic cascade Ag----Ab1----Ab2----Ab3 has been analysed by direct nucleotide sequencing of H- and L-enriched mRNA. Ab1 and Ab3 expressing the major public idiotypes used similar, if not identical, VH and VK genes. The VH Ab3 of the Ab1 type (Ab1') appeared highly conserved. Ab2 also use a small number of germ-line genes. The D region of Ab2 is of particular interest since it contains either a Tyr-Tyr-Glu or a Glu-Glu-Tyr sequence, characteristic of the GAT major determinants. It is therefore suggested that this D region contains the internal image of the antigen. A large number of VH germ-line genes have been isolated and sequenced. They all pertain to the VH-II family, which contains a large number of members, some of them being very close in sequence.

Methods for cDNA cloning and sequencing tobacco mosaic virus RNA

DNA complementary to tobacco mosaic virus (TMV) RNA (cDNA) was prepared by priming reverse transcription with synthetic oligonucleotides. The cDNAs terminated prematurely at many specific sites and no transcripts longer than about 2000 nucleotides were obtained. However, the entire 6395 nucleotide long TMV RNA could be copied into cDNA by specific priming with a series of 13 to 17 residue long oligonucleotides or by non-specific priming with short, 4 to 7 residue, oligonucleotides. A number of different priming methods were used to convert the cDNA into double-stranded DNA (dsDNA). The double-stranded cDNA was recovered by shotgun cloning into M13 and analysed by sequencing. The frequency at which cDNA clones were recovered has been used to compare various cDNA cloning strategies.

A labile phosphodiester bond at the ligation junction in a circular intervening sequence RNA

The excised intervening sequence of the Tetrahymena ribosomal RNA precursor mediates its own covalent cyclization in the absence of any protein. The circular molecule undergoes slow reopening at a single phosphodiester bond, the one that was formed during cyclization. The resulting linear molecule has 5'-phosphate and 3'-hydroxyl termini; these are unusual products for RNA hydrolysis but are typical of the other reactions mediated by this molecule. The reopened circle retains cleavage-ligation activity, as evidenced by its ability to undergo another round of cyclization and reopening. The finding that an RNA molecule can be folded so that a specific phosphate can be strained or activated helps to explain how the activation energy is lowered for RNA self-splicing. The proposed mechanisms may be relevant to several other RNA cleavage reactions that are RNA-mediated.

Complete sequences of the intergenic and mRNA start signals in the Sendai virus genome: homologies with the genome of vesicular stomatitis virus

All of the consensus intergenic and transcription initiation sequences of the genome of Sendai virus, a paramyxovirus, have been determined. The boundary between the intergenic sequence, 3'-GAA, and the mRNA start signal, 3'- UCCCANUUUC , was identified by sequencing the 5' termini of specific viral mRNA molecules. One of the five intergenic trinucleotides differed from the rest, consisting of 3'- GGG , and single base substitutions were observed in two of the mRNA start signals. The Sendai virus intergenic sequence was similar to the analogous sequence (3'-GA) of vesicular stomatitis virus (VSV), a member of another family of negative-strand RNA viruses, the rhabdoviruses , but there was no sequence homology between the mRNA start signals of the two viruses. Nevertheless, these mRNA start signals were organized in the same way, being ten bases long and possessing two consensus regions, divided by one (Sendai virus) or two (VSV) variable internal nucleotides. These findings extend the evidence that both families of negative-strand RNA viruses descended from a common ancestor and that an archetypal mechanism of transcriptional regulation has been conserved in their evolution.

"Dideoxy" RNA sequencing: a rapid method for studying genetic information

The chain termination sequencing technique on RNA is a very rapid, direct method for the analysis of genetic information. It is particularly suitable for analysing systems on which microgram amounts of 50% pure RNA can be made available and for which numerous data are needed in order to derive genetic or structural information. The usefulness and limitations of the technique are discussed.

Structural organization of the 3' half of the rat thyroglobulin gene

We report the structural organization of an 80 Kb segment of rat DNA, which encodes for about 40% of Thyroglobulin mRNA at the 3' end. The codogenic information included in this segment is splitted in 17 exons of homogeneous size (about 200 bp). The seven exons at the extreme 3' end have been precisely defined by DNA sequence analysis. No clear sequence homology is found among the exons, even though their coding capacity is quite similar, from 55 to 63 aminoacids residues. We located 2 hormonogenic (T4 forming) sites on the extreme 3' end of the gene in different exons. The DNA sequence coding for these functional sites shows a 70% homology in a 50 nucleotides segment. In addition we found a remnant of this sequence in other exons of the gene. Two large introns have been found on the 3' end of the gene: one is 17 Kb and the other one is more than 30 Kb long. On the basis of these findings and of preliminary studies on the remaining 5' end of the gene, we can predict that the minimum length of the rat TGB gene will be 150 Kb, which makes this gene the largest so far identified eukaryotic gene. We propose in addition that the 3' end exons arose by duplication of a common ancestor.

Isolation of hybridomas expressing a specific heavy chain variable region gene segment by using a screening technique that detects mRNA sequences in whole cell lysates

A technique is described that allows single hybridoma cell colonies to be assayed for the productive rearrangement of a single immunoglobulin variable region (V) gene segment by utilizing expression of V mRNA for analysis. Hybridomas growing in microwell tissue culture plates are lysed in situ, cellular RNA is directly transferred to nitrocellulose by filtration, and specific immunoglobulin mRNA is detected by hybridization of the filter with a DNA probe. The method is simple and sensitive. A single species of mRNA can be detected in a lysate of 1000 cells; 5000 hybridoma colonies can be easily screened per day. The technique has been successfully used to isolate cell lines from nonimmune mice expressing a particular heavy chain variable region (VH) gene segment.

Secretion and processing of an immunoglobulin light chain in Escherichia coli

When a cDNA coding for the kappa light chain (L-321) from the mouse MOPC321 myeloma was cloned into Escherichia coli, L-321 antigens were found in both cytoplasmic and periplasmic fractions. In cells synthesizing the intact chain, starting with its signal peptide, the periplasm contained a mature-size immunoglobulin indicating that the eukaryotic signal peptide can initiate secretion and be processed. When the entire cDNA for L-321 (including its signal peptide) was inserted in the gene for bacterial beta-lactamase, processing cleaved only the first bacterial signal sequence of the hybrid protein synthesized. Removal of the beta-lactamase signal peptide was also observed with another beta-lactamase-L-321 hybrid which did not include the immunoglobulin signal peptide and the adjacent part of the variable region. The two hybrid proteins may, however, differ in their mode of secretion.

Complete nucleotide sequence of the messenger RNA coding for chicken muscle glyceraldehyde-3-phosphate dehydrogenase

The complete nucleotide sequence for chicken glyceraldehyde-3-phosphate dehydrogenase mRNA has been determined, thereby extending the longest such sequence previously reported (Dugaiczyk et al. Biochemistry, 1983, 22, 1605-1613) by 27 nucleotides. The complete mRNA with the exclusion of poly(A) is 1284 nucleotides long and contains 56 nucleotides of 5' non coding sequence and 229 nucleotides of 3' non coding region. Knowledge of the complete sequence allows us to propose secondary structures models which may be of biological significance.

A new rule for analyzing homologous coding sequences in DNA

A new rule is proposed for detecting homology between DNA sequences coding for proteins. Simple coding considerations predict that if two DNA sequences are homologous because of a common ancestry, they should share sequence similarities primarily in the same translation phase, with their codons aligned. Similarities which are in phase are shown to be more frequent between related sequences than between unrelated or random ones. But similar segments which are out of translation phase are no more frequent between related than unrelated sequences. Duplication and concatenation of genetic elements, followed by gene duplication and random mutations would lead to the patterns observed. Similarities are examined between various immunologically important sequences, including immunoglobulins, MHC products, and the T lymphocyte antigen Thy 1.

Molecular analysis of the anti-GAT repertoire in three strains of mice

GAT-specific antibodies which express the CGAT (or pGAT) public idiotypic specificities are encoded by a paucigene system. Antibodies expressing discrete specificities, i.e. anti-GAT and anti-NP, appeared to use the same VH germ-line genes, an observation which directly supports the importance of random H-L pairing to generate a large number of distinct antibody molecules.

V kappa gene family in (Glu60 Ala30 Tyr10)n (GAT)-specific antibodies that express CGAT (or pGAT) public idiotypic specificities. Protein and mRNA sequencing of eight monoclonal V kappa chains

A large proportion of (Glu60 Ala30 Tyr10)n (GAT)-specific antibodies expresses public idiotypic specificities, termed CGAT (or pGAT), that require the presence of both the heavy and the light chains in order to be expressed. We report in this paper the complete sequence of eight V kappa regions pertaining to eight anti-GAT monoclonal antibodies derived from three strains of mice: BALB/c, DBA/2, and C57BL/6. The methodology used a combination of NH2-terminal amino acid and mRNA nucleotide sequencing. All eight sequences analyzed, although highly homologous and all pertaining to the same V kappa 1 subgroup, allowed definition of three germline genes that are likely to be present in all three strains of mice and also in NZB. It seems likely, however, that any given strain may not necessarily use all three genes for making anti-GAT antibodies. The search for structural correlates of idiotypes could not be framed in a simple picture, but our data suggest that similar idiotopes may result from different interacting primary structures, leading to structural homologies that should be visualized at three-dimensional level.