A systematic approach to chemical DNA sequencing by subcloning in pGV451 and derived vectors.
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Base Sequence↗
Biomedical subjects
G Volckaert
Publications and source records attributed to G Volckaert.
Structural analysis of the sequence coding for an inducible 26-kDa protein in human fibroblasts.
When human fibroblast cells were stimulated with poly(I) X poly(C) in the presence of cycloheximide for the production of interferon-beta (IFN-beta), a 26-kDa protein could be immunoprecipitated by antiserum raised against partially purified human IFN-beta [Content, J., De Wit, L., Pierard, D., Derynck, R., De Clercq, E. & Fiers, W. (1982) Proc. Natl Acad. Sci. USA 79, 2768-2772]. In our hands this 26-kDa protein showed no antiviral activity. Other investigators have, however, reported the presence in the same conditions of a second type of IFN, a so-called beta 2 species [Weissenbach, J., Chernajovsky, Y., Zeevi, M., Shulman, L., Soreq, H., Nir, U., Wallach, D., Perricaudet, M., Tiollais, P. & Revel, M. (1980) Proc. Natl Acad. Sci. USA 77, 7152-7156] of which the mRNA structure and protein characteristics strongly suggests identity with the 26-kDa product. In this paper we describe the nucleotide sequence of the 26-kDa cDNA and part of the corresponding genomic clone. The cDNA clones were isolated from a library made with mRNA from induced human fibroblasts. As, however, the information thus obtained was still incomplete, genomic clones were isolated from a total human DNA library. In this way, the entire region coding for the 26-kDa protein was established, as well as the neighbouring sequences including the inducible promoter area. From the deduced polypeptide sequence a number of characteristics of the 26-kDa protein can be explained. It turns out that the 26-kDa protein gene and the so-called 'IFN-beta 2' gene are identical. However, extensive homology searches indicate that the 26-kDa protein does not show statistically significant sequence homology with any known interferon species. Hence, the question of whether the 26-kDa product represents a novel IFN species remains open.
Amino Acid Sequence↗
Cloning of cDNA coding for human tissue-type plasminogen activator and its expression in Escherichia coli.
cDNA clones of the mRNA coding for tissue-type plasminogen activator (t-PA) have been obtained and their nucleotide sequences compared to those reported previously. A gene coding for t-PA has been reconstructed and inserted into vectors for expression in prokaryotic cells. Relatively high levels of t-PA accumulated in inclusion bodies in Escherichia coli containing an optimized expression plasmid, but only a small proportion of the insoluble protein was recovered as active enzyme using a variety of solubilization procedures.
Amino Acid Sequence↗
Human tissue-type plasminogen activator gene located near chromosomal breakpoint in myeloproliferative disorder.
Plasminogen activators (PA) convert the inactive proenzyme plasminogen into plasmin, which is involved in the process of fibrinolysis, tissue remodeling, and cell migration. There are two distinct forms of PA: urokinase (u-PA) and tissue-type plasminogen activator (t-PA). t-PA has higher affinity for fibrin and is the main form involved in thrombolysis. By in situ chromosomal hybridization and Southern blot analysis of somatic cell hybrid DNA, we have assigned the human t-PA gene to chromosome 8, bands 8p12----q11.2. We have detected a common EcoRI restriction fragment length polymorphism within the t-PA gene that thus provides a precisely localized highly informative marker for genetic linkage studies. The t-PA gene localization coincides with a translocation breakpoint observed in myeloproliferative disorders. Whereas leukemic cells usually secrete both types of PA, a correlation exists between acute myeloid leukemic cells that release only t-PA and failure to respond to chemotherapy.
Animals↗
Determination of tissue-type plasminogen-activator mRNA in human and non-human cell lines by dot-blot hybridization.
A labelled cDNA clone was used in DNA-RNA hybridization on nitrocellulose filter paper (dot-blot technique) to detect and quantify mRNA for endogenous tissue plasminogen activator (PA) in cell extracts and samples of RNA purification runs. Although, for detection purposes, the assay was less sensitive than translation in Xenopus oocytes, it was at least as reliable and much more convenient for the purpose of quantitative determination. In particular, the technique was used to study the kinetics of PA mRNA formation in a human melanoma cell line (Bowes) after exposure to the tumour promoter 12-O-tetradecanoylphorbol 13-acetate (TPA). Incubation of the cells with TPA resulted in a 15-20-fold increase in cellular PA mRNA content. The effect was time- and dose-dependent: the increase in PA-specific mRNA was clearly visible as early as 4 h after initiation of TPA treatment in Bowes cells. It was blocked completely by pretreatment of the cells with actinomycin D, indicating that TPA caused enhancement of synthesis of PA mRNA rather than inhibition of PA mRNA degradation. The use of the nitrocellulose dot-blot technique also revealed that two non-human cell lines produce mRNAs which cross-react with the human PA mRNA, namely the mouse melanoma cell line B16 and the rat brain-tumour cell line, RT4-71-1. TPA was found to exert similar stimulatory effects on the synthesis of mRNAs in these cell lines as in Bowes cells.
Animals↗
A restriction endonuclease map of Streptomyces phage VWB.
A physical map of the actinophage VWB has been constructed using the restriction endonucleases BglII, ClaI, EcoRI, EcoRV, HindIII, KpnI and SphI. Phage VWB, genome size 47.3 kb, propagates on Streptomyces venezuelae, and it can also lysogenise this species. The three BglII-generated fragments of VWB DNA were cloned in pBR322, and subsequently mapped. In this manner the restriction map of the VWB phage genome was constructed.
Bacteriophages↗
Molecular cloning of murine interferon gamma (MuIFN-gamma) cDNA and its expression in heterologous mammalian cells.
A complete cDNA clone of murine interferon-gamma (MuIFN-gamma) was obtained by recombining two appropriate segments from partial cDNA clones originally identified by colony hybridization with rat IFN-gamma chromosomal gene fragments as probes. An expression vector was constructed in which the cDNA was placed under control of the SV40 early promoter. Transient expression of MuIFN-gamma was obtained by transformation of COS-1 cells. Subsequently, this interferon expression unit was linked to a vector containing a dihydrofolate reductase (DHFR) modular gene and used to transform DHFR(-)-CHO cells. Cell clones were selected that constitutively produce an interferon activity which by several criteria was found to be indistinguishable from natural, splenocyte-derived MuIFN-gamma.
Animals↗
Nucleotide sequence of a crustacean 18S ribosomal RNA gene and secondary structure of eukaryotic small subunit ribosomal RNAs.
The primary structure of the gene for 18 S rRNA of the crustacean Artemia salina was determined. The sequence has been aligned with 13 other small ribosomal subunit RNA sequences of eukaryotic, archaebacterial, eubacterial, chloroplastic and plant mitochondrial origin. Secondary structure models for these RNAs were derived on the basis of previously proposed models and additional comparative evidence found in the alignment. Although there is a general similarity in the secondary structure models for eukaryotes and prokaryotes, the evidence seems to indicate a different topology in a central area of the structures.
Animals↗
The nucleotide sequences of the 5 S rRNAs of seven molds and a yeast and their use in studying ascomycete phylogeny.
The sequences of the 5 S rRNAs isolated from 8 ascomycete species belonging to the genera Aspergillus, Penicillium, Acremonium and Candida are reported. Two of the examined strains each yielded a mixture of 3 slightly different 5 S RNAs, which were individually sequenced after fractionation. A previously published sequence for Aspergillus nidulans 5 S RNA was found to contain errors. Reconstruction of an evolutionary tree based on 5 S RNA sequences showed that the 16 presently examined ascomycetes form three clusters. The same threefold partition can be observed in the secondary structure pattern, each cluster showing a slightly different variant of the general 5-helix model for 5 S rRNA (De Wachter, Chen and Vandenberghe (1982) Biochimie 64, 311-329), and different sets of secondary structure equilibrium forms in helices C and E of the aforementioned model.
Aspergillus flavus↗
Base specific interaction of reductively activated nitroimidazoles with DNA.
To exert biological activity, nitroimidazole drugs require reductive activation in vivo. Nucleic acids are susceptible to the activated drug in vitro and are presumably the major target in vivo. We carried out electrolytical reduction of several 5-nitroimidazoles at a controlled potential either in the presence or prior to the addition of DNA. Using a nucleotide sequence specific test to analyse cleavage products, specific interaction of the reduced nitroimidazole intermediate(s) towards the guanine residues is prominent. Since the strand scission depends on subsequent piperidine treatment, it can be concluded that the primary interaction between the activated drug and guanine is a covalent modification weakening the glycosidic bond.
Base Composition↗
Heterogeneity of alpha 2u-globulin gene products in different translational systems, plasma and urine.
alpha 2u-Globulin, an androgen dependent rat urinary protein, displays considerable microheterogeneity. To explore whether this microheterogeneity of alpha 2u-globulin in male rat urine is related to the heterogeneity at the level of the genes encoding this protein, or whether it is due to post-translational processing we studied the alpha 2u-globulin mRNA translation products in rabbit reticulocyte and Xenopus oocytes. Comparison of the alpha 2u-globulin species produced in these two heterologous systems with those observed in plasma and urine indicates that the heterogeneity of this protein in urine is mainly due to heterogeneity at the level of the corresponding mRNAs.
Alpha-Globulins↗
The nucleotide sequence of cDNA complementary to the C1 component of rat prostatic binding protein.
The mRNA for component C1 of rat prostatic binding protein has been cloned and characterized. A partially purified mRNA fraction for this complex protein was reverse-transcribed into double-stranded cDNA and cloned into the PstI site of plasmid pBR 322. The 426-base-pair insert of the recombinant plasmid pC1A75 was completely sequenced. The coding region corresponds precisely to the 88 amino acid residues of C1 and in addition contains the information of a signal peptide of 23 residues. The 5' non-coding region counts only 19 nucleotides and is incomplete but the 3'-terminal non-coding part of 60 nucleotides extends into the poly(A) tail. Sequence analysis of other C1-positive clones indicates the presence of sequence rearrangements which must have occurred during the cloning procedure. Possible mechanisms for the generation of these cloning artefacts are discussed.
Androgen-Binding Protein↗
Molecular mechanisms of nucleotide-sequence rearrangements in cDNA clones of human fibroblast interferon mRNA.
The characterization and nucleotide sequencing of cDNA clones of human fibroblast interferon (HFIF) mRNA (Derynck et al., 1980) revealed two types of structural inversions :(i) an inverted repeat of a 3'-proximal segment at the 5'end, or (ii) an inverted 5'-terminal segment. Based on the nucleotide sequence of these inverted clones, we have deduced molecular mechanisms to explain how the rearrangements could have arisen. We propose that the usual small 3'-terminal hairpin does not form after the reverse transcription produces the first cDNA strand. Instead, base pairing occurs between the 3'-terminal segment and the more distal region of the first cDNA strand, forming a much larger hairpin loop. Second-strand synthesis followed by either nicking or unfolding of the loop structure and continuation of the polymerase reaction would lead to the observed types of inversions. The 5'-truncated clone, pHFIF-1, whose new 5'-terminal sequence diverges from that of the corresponding region in the mRNA, can also be explained by such a mechanism.
Base Sequence↗
Isolation and structure of a human fibroblast interferon gene.
Chimaeric plasmids containing double-stranded cDNA copies of mRNA induced in human fibroblasts by poly I . C were screened by an RNA selection method. A series of clones to which human fibroblast interferon mRNA selectively hybridized was identified. From the nucleotide sequence of the gene, the complete amino acid sequence of human fibroblast interferon was deduced. The protein is 166 amino acids long and is preceded by a 21-amino acid signal sequence.
Amino Acid Sequence↗
Nucleotide sequence of the simian virus 40 HindII + III restriction fragment A (second part of the T antigen gene).
The nucleotide sequence of the second part of the simian virus 40 DNA HindII + III restriction fragment A is presented. The sequence extends from map position 0.533 to 0.424 and together with the first part of Hind-A [Volckaert et al. Proc. Natl Acad. Sci. U.S.A. 75, 2160--2164 (1978)] completes the total hind-A sequence, comprising 1169 base pairs. The second half of Hind-A includes the region corresponding to the second splicing boundary common to small tumor antigen (small-t) and large tumor antigen (large-T) mRNA and it contains coding information for an internal portion of large-T antigen. Two similar secondary structures of reasonable thermodynamic stability can be proposed for the nucleotide sequence of the pre-mRNA corresponding to the region reported here. Their possible relevance to the splicing of the SV40 early mRNAs is discussed. The deduced amino acid sequence is 188 residues long and contains a Lys-Lys-Lys-Arg-Lys-stretch which may be involved in the DNA binding capacity of large-T. A presumptive phosphorylation site is also present.
Amino Acid Sequence↗
Nucleotide sequence of simian virus 40 DNA: structure of the middle segment of the HindII + III restriction fragment B (sixth part of the T antigen gene) and codon usage.
We report here the nucleotide sequence of the simian virus 40 DNA region that lies between the EcoRII restriction endonuclease cleavage sites at map positions 0.214 and 0.281. The sequence was determined by partial chemical degradation of terminally labeled DNA fragments according to the procedure of Maxam and Gilbert. This region represents 6.7% of the SV40 genome and is located in the middle of HindII + III restriction fragment B. It is expressed as part of the early 19-S messenger RNA, which codes for the large-T antigen protein. Only one open reading frame for translation can be deduced from the message strand of the DNA and this reading frame connects in phase with the one of both neighboring fragments. This publication is the last in a series of papers about the T-antigen gene, and several properties of this gene and its product are discussed. The non-randomness of codon usage is similar to that previously discussed for the late part of the genome. Moreover, it appears that the choice of a third letter can be determined by the nature of the following codon; some codons which start with a pyrimidine are almost never preceded by an adenosine and some ANN-type codons are almost never preceded by a guanosine.
Amino Acid Sequence↗
Nucleotide sequence deletions within the coding region for small-t antigen of simian virus 40.
Simian virus 40 early mutants with deletions mapping in the 0.53-0.60 region have been sequenced by the Maxam and Gilbert approach. All these deletions effect the small-t gene. The size of the shortened small-t-related polypeptides produced by several of the mutants has been compared with the molecular weight as deduced from the nucleotide sequence. There was good agreement for the mutants dl890, dl891, and dl2102. For dl2121 and dl2122 the small-t-related protein was considerably larger than expected. It is possible to explain this result on the basis of the nucleotide sequence: the normal splicing event of the small-t mRNA still occurs, but as the deletion shifts the reading frame, translation of the small-t-related polypeptide continues beyond the small-t splice, but in a different reading frame than large-T. Mutants dl883, dl884, and dl2112 have lost one of the small-t splicing boundaries, and no (or minute amonts of) small-t-related protein has been observed in mutant-infected cells. The possible relationship between splicing and transport of polyadenylic acid-containing mRNA from the nucleus to the cytoplasm in vertebrae cells is discussed.
Antigens, Viral↗
Complete nucleotide sequence of SV40 DNA.
The determination of the total 5,224 base-pair DNA sequence of the virus SV40 has enabled us to locate precisely the known genes on the genome. At least 15.2% of the genome is presumably not translated into polypeptides. Particular points of interest revealed by the complete sequence are the initiation of the early t and T antigens at the same position and the fact that the T antigen is coded by two non-contiguous regions of the genome; the T antigen mRNA is spliced in the coding region. In the late region the gene for the major protein VP1 overlaps those for proteins VP2 and VP3 over 122 nucleotides but is read in a different frame. The almost complete amino acid sequences of the two early proteins as well as those of the late proteins have been deduced from the nucleotide sequence. The mRNAs for the latter three proteins are presumably spliced out of a common primary RNA transcript. The use of degenerate codons is decidedly non-random, but is similar for the early and late regions. Codons of the type NUC, NCG and CGN are absent or very rare.
Antigens, Neoplasm↗