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PubMed1991

Mitochondrial DNA sequence analysis in congenital myotonic dystrophy.

Mitochondrial genetic modifying factors have been suspected in several autosomally inherited diseases. The congenital variant of myotonic dystrophy, in which there is striking maternal inheritance pattern, is a likely candidate disease. To investigate this possibility, we sequenced completely the mitochondrial genome in 2 patients with congenital myotonic dystrophy. Comparison of the two sequences with control data failed to reveal a specific nucleotide variant or length variant in this disease. We conclude that a mitochondrial genetic modifying factor is not present in congenital myotonic dystrophy.

Adult↗
PubMed1989

Expression and DNA sequence analysis of a human embryonic skeletal muscle myosin heavy chain gene.

Vertebrate myosin heavy chains (MHC) are represented by multiple genes that are expressed in a spatially and temporally distinct pattern during development. In order to obtain molecular probes for developmentally regulated human MHC isoforms, we used monoclonal antibodies to screen an expression cDNA library constructed from primary human myotube cultures. A 3.4 kb cDNA was isolated that encodes one of the first MHCs to be transcribed in human skeletal muscle development. A portion of the corresponding gene encoding this isoform has also been isolated. Expression of this embryonic MHC is a hallmark of muscle regeneration after birth and is a characteristic marker of human muscular dystrophies. During normal human development, expression is restricted to the embryonic period of development prior to birth. In primary human muscle cell cultures, devoid of other cell types, mRNA accumulation begins as myotubes form, reaches a peak 2 days later and declines to undetectable levels within 10 days. The expression of the protein encoded by the embryonic skeletal MHC gene follows a similar time course, lagging behind the mRNA by approximately two days. Thus, expression of the human embryonic gene is efficiently induced and then repressed in cultured muscle cells, as it is in muscle tissue. The study of the regulation of a human MHC isoform with a central role in muscle development and in muscle regeneration in disease states is therefore amendable to analysis at a molecular level.

Amino Acid Sequence↗
PubMed1979

DNA sequence analysis of the transposon Tn3: three genes and three sites involved in transposition of Tn3.

The complete nucleotide sequence of the transposon Tn3 and of 20 mutations which affect its transposition are reported. The mutations, generated in vitro by random insertion of synthetic restriction sites, proved to contain small duplications or deletions immediately adjacent to the new restriction site. By determining the phenotype and DNA sequence of these mutations we were able to generate an overlapping phenotypic and nucleotide map. This 4957 bp transposon encodes three polypeptides which account for all but 350 bp of its total coding capacity. These proteins are the transposase, a high molecular weight polypeptide (1015 amino acids) encoded by the tnpA gene; the Tn3-specific repressor, a low molecular weight polypeptide (185 amino acids) encoded by the tnpR gene; and the 286 amino acid beta-lactamase. The 38 bp inverted repeats flanking Tn3 appear to be absolutely required in cis for Tn3 to transpose. Genetic data suggest that Tn3 contains a third site (Gill et al., 1978), designated IRS (internal resolution site), whose absence results in the insertion of two complete copies of Tn3 as direct repeats into the recipient DNA. We suggest that these direct repeats of complete copies of Tn3 are intermediates in transposition, and that the IRS site is required for recombination and subsequent segregation of the direct repeats to leave a single copy of Tn3 (Gill et al., 1978). A 23 nucleotide sequence within the amino terminus of the transposase which shares strong sequence homology with the inverted repeat may be the internal resolution site.

Base Sequence↗
PubMed1987

DNA sequence analysis suggests that expression of flagellar and chemotaxis genes in Escherichia coli and Salmonella typhimurium is controlled by an alternative sigma factor.

Biosynthesis of bacterial flagella involves the coordinated expression of 30 or more genes in several separate operons. We have recently shown that in Bacillus subtilis, the sigma 28 factor is essential for flagellar synthesis, suggesting that transcription of these genes is directly under the control of this alternative sigma factor. In enteric bacteria structural genes for flagellar, chemotaxis, and motility operons appear to be under coordinate control, however, the nature of the regulatory factors has not been determined. Sequence analysis of many such genes has failed to reveal plausible promoter sequences for the predominant bacterial RNA polymerase, and several such genes are not transcribed effectively in vitro by the Escherichia coli sigma 70 RNA polymerase. However, all of the sequenced flagellar, chemotaxis, and motility operons from the enteric bacteria are preceded by DNA sequences highly homologous to B. subtilis sigma 28 promoters. We propose that an alternative sigma factor controls expression of the flagellar regulon in both B. subtilis and in the enteric bacteria.

Bacterial Proteins↗
PubMed1993

DNA sequence analysis of an allelic variant of the Actinobacillus pleuropneumoniae-RTX-toxin I (ApxIA) from serotype 10.

The structural gene encoding Actinobacillus pleuropneumoniae-RTX-toxin I (ApxIA), one of the major hemolytic and cytolytic toxins of the organism, was cloned from serotype 10. The nucleotide sequence data showed that the gene from serotype 10 was 98% identical to that from serotype 1 at both DNA and amino acid levels. The sequence difference was found to localize at the 3' terminal region of the gene. We then analyzed the 3' terminal region of the apxIA gene from other serotypes, 5a, 5b, 9 and 11, using polymerase chain reaction-amplified DNA fragments. Results of DNA sequence indicated that apxIA gene can be divided into the original form including serotypes 1, 9 and 11, and the allelic variant including serotypes 5a, 5b and 10. These gene products, ApxIA proteins, appear to have different second structures at the carboxyl terminal proximal region.

Actinobacillus pleuropneumoniae↗
PubMed1983

DNA sequence analysis of the EcoRI Dhet fragment of B95-8 Epstein-Barr virus containing the terminal repeat sequences.

An analysis of the approximately 12,440 base-pair sequence of the EcoRI Dhet fragment isolated from the circular episomal form of the B95-8 strain of Epstein-Barr virus is presented. This fragment contains the covalently joined ends of the intracellular episomal form of the molecule. In the viral capsid the DNA is linear and the joining is mediated via the terminal repeated DNA. Four copies of tandem repeated DNA were present in this clone, three with a repeat size of 538 and one of 523. The positions of a number of possible protein coding regions and transcription signals are discussed. In particular a possible spliced coding region for an approximately 45,000 Mr protein expressed in latently infected transformed cells is proposed. The predicted protein sequence contains hydrophobic regions separated by charged amino acids reminiscent of a membrane protein.

Animals↗
PubMed1990

DNA sequence analysis of mutations induced by N-2-acetylamino-7-iodofluorene in plasmid pBR322 in Escherichia coli.

The spectrum of mutations induced by N-2-acetylamino-7-iodofluorene (AAIF) was analyzed in a forward mutation system based on mutagenesis directed to a small restriction fragment in the tetracycline resistance gene of plasmid pBR322. AAIF was found to induce frameshift mutations and base-pair substitutions at approximately equal frequencies. The frameshift mutations were mostly deletions of single base-pairs, but -2 frameshifts and +1 frameshifts were also detected. With one exception, the substitutions were transversions initiated at a G.C base-pair. Both frameshift mutations and transversions occurred preferentially at sites of repetitive guanine residues. Although AAIF and the related aromatic amines N-2-acetylaminofluorene (AAF) and N-2-aminofluorene (AF) all bind to the C-8 position of guanine, they have different effects on DNA conformation, and these differences are reflected in their mutation spectra. Previous studies have provided evidence that AAF adducts can trigger a B to Z conformational change in alternating GC sequences or displacement of the guanine by the fluorene ring in other sequences; the principal result is two classes of frameshift mutations. AF, whose DNA interaction involves outside binding rather than insertion and denaturation, primarily induces base-pair substitutions. AAIF adducts are chemically similar to AAF adducts, but the iodo group apparently hinders insertion of the fluorene ring into DNA. Consistent with this model, the mutation spectrum of AAIF combines properties of the mutation spectra of both AAF and AF.

2-Acetylaminofluorene↗
PubMed1996

Human colonic biota studied by ribosomal DNA sequence analysis.

Human colonic biota is a complex microbial ecosystem that serves as a host defense. Unlike most microbial ecosystems, its composition has been studied extensively by relatively efficient culture methods. We have compared an established culture-based method with direct amplification and partial sequencing of cloned 16S rRNA genes from a human fecal specimen. Nine cycles of PCR were also compared with 35 cycles. Colonies and cloned amplicons were classified by comparing their ribosomal DNA (rDNA; DNA coding for rRNA) sequences with rDNA sequences of known phylogeny. Quantitative culture recovered 58% of the microscopic count. The 48 colonies identified gave 21 rDNA sequences; it was estimated that 72% of the rDNA sequences from the total population of culturable cells would match these 21 sampled sequences (72% coverage). Fifty 9-cycle clones gave 27 sequences and 59% coverage of cloned rDNAs. Thirty-nine rDNAs cloned after 35 cycles of PCR gave 13 sequences for 74% coverage. Thus, the representation of the ecosystem after 35 cycles of PCR was distorted and lacked diversity. However, when the number of temperature cycles was minimized, biodiversity was preserved, and there was good agreement between culturing bacteria and sampling rDNA directly.

Bacteria↗
PubMed2004

DNA sequence analysis of regions surrounding blaCMY-2 from multiple Salmonella plasmid backbones.

The emergence in the United States of resistance to expanded-spectrum cephalosporin (e.g., ceftriaxone) within the salmonellae has been associated primarily with three large (>100-kb) plasmids (designated types A, B, and C) and one 10.1-kb plasmid (type D) that carry the blaCMY-2 gene. In the present study, the distribution of these four known blaCMY-2-carrying plasmids among 35 ceftriaxone-resistant Salmonella isolates obtained from 1998 to 2001 was examined. Twenty-three of these isolates were Salmonella enterica serotype Newport, 10 were Salmonella enterica serotype Typhimurium, 1 was Salmonella enterica serotype Agona, and 1 was Salmonella enterica serotype Reading. All 23 serotype Newport isolates carried a type C plasmid, and 5, 4, and 1 serovar Typhimurium isolate carried type B, A, and C plasmids, respectively. Both the serotype Agona and serotype Reading isolates carried type A plasmids. None of the isolates carried a type D plasmid. Hybridization data suggested that plasmid types A and C were highly related replicons. DNA sequencing revealed that the region surrounding blaCMY-2 was highly conserved in all three plasmid types analyzed (types B, C, and D) and was related to a region surrounding blaCMY-5 from the Klebsiella oxytoca plasmid pTKH11. These findings are consistent with a model in which blaCMY-2 has been disseminated primarily through plasmid transfer, and not by mobilization of the gene itself, to multiple Salmonella chromosomal backbones.

Bacterial Typing Techniques↗
PubMed1992

DNA sequence analysis and comparison of the variable heavy and light chain regions of two IgM, monoclonal, anti-myelin associated glycoprotein antibodies.

The complete variable heavy and light chain gene sequences of two monoclonal, IgM, anti-myelin associated glycoprotein (MAG) antibodies associated with peripheral neuropathy, are presented. Comparative analysis of the two VH regions has revealed that they are 88% homologous to one another and are both members of the VH3 gene family. They are also highly homologous to a gene which is frequently utilized in the fetal B-cell repertoire. The V kappa light chain gene of one of the antibodies is 99% homologous to a V kappa II gene and the V lambda light chain gene of the other antibody is only 72% homologous to other known V lambda genes. Further analysis of V genes utilized by anti-MAG antibodies should reveal the structural basis for their binding activity.

Amino Acid Sequence↗
PubMed1986

Cloning and DNA sequence analysis of the cDNA for the precursor of the beta chain of bovine follicle stimulating hormone.

Follicle stimulating hormone (FSH) plays essential roles in the maintenance and development of oocytes and spermatozoa in normal reproductive physiology. FSH possesses two subunits, alpha and beta, the latter being responsible for FSH biological specificity. We have cloned and sequenced the cDNA encoding the FSH beta chain from a bovine anterior pituitary cDNA library. The mature molecule is 109 amino acids long and is preceded by a 20-amino acid putative signal peptide. RNA gel blot analysis of bovine pituitary RNA shows that the mRNA encoding beta chain of FSH is approximately 1.7 kilobases in length.

Amino Acid Sequence↗
PubMed1990

A rapid method for partial mRNA and DNA sequence analysis of the photosystem IIpsbA gene.

Single amino acid substitutions in the D1 protein of photosystem II may cause resistance to various herbicides. In all organisms studied these substitutions are located in or between helices IV and V of the protein. The increasing number of herbicide-resistant organisms necessitates development of a rapid methodology to characterize deviations from the wildtype sequence. Here, two procedures are described to identify mutations in the psbA gene, which is coding for D1. These procedures involve the isolation and amplification of DNA and RNA and subsequent sequencing reactions without the need to clone the psbA gene. A triazine-resistant and a -susceptible biotype of Chenopodium album were used as model species. An A to G transition, giving rise to a serine to glycine mutation at position 264 in the D1 protein, is found in the resistant plant.

Base Sequence↗
PubMed1990

Characterization of the antigenic structure of herpes simplex virus type 1 glycoprotein C through DNA sequence analysis of monoclonal antibody-resistant mutants.

Earlier studies of a group of monoclonal antibody-resistant (mar) mutants of herpes simplex virus type 1 glycoprotein C (gC) operationally defined two distinct antigenic sites on this molecule, each consisting of numerous overlapping epitopes. In this report, we further define epitopes of gC by sequence analysis of the mar mutant gC genes. In 18 mar mutants studied, the mar phenotype was associated with a single nucleotide substitution and a single predicted amino acid change. The mutations were localized to two regions within the coding sequence of the external domain of gC and correlated with the two previously defined antigenic sites. The predicted amino acid substitutions of site I mutants resided between residues Gln-307 and Pro-373, whereas those of site II mutants occurred between amino acids Arg-129 and Glu-247. Of the 12 site II mutations, 9 induced amino acid substitutions within an arginine-rich segment of 8 amino acids extending from residues 143 to 151. The clustering of the majority of substituted residues suggests that they contribute to the structure of the affected sites. Moreover, the patterns of substitutions which affected recognition by antibodies with similar epitope specificities provided evidence that epitope structures are physically linked and overlap within antigenic sites. Of the nine epitopes defined on the basis of mutations, three were located within site I and six were located within site II. Substituted residues affecting the site I epitopes did not overlap substituted residues of site II, supporting our earlier conclusion that sites I and II reside in spatially distinct antigenic domains. A computer analysis of the distribution of charged residues and the predicted secondary structural features of wild-type gC revealed that the two antigenic sites reside within the most hydrophilic regions of the molecule and that the antigenic residues are likely to be organized as beta sheets which loop out from the surface of the molecule. Together, these data and our previous studies support the conclusion that the mar mutations identified by sequence analysis very likely occur within or near the epitope structures themselves. Thus, two highly antigenic regions of gC have now been physically and genetically mapped to well-defined domains of the protein molecule.

Animals↗
PubMed1997

Assignment of the beta-subunit of wheat eIF2 by protein and DNA sequence analysis and immunoanalysis.

Wheat germ initiation factor 2 (eIF2), like mammalian and yeast eIF2, contains three nonidentical subunits. The estimated molecular weights for the wheat subunits are 38,000 (p38), 42,000 (p42), and 50,000 (p50). Peptide sequence was obtained for the p38 subunit of wheat eIF2 and the resulting amino acid sequence suggested that it was actually the equivalent of the mammalian beta-subunit. A wheat sprout cDNA expression library was screened with antibody affinity purified to the p38 subunit. The DNA sequence of the clones obtained also indicated that the p38 subunit was the equivalent to the mammalian beta-subunit. The wheat p38 subunit was then expressed in Escherichia coli and antibodies raised to the purified recombinant protein. Only the p38 subunit of purified wheat germ eIF2 reacted with the antisera. The p38 subunit of wheat eIF2 is therefore the equivalent of mammalian eIF2beta.

Amino Acid Sequence↗
PubMed1994

Identification of the proteoglycan versican in aorta and smooth muscle cells by DNA sequence analysis, in situ hybridization and immunohistochemistry.

Versican is a large chondroitin sulfate proteoglycan (CSPG) initially identified in cultured human fibroblasts. Previous studies have shown that there is a versican-like molecule in cultured monkey smooth muscle cells. In this study, we have cloned and sequenced the large CSPG from cultured monkey smooth muscle cells, fetal and juvenile monkey aorta, and human fetal aorta. The cDNA sequence from human fetal aorta is completely homologous to the human fibroblast versican. We obtained 2.5 kb of cDNA sequence from monkey aortic RNA and cultured monkey smooth muscle cell RNA. This sequence covers three distinct domains of versican (hyaluronic acid binding domain, glycosaminoglycan attachment domain and protein binding domain) and demonstrates over 90% homology to the human versican sequence. In situ hybridization histochemistry indicates that the versican RNA transcript is located in the epithelium throughout the tunica media of the aorta. Western blot analysis and immunohistochemistry also confirm the presence of versican in human and monkey aorta.

Amino Acid Sequence↗
PubMed2001

Spiroplasma sp. 16S rDNA in Creutzfeldt-Jakob disease and scrapie as shown by PCR and DNA sequence analysis.

The pathogenesis of the transmissible spongiform encephalopathies (TSE), which include Creutzfeldt-Jakob disease (CJD) in humans and scrapie in sheep, remains an enigma. In this paper we present evidence for the association of Spiroplasma sp., a wall-less prokaryote, with TSE. We have shown PCR amplification of Spiroplasma 16S rDNA in TSE-infected brain tissues (13 of 13 CJD cases and 5 of 9 scrapie cases) and not in control brains (0 of 50). Direct sequencing of the amplified PCR products has confirmed the presence of Spiroplasma-like DNA in all 5 of the TSE brains tested. Our evidence is not necessarily in conflict with involvement of a PrPres--a protease-resistant host-derived protein referred to as the prion--in the pathogenesis of TSE, since there is evidence that another factor is involved. We propose a bacterium, namely Spiroplasma, as this associated factor although the role of Spiroplasma in TSE cannot be determined from these experiments. The presence of the nucleic acid sequence of this microbe in all cases of TSE in our laboratory and not in controls provides direct evidence of the association of Spiroplasma sp. with TSE.

Animals↗