Genetic basis for the cross-reactive idiotypes on the light chains of human IgM anti-IgG autoantibodies

The role of immunoglobulin structural genes in the generation of autoantibodies in humans has not been elucidated. Human monoclonal IgM anti-IgG autoantibodies (rheumatoid factors, RFs) from unrelated people often share idiotypic antigens. Antibodies against synthetic peptides have localized two of the shared idiotypic determinants to the second and third complementarity-determining regions of the kappa light chain. The reported sequences of several human RF light chains are remarkably homologous in these regions. Animal studies have shown that some shared idiotypic antigens represent serological markers for immunoglobulin variable (V)-region genes. Therefore, we hypothesized that human RF light chains derived from a single germ-line gene, designated V kappa-(RF), or from a small family of very closely related genes. In the present experiments, we have isolated and sequenced two human V kappa germ-line genes that encode kappa light chains, which are identical or closely related to the light chains of human RF. The data indicate that the shared idiotypic antigens on RF are phenotypic markers for a kappa V-region gene that is highly conserved in the human population. The results also imply that the light chains of IgM anti-IgG autoantibodies can be encoded by germ-line genes without any somatic mutation.

A 24-base-pair DNA sequence from the MAT locus stimulates intergenic recombination in yeast

HO nuclease is a site-specific double-strand endonuclease present in haploid Saccharomyces cerevisiae undergoing mating type interconversion. HO nuclease initiates mating type interconversion by making a double-strand break within the MAT locus. To define the recognition site for the enzyme in vitro, we have constructed a number of point mutations and deletions within or adjacent to the HO recognition site. Digestion of these substrates with HO in vitro reveals that the minimal recognition site is 18 base pairs long, although several shorter substrates and substrates containing point mutations are cleaved at low levels in vitro. A 24-base-pair HO recognition site stimulates homologous recombination when present in a region unrelated to MAT. Recombinants arise from both gene conversion and crossover events. The identification of the HO recognition site provides a way of introducing a defined initiation site for recombination.

Structure of the receptor for platelet-derived growth factor helps define a family of closely related growth factor receptors

The primary structure of the receptor for platelet-derived growth factor (PDGF), determined by means of cloning a cDNA that encodes the murine pre-PDGF receptor, is closely related to that of the v-kit oncogene product and the receptor for macrophage colony stimulating factor (CSF-1). Common structural features include the presence of long sequences that interrupt the tyrosine-specific protein kinase domains of each molecule. The PDGF and CSF-1 receptors also share a characteristic distribution of extracellular cysteine residues. Ubiquitin is covalently bound to the purified PDGF receptor, the human gene for which is on chromosome 5.

The avian beta-adrenergic receptor: primary structure and membrane topology

Partial amino acid sequence information allowed the isolation of cDNA clones encoding the turkey erythrocyte beta-adrenergic receptor. Antisera raised against synthetic peptides encoded by the cDNA crossreacted with the purified receptor and appropriate tryptic fragments, confirming the identity of the cDNA. The receptor is composed of 483 amino acids and has a molecular mass of 54 kDa. Its sequence suggests that it is arranged predominantly in seven membrane-spanning sequences and a long cytoplasmic carboxyl-terminal domain. The extracellular amino-terminal domain contains a consensus sequence for N-glycosylation. The beta-adrenergic receptor displays overall structural similarity and weak sequence homology with rhodopsin. Because both proteins act by regulating GTP-binding proteins, a compact structure based on seven membrane-spanning regions may be a general model for receptors that act on G proteins.

The murine transforming growth factor-beta precursor

Transforming growth factor-beta (TGF-beta) is a homodimeric polypeptide which can act, often in cooperation with other growth factors, as a mitogenic factor for a variety of cells. TGF-beta can also exert growth inhibitory activity on many other cell lines. We have isolated cDNAs coding for the murine TGF-beta cDNA precursor. The deduced amino acid sequence localizes the 112-amino acid long TGF-beta monomer to the C terminus of the precursor. Two areas of the precursor exhibit a marked degree of homology to the human counterpart. One of these regions comprises the mature TGF-beta monomer, while the other corresponds to the NH2 terminus of the precursor and suggests an important biological function for this area. Northern hybridization results identify a major 2.5-kilobase TGF-beta mRNA and several minor TGF-beta mRNA species.

Shuttle mutagenesis: a method of transposon mutagenesis for Saccharomyces cerevisiae

We have extended the method of transposon mutagenesis to the eukaryote, Saccharomyces cerevisiae. A bacterial transposon containing a selectable yeast gene can be transposed into a cloned fragment of yeast DNA in Escherichia coli, and the transposon insertion can be returned to the yeast genome by homologous recombination. Initially, the cloned yeast DNA fragment to be mutagenized was transformed into an E. coli strain containing an F factor derivative carrying the transposable element. The culture was grown to allow transposition and cointegrate formation and, upon conjugation, recipients were selected that contained yeast sequences with transposon insertions. The yeast DNA was removed from the vector by restriction endonuclease digestion, and the transposon insertion was transformed into yeast. The procedure required a minimum number of manipulations, and each transconjugant colony contained an independent insertion. We describe 12 transposon Tn3 derivatives for this procedure as well as several cloning vectors to facilitate the method.

Nucleotide sequence of the alkaline phosphatase gene of Escherichia coli

The nucleotide sequence of the alkaline phosphatase (APase) gene (phoA) of Escherichia coli strain 294 has been determined. Pre-APase has a total of 471 amino acids (aa) including a signal sequence of 21 aa. The derived aa sequence differs from that obtained by protein sequencing by the presence of aspartic acid instead of asparagine at positions 16 and 36, and glutamic acid instead of glutamine at position 197. Two open reading frames (ORF1 and ORF2) located downstream from phoA or upstream from proC have been found. ORF1 encodes a putative presecretory protein of 106 aa with a signal sequence of 21 or 22 aa. If this protein is actually produced, it may be one of the smallest periplasmic proteins in E. coli.

Human transforming growth factor-beta complementary DNA sequence and expression in normal and transformed cells

The partial amino-acid sequence of purified human transforming growth factor-beta (TGF-beta) was used to identify a series of cDNA clones encoding the protein. The cDNA sequence indicates that the 112-amino acid monomeric form of the natural TGF-beta homodimer is derived proteolytically from a much longer precursor polypeptide which may be secreted. TGF-beta messenger RNA is synthesized in various normal and transformed cells.

Supercoil sequencing: a fast and simple method for sequencing plasmid DNA

A method for obtaining sequence information directly from plasmid DNA is presented. The procedure involves the rapid preparation of clean supercoiled plasmid DNA from small bacterial cultures, its complete denaturation by alkali, and sequence determination using oligodeoxyribonucleotide-primed enzymatic DNA synthesis in the presence of dideoxynucleoside triphosphates. The advantages of the method include speed, simplicity, avoidance of additional cloning steps into single-stranded phage M13 vectors, and hence applicability to sequencing large numbers of samples.

Characterization of the human factor VIII gene

The complete 186,000 base-pair (bp) human factor VIII gene has been isolated and consists of 26 exons ranging in size from 69 to 3,106 bp and introns as large as 32.4 kilobases (kb). Nine kb of mRNA and protein-coding DNA has been sequenced and the mRNA termini have been mapped. The relationship between internal duplications in factor VIII and evolution of the gene is discussed.

Human transforming growth factor-alpha: precursor structure and expression in E. coli

Transforming growth factor-alpha (TGF-alpha) is secreted by many human tumors and can induce the reversible transformation of nontransformed cell lines. Using long synthetic deoxyoligonucleotides as hybridization probes we isolated an exon coding for a portion of TGF-alpha from a human genomic DNA library. Utilizing this exon as a probe, a cell line derived from a human renal cell carcinoma was identified as a source of TGF-alpha mRNA. A cloned TGF-alpha cDNA was isolated from a cDNA library prepared using RNA from this cell line, and was found to encode a precursor polypeptide of 160 amino acids. The 50 amino acid mature TGF-alpha produced by expression of the appropriate coding sequence in E. coli binds to the epidermal growth factor receptor and induces the anchorage independence of normal mammalian cells in culture.

Cloning, nucleotide sequence, and expression in Escherichia coli of the exotoxin A structural gene of Pseudomonas aeruginosa

A 2760-base pair DNA segment of the Pseudomonas aeruginosa strain PA103 chromosome encoding the exotoxin A (ETA) structural gene has been cloned in Escherichia coli and the nucleotide sequence has been determined. Analysis of the 5'- and 3'-flanking regions indicate that ETA is translated from a monocistronic message. Comparison of the deduced NH2-terminal amino acid sequence with that determined by sequence analysis of the secreted protein indicates that ETA is made as a 638 amino acid precursor from which a highly hydrophobic leader peptide of 25 amino acids is removed during the secretion process. Data are presented that indicate a COOH-terminal location of the ADP-ribosylation activity of the molecule. Expression of the ETA coding sequence in E. coli under control of the E. coli trp promoter, but not the ETA promoter, results in the production of enzymatically and immunologically active protein. However, most of this material appears to be neither processed nor secreted. Comparison of the ETA amino acid and nucleotide sequences to those of diphtheria toxin revealed no significant homologies, indicating that these functionally similar toxins evolved from different genes.

Cloning and sequencing of the xylose isomerase and xylulose kinase genes of Escherichia coli

A 4.2-kilobase-pair fragment of the Escherichia coli chromosome which contains the genes for xylose isomerase and xylulose kinase was cloned into plasmid pBR322. The hybrid plasmid (designated pECX14) complements strains deficient in either or both of the two enzymes. Deletion derivatives of pECX14 were used to localize the two genes on the cloned fragment. The entire nucleotide sequence of the cloned fragment was determined. Open reading frames which, if translated, would encode proteins of molecular weights 54,000 and 52,000 were found. These were identified as the isomerase and kinase structural genes, respectively.

Cloning, sequencing, and secretion of Bacillus amyloliquefaciens subtilisin in Bacillus subtilis

The subtilisin gene from B. amyloliquefaciens has been cloned and expressed under its own promoter on a high copy plasmid, pBS42, in Bacillus subtilis I-168 (Marburg strain). Greater than 95 percent of the expressed protease activity is secreted, and the activity is sensitive to inhibition by phenylmethylsulfonyl fluoride as expected for subtilisin. Bacillus subtilis transformants carrying the Bacillus amyloliquefaciens subtilisin gene in pBS42 (called pS4) secreted large amounts of a protein not seen in control pBS42 transformants. This protein migrated in SDS gels near the position of authentic subtilisin. The complete nucleotide sequence of the cloned gene has been determined using dideoxy sequencing methods. Ba131 exonuclease digestion studies at the 5' end of the gene have defined a 31 base pair stretch necessary for efficient expression of subtilisin. In addition to this putative promoter region, sequences have been assigned for ribosome binding, translation initiation, a signal peptide, the mature enzyme, and translation and transcription termination. A most interesting feature of the gene is a sequence of unknown function coding for roughly 75 amino acids between the signal sequence and the mature enzyme. It is proposed that this region serve as a pro-peptide as is commonly found in eukaryotic secreted proteases.

Identification of the type I trimethoprim-resistant dihydrofolate reductase specified by the Escherichia coli R-plasmid R483: comparison with procaryotic and eucaryotic dihydrofolate reductases

We have isolated and determined the nucleotide sequence of a 1,626-base-pair fragment from R-plasmid R483 which encodes a trimethoprim-resistant dihydrofolate reductase. Analysis of the nucleotide sequence of this fragment revealed the presence of two open reading frames, each sufficient to encode polypeptides of approximately 17,000 daltons. Both open regions are preceded by sequences conforming closely to the canonical description of procaryotic promoters. A 490-base-pair HpaI fragment spanning one of the potential coding regions was inserted into a plasmid vector under the transcriptional control of the trp promoter. Cells transformed with this plasmid were trimethoprim resistant and produced dihydrofolate reductase activity which in vitro was resistant to moderate levels of trimethoprim. Analysis of the predicted amino acid sequence of this protein indicated that the R483-encoded trimethoprim-resistant enzyme was distantly related to the trimethoprim-sensitive bacterial homologs. The conserved amino acids were localized primarily to the region of the enzyme previously shown to comprise the hydrophobic substrate binding pocket.

Structure and organization of the human Ki-ras proto-oncogene and a related processed pseudogene

Analysis of the organization and nucleotide sequence of two human loci related to the transforming gene of Kirsten murine sarcoma virus establishes one as a functional gene and the other as a processed pseudogene. The two final coding exons of the functional gene seem to have arisen by duplication. Differentially spliced mRNAs incorporating one or other of the duplicated exons probably served as the intermediates by which the viral transforming gene and the pseudogene were generated. This suggests that the functional gene may specify either of two related polypeptides depending on the pattern of RNA splicing.

Saccharomyces cerevisiae contains two discrete genes coding for the alpha-factor pheromone

Two genes, MF alpha 1 and MF alpha 2, coding for the alpha-factor in yeast Saccharomyces cerevisiae were identified by in situ colony hybridization of synthetic probes to a yeast genomic library. The probes were designed on the basis of the known amino acid sequence of the tridecapeptide alpha-pheromone. The nucleotide sequence revealed that the two genes, though similar in their overall structure, differ from each other in several striking ways. MF alpha 1 gene contains 4 copies of the coding sequence for the alpha-factor, which are separated by 24 nucleotides encoding the octapeptide Lys-Arg-Glu-Ala-Glu(or Asp)-Ala-Glu-Ala. The first alpha-factor coding block is preceded by a sequence for the hexapeptide Lys-Arg-Glu-Ala and 83 additional amino acids. MF alpha 2 gene contains coding sequences for two copies of the alpha-factor that differ from each other and from alpha-factor encoded by MF alpha 1 gene by a Gln leads to Asn and a Lys leads to Arg substitution. The first copy of the alpha-factor is preceded by a sequence coding for 87 amino acids which ends with Lys-Arg-Glu-Ala-Val-Ala-Asp-Ala. The coding blocks of the two copies of the pheromone are separated by the sequence for Lys-Arg-Glu-Ala-Asn-Ala-Asp-Ala. Thus, the alpha-factor can be derived from 2 different precursor proteins of 165 and 120 amino acids containing, respectively, 4 and 2 copies of the pheromone.

Comparative analysis of the human type 1a and bovine type 1 papillomavirus genomes

The DNA sequences of the genomes of the bovine type 1 and human type 1a papillomaviruses were compared. The overall organization of both genomes is very similar. Three areas of maximal homology were found in the L1 and E1/E2 genes, and at the beginning of L2. The conservation of homologous amino acid sequences encoded in the open reading frames argues that these segments represent real genes or exons. Within these segments, however, only certain domains of the putative proteins are preferentially conserved. Two polypeptide chains show homologous arrangement of the cysteine residue clusters Cys-X-X-Cys, despite a lack of conservation of the rest of the amino acid sequence. A significant sequence divergence in a region where the three reading frames are open suggests that papillomavirus genomes have evolved not solely by accumulation of point mutations. Conserved sequences were also found in the noncoding region, and their possible involvement in regulation of viral gene expression is discussed.

Complete nucleotide sequences of the T24 human bladder carcinoma oncogene and its normal homologue

DNA sequence analysis of the activated oncogene from the T24 human bladder carcinoma line and two alleles of its normal cellular progenitor (c-Ha-ras-1) indicates that the genes encompass at least four exons, and that only a single point mutation residing within the first exon distinguishes the coding region of both alleles of the normal gene from their activated counterpart. Both versions of the gene encode a protein which is predicted to differ from the corresponding viral gene product at three amino acid residues, one of which was previously shown to represent the major site of phosphorylation of the viral polypeptide.

Identification and nucleotide sequence of a human locus homologous to the v-myc oncogene of avian myelocytomatosis virus MC29

Avian myelocytomatosis virus MC29 is a replication-defective acute leukaemia virus which induces a variety of tumours in chickens including sarcomas, renal and hepatic carcinomas, and myelocytomatosis. The oncogenic potential of the virus is mediated by the gene v-myc, acquired from sequences (c-myc) present in normal uninfected chicken DNA. Sequences closely related to chicken c-myc have been highly conserved throughout evolution, from Drosophila to vertebrates. The hypothesis that c-myc may be involved in neoplastic transformation has been strengthened by the finding that B-cell lymphomas induced in chickens by avian leukosis virus (ALV) are often associated with increased expression of c-myc resulting from integration of the ALV provirus adjacent to the c-myc gene. More recently, it has been demonstrated that the malignant human cell line HL-60, derived from the peripheral blood leukocytes of a patient with acute promyelocytic leukaemia, expresses elevated levels of myc-related mRNA associated with an amplification of the c-myc gene. To explore the relationship of the human cellular myc gene with the corresponding viral oncogene from MC29, and to provide a framework for the analysis of the mechanism and significance of c-myc amplification in human tumours, we have isolated and determined the nucleotide sequence of a genomic clone prepared from a normal human library which contains all domains sharing homology with v-myc.

Nucleotide sequence to the v-myc oncogene of avian retrovirus MC29

Avian myelocytomatosis viruses are retroviruses whose oncogene (v-myc) induces an unusually wide variety of tumors, including carcinomas, endotheliomas, sarcomas, and myelocytomatoses. The viral gene v-myc arose by transduction of an undetermined portion of a cellular gene known as c-myc. In order to facilitate further studies of the functions of v-myc and c-myc and to permit detailed comparisons between the two genes, we have determined the nucleotide sequence of v-myc in the genome of the MC29 strain of myelocytomatosis virus. The v-myc domain in MC29 virus encodes a hydrophilic polypeptide with a molecular weight of 47,000, fused to a portion of the polyprotein encoded by the viral structural gene gag. The carboxyl-terminal half of the v-myc polypeptide is rich in basic amino acid residues. This feature may account for the DNA-binding properties of the hybrid gag-myc-encoded protein which would have a molecular weight of approximately 100,000, in accord with results from previous studies of the protein encoded by v-myc. The junctions between v-myc and the genome of the transducing virus are apparent but reveal no clues to the mechanism by which transduction might occur.

The primary structure and genetic organization of the bovine papillomavirus type 1 genome

The complete nucleotide sequence of the doubt-stranded circular DNA of bovine papillomavirus type 1 (BPV-1) was determined. Analysis of this sequence in conjunction with known transcriptional data for the virus provides a basis of determining the organization of the papillomavirus genome. All the major open reading frames are located on the same DNA strand. The region transcribed in BPV-transformed cells contains open frames in all three translational frames whereas the region transcribed in productively infected bovine fibropapillomas is characterized by two large open reading frames partitioned by a single translational stop codon. The localization of sequences diagnostic of promoters and polyadenylation sites suggests that splicing is involved in the biosynthesis of the viral mRNAs. A sequence comparison indicates the genome organization of the bovine papillomavirus and that of the members of the simian virus 40-polyomavirus subgroup to be distinct, suggesting that these two groups of viruses are evolutionarily unrelated.

Structural comparison of human, bovine, rat, and Walker 256 carcinosarcoma asparaginyl-tRNA

The complete nucleotide sequences of human placenta, human liver, and bovine liver tRNAAsn have been determined. A comparison of these tRNA structures with the previously reported nucleotide sequences of rat liver and Walker 256 carcinosarcoma tRNAAns reveals that the primary nucleotide sequences of the major species of mammalian cytoplasmic tRNAasn are conserved in higher eucaryotes. The complete nucleotide sequence of these tRNAs is: pG-U-C-U-C-U-G-U-m1G-m2G-C-G-C-A-A-D-C-G-G-D-X-A-G-C-G-C-m2(2)G-psi-psi-C-G-G-C-U-Q(G)-U-U-t6A-A-C-C-G-A-A-A-G-m7G-D-U-G-G-U-G-G-Z-psi-C-G-m1A-G-C-C-C-A-C-C-C-A-G-G-G-A-C-G-C-C-AOH where X is 3-(3-amino-3-carboxyl-n-propyl)uridine, Q is 7-(4,5-cis-dihydroxyl-1-cyclopenten-3-yl-aminomethyl)-7-deazaguanosine, Z is an unknown modified nucleotide, and Q(G) represents the replacement of Q nucleoside by G nucleoside in Walker 256 carcinosarcoma tRNAAsn. These primary structures were determined by combined use of the 3H- and 32P-post-labeling techniques. Sequences were compared by tritium nucleoside trialcohol analysis, completed RNAase T1 digestion followed by 3H-labeled fingerprinting on polyethylenimine-impregnated cellulose by two-dimensional thin-layer chromatography (TLC), and polyacrylamide gel electrophoresis of either 5'-32P- and/or 3'-[32P]pCp-labeled tRNA after partial ribonuclease digestions.

A mammalian mitochondrial serine transfer RNA lacking the "dihydrouridine" loop and stem

A unique transfer RNA has been identified in human and bovine mitochondria that lacks the "dihydrouridine" loop and stem structure. This tRNA is mitochondrially coded as shown by DNA sequence analysis of the human and bovine mitochondrial DNA. Sequence analysis of the RNA shows that it is post-transcriptionally modified by the addition of CCA at the 3' terminus and that at least one base is modified. As predicted by its anticodon (GCU, corresponding to the serine codons AGU/C) this tRNA can be aminoacylated with serine when purified mitochondria are incubated in a medium containing 3H-serine.