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At least 163 records · Page 9Linked to original sources
PubMed1990

Comparative DNA sequence analysis of the host shutoff genes of different strains of herpes simplex virus: type 2 strain HG52 encodes a truncated UL41 product.

Herpes simplex virus (HSV) particles contain a factor which can shut off host protein synthesis during the earliest stages of infection. The efficiency of shutoff varies between different strains of virus, type 2 strains being generally more active than type 1 strains. However, HSV-2 strain HG52 is deficient in host cell shutoff. We have investigated the basis of the different shutoff phenotypes of a strong shutoff strain (HSV-2 strain G), a weak shutoff virus (HSV-1 strain 17 syn+) and HG52 by comparative DNA sequence analysis of gene UL41, which encodes the virion-associated host shutoff factor. The results show that the UL41 genes of strains G and 17 are 86% homologous and that the lack of shutoff by HG52 is likely to be explained by a frameshift mutation within its UL41 coding sequence.

Amino Acid Sequence↗
PubMed1993

Cloning, DNA sequence analysis and partial characterization of pepN, a lysyl aminopeptidase from Lactobacillus delbrückii ssp. lactis DSM7290.

In cell extracts of Lactobacillus delbrückii ssp. lactis DSM7290 a peptidase with the ability to hydrolyse Phe-beta-naphthylamide (Phe-beta-NA) and His-beta-NA could be detected. Escherichia coli lacking the enzyme activity in an enzymic plate assay was used to screen high-copy-number and low-copy-number plasmid libraries of size-fractionated Lactobacillus DNA. Clones with the desired phenotype were detected, and the gene, designated pepN, was further subcloned and sequenced. A large open reading frame of 2529 nucleotides is predicted to encode a protein of 843 amino acids (95358 Da). Comparison of the pepN gene from Lb. delbrückii ssp. lactis DSM7290 indicates that it is homologous to genes of the family of Zn(2+)-metallohydrolases and PepN shows identity with the active centre Zn(2+)-binding motif of these enzymes. The substrate Lys-beta-NA is more effectively cleaved than Phe-beta-NA or His-beta-NA which were used for screening in E. coli. The cloned pepN gene was efficiently overexpressed in E. coli and subcloning of the gene in Lactobacillus casei resulted in a moderate overexpression of approximately 20-fold. The pepN gene product was purified from the pepN-deficient E. coli strain CM89, using the substrate Lys-p-nitroanilide (Lys-NH-Ph) in the assay procedure. In a four-step procedure including streptomycin sulfate precipitation, anion-exchange chromatography and gel filtration the peptidase was purified to electrophoretic homogeneity.

Amino Acid Sequence↗
PubMed1990

DNA sequence analysis of five genes; tnsA, B, C, D and E, required for Tn7 transposition.

A region of DNA sequence of the bacterial transposon Tn7, which is required for transposition, has been determined. This DNA sequence completes an 8351 base pair (bp) region containing five long open reading frames (ORF's) that correspond to the genetically defined genes, tnsA, B, C, D and E, required for Tn7 transposition. All of the ORF's are oriented in the same direction, ie. inward from the element's right end. The genes are in a very compact arrangement with the presumed initiation codons never more than two bases beyond the preceding termination codon. Domains with similarity to the helix-turn-helix genre of Cro-like, sequence specific DNA binding sites occur within the deduced amino acid (a.a.) sequence of the TnsA, TnsB, TnsD and TnsE proteins. Translation of the tnsC ORF reveals strong homology to a consensus sequence for nucleotide binding sites as well as a region of similarity to a transcriptional activator (MalT). No striking a.a. sequence similarity to other DNA recombinases is observed. The possible roles of these proteins in Tn7 transposition is discussed in light of the analysis presented.

Amino Acid Sequence↗
PubMed1991

DNA sequence analysis and restriction fragment length polymorphism (RFLP) typing of the HLA-DQw2 alleles associated with dermatitis herpetiformis.

Dermatitis herpetiformis (DH) is a blistering autoimmune skin disease associated with a 95-100% incidence of the HLA class II antigen HLA-DQw2. Although the precise role of this antigen in the pathogenesis of DH is unclear, one theory proposes that patients with DH possess a molecularly unique subtype of the HLA-DQw2 antigen that causes immune abnormalities eventuating in the clinical manifestations of DH. To test this hypothesis, we performed DNA sequence analysis on the highly polymorphic HLA-DQB1 and HLA-DQA1 loci of eight patients with dermatitis herpetiformis. All DQB1 alleles sequenced were identical to the previously described HLA-DQB*0201 allele from HLA-DQw2 normal subjects. In addition, DQA1 alleles sequenced were identical to those alleles previously associated with HLA-DQw2 (DQA*0201, DQA*0501). These data document that although HLA-DQw2 appears to be a necessary element in the pathogenesis of DH, the development of DH is not dependent on the presence of a unique HLA-DQw2 antigen. HLA-DQ allelic typing by restriction fragment length polymorphism analysis of PCR-amplified HLA-DQA1 and HLA-DQB1 fragments was also performed in ten patients with DH to determine the allelic distribution among both HLA-DR3 (eight patients) and non-DR3 (two patients) DH patients. At the HLA-DQ beta chain locus, all patients possessed the DQB1*0201 allele. At the HLA-DQ alpha chain locus, all HLA-DR3 patients and one non-DR3 patient displayed a pattern consistent with the DQA1*0501 allele, whereas one non-DR3 patient displayed a pattern consistent with the DQA1*0201 allele. These data document that patients with DH do not express a unique HLA-DQw2 heterodimer, that the HLA-DQw2 molecules present in patients with DH have no DNA sequence differences from those found in normal HLA-DQw2 subjects and therefore that susceptibility to DH is not due to a unique HLA-DQw2 molecule.

Alleles↗
PubMed1990

[DNA sequence analysis of HLA-DQB genes associated with insulin-dependent diabetes mellitus in Japanese].

Recently it has been reported that 57th amino acid of DQ beta antigen was a non-aspartic acid in the most Caucasian patients with insulin-dependent diabetes mellitus (IDDM). Using serological analysis, HLA-DQ antigens show a strong association with IDDM rather than the HLA-DR antigens. In the Caucasian population, IDDM is associated with DQw2 and DQw3 antigens. However, in the Japanese population, DQw4 and DQw9 antigens are strongly associated with IDDM. In order to determine the possible significance of the 57th amino acid of DQ beta chain for the susceptibility to IDDM in Japanese, we performed DNA Sequence analysis of HLA-DQB from Japanese IDDM patient, its same HLA genotyped healthy sibling and B cell line with Japanese IDDM associated haplotype. The results revealed that all of the 57th amino acid are aspartic acid which is thought to contribute to develop IDDM resistance in Caucasian. Furthermore we could not find any other amino acid sequence of DQ beta chain which might contribute to the susceptibility of the Japanese IDDM.

Amino Acid Sequence↗
PubMed1991

The 1-aminocyclopropane-1-carboxylate synthase of Cucurbita. Purification, properties, expression in Escherichia coli, and primary structure determination by DNA sequence analysis.

The key regulatory enzyme in the biosynthetic pathway of the plant hormone ethylene is 1-aminocyclopropane-1-carboxylic acid (ACC) synthase (EC 4.4.1.14). We have partially purified ACC synthase 6,000-fold from Cucurbita fruit tissue treated with indoleacetic acid + benzyladenine + aminooxyacetic acid + LiCl. The enzyme has a specific activity of 35,000 nmol/h/mg protein, a pH optimum of 9.5, an isoelectric point of 5.0, a Km of 17 microM with respect to S-adenosylmethionine, and is a dimer of two identical subunits of approximately 46,000 Da each. The subunit exists in vivo as a 55,000-Da species similar in size to the primary in vitro translation product. DNA sequence analysis of the cDNA clone pACC1 revealed that the coding region of the ACC synthase mRNA spans 493 amino acids corresponding to a 55,779-Da polypeptide; and expression of the coding sequence (pACC1) in Escherichia coli as a COOH terminus hybrid of beta-galactosidase or as a nonhybrid polypeptide catalyzed the conversion of S-adenosylmethionine to ACC (Sato, T., and Theologis, A. (1989) Proc. Natl. Acad. Sci. U.S.A. 86, 6621-6625). Immunoblotting experiments herein show that the molecular mass of the beta-galactosidase hybrid polypeptide is 170,000 Da, and the size of the largest nonhybrid polypeptide is 53,000 Da. The data suggest that the enzyme is post-translationally processed during protein purification.

Amino Acid Sequence↗
PubMed1996

Construction of cDNA library from liver RNA of heat shocked rats and DNA sequence analysis of the clone containing the 3'-end untranslated region (3'UTR) of the heat inducible gene hsp70.2.

cDNA library constructed from liver RNA of rats subjected to hyperthermia was used to isolate divergent 3' end untranslated regions (3'UTR) of heat inducible hsp70.1 and hsp70.2 genes. As a result of a double selection procedure with the use of DNA-DNA hybridization and PCR analysis 9 clones containing cDNA sequences derived from the 3'UTR of the hsp70.2 gene were selected. Nucleotide sequence of the cloned inserts was established and the Northern blot analysis was performed to identify the heat inducible transcript encoded by the hsp70.2 gene.

Animals↗
PubMed1990

Genetic and DNA sequence analysis of the Salmonella typhimurium virulence plasmid gene encoding the 28,000-molecular-weight protein.

We have confirmed that the 28,000-molecular-weight (28K) protein encoded by the virA gene of the 90-kilobase Salmonella typhimurium virulence plasmid is a virulence factor. It was previously shown that a Tn5 insertion, vir-22::Tn5, located in the virulence plasmid greatly attenuated virulence for mice and inhibited the production of a 28K protein (P.A. Gulig and R. Curtiss III, Infect. Immun. 56:3262-3271, 1988). Plasmid pYA426 fully complemented vir-22::Tn5 to virulence by increasing splenic infection after oral inoculation and encoded the 28K protein. To identify the virulence gene(s) of pYA426 mutated by vir-22::Tn5, we constructed nested deletions in pYA426 and examined deletion derivatives for their abilities to complement vir-22::Tn5. Only derivatives still producing the 28K protein complemented vir-22::Tn5. Furthermore, the smallest complementing derivative encoded only the 28K protein, as determined by DNA sequence analysis. Therefore, the 28K protein is sufficient for complementation of the attenuating mutation vir-22::Tn5 and must be the virulence factor inhibited by the insertion. We determined the nucleotide sequence of the 1.2-kilobase BamHI-EcoRI fragment encoding the 28K protein and identified the structural gene, virA. A 723-base-pair open reading frame which encodes a peptide with a molecular weight of 27,572 was found.

Amino Acid Sequence↗
PubMed1993

Mapping and DNA sequence analysis of the cytomegalovirus transforming domain III (mtrIII).

The transforming activity of XbaI fragment E (map units 0.685-0.770) of human cytomegalovirus Towne strain was originally localized in two terminal segments, 3 kb XbaI-BamHI EM (mtrII) and 7.5 kb BamHI-XbaI EJ (mtrIII). Three immediate-early genes, IE1 to IE3, are located in the same region (map unit 0.685-0.770), and IE1 is located in the EJ fragment. IE1 protein increases chromatin transcriptional activity and causes alteration in chromatin conformation. In this study, we have investigated the potential transforming activity of IE1, IE1 plus its promoter-regulatory region (IE P/R), and the remaining fragment of EJ after deletion of IE1 plus IE P/R. Our results clearly demonstrate that IE1 or IE1 plus IE P/R is not involved in transformation, and that the transforming activity of mtrIII is located in a 2.1 kb SalI-XbaI subfragment of EJ. DNA sequence analysis reveals four putative open reading frames (ORFs) L1, L2, L3 and R1 in the 2.1 kb fragment. The data from the deletion clones of the 2.1 kb fragment and also by disruption of individual ORFs by restriction enzyme digestion, suggest that a complete ORF L3 or R1 may be essential but not sufficient for the transforming activity. Because significant reduction in transforming activity is obtained by interrupting ORFs LI and L2, these ORFs may be required for the full transforming activity.

3T3 Cells↗
PubMed1994

Cloning and DNA sequence analysis of bmpC, a gene encoding a potential membrane lipoprotein of Borrelia burgdorferi.

Immunoscreening of a lambda gt11 genomic library of Borrelia burgdorferi expressed in Escherichia coli permitted detection of a clone containing a partial sequence of a B. burgdorferi gene encoding a protein with significant homology to TmpC of Treponema pallidum. Subsequent cloning and DNA sequence analysis revealed an open reading frame encoding a protein with 353 amino acid residues. The open reading frame is preceded by putative promoter sequences and a ribosome binding site, and is initiated with a TTG. The putative protein shares 26% identity with TmpC, contains a signal peptidase II sequence, and is also homologous to the gene products of the recently described bmpA and bmpB of B. burgdorferi. This gene has been designated bmpC. Additional sequencing and restriction analysis indicate that it is located at approximately 400 kbp on the chromosomal map of B. burgdorferi, immediately upstream of bmpA and bmpB.

Amino Acid Sequence↗
PubMed1986

Rat liver glutathione S-transferases. DNA sequence analysis of a Yb2 cDNA clone and regulation of the Yb1 and Yb2 mRNAs by phenobarbital.

We have constructed a cDNA clone, pGTA/C48, which is complementary to the rat liver glutathione S-transferase Yb2 mRNA. Recombinant clone pGTA/C48 contains a cDNA insert of 845 base pairs which overlaps nucleotides 108-952 of the Yb1 cDNA clone, pGTA/C44, described previously by our laboratory (Ding, G. J.-F., Lu, A. Y. H., and Pickett, C. B. (1985) J. Biol. Chem. 260, 13268-13271). Over the protein coding region of the Yb1 and Yb2 cDNA clones there is an 84% nucleotide sequence homology, whereas the 3' untranslated regions are only 32% homologous. The complete amino acid sequence of the Yb2 subunit has been determined from a combination of DNA sequence analysis of pGTA/C48 and conventional protein sequence analysis of the glutathione S-transferase Yb1 Yb2 heterodimer. The Yb2 subunit is comprised of 218 amino acids with a molecular weight of 25,705 and has an amino acid sequence which is 79% homologous to the sequence of the Yb1 subunit. We have utilized the divergent 3' untranslated regions of three rat liver glutathione S-transferase cDNA clones as specific probes to determine the effect of phenobarbital on the level of Yb1, Yb2, and Yc mRNAs. Our results clearly show that the Yb1 and Yb2 mRNAs are elevated approximately 5-6-fold by phenobarbital administration; whereas the Yc mRNA is only modestly elevated by this xenobiotic. Finally, our data suggest that the Yb2 subunit is encoded by a gene(s) which is distinct from the Yb1 gene(s) and provides direct evidence for the existence of multiple glutathione S-transferase Yb genes in the rat.

Amino Acid Sequence↗
PubMed2001

[DNA sequence analysis and expression of the recombinant plasmid pBX1 from Borrelia burgdorferi B31 strain].

OBJECTIVE: This study was to provide the target antigen for the development of a Lyme disease vaccine and serodiagnosis reagent. METHODS: We used the automatic DNA sequencing machine (Model 377) to detect the nucleotide sequence of the inserted part of the recombinant plasmid pBX1 from Borrelia burgdorferi B31 strain. The restriction enzyme map of the inserted part of pBX1 was analysed by using computer software. The expressed product of pBX1 in E. coli XLI-Blue MRF was analysed by using SDS-PAGE and western-blotting. RESULTS: 1. DNA sequencing showed that pBX1 contained a 477bp inserted gene fragment, and when it was compared with the published sequence of the specific region of the gene of the 83 kd antigen protein from Borrelia burgdorferi B31 strain, only one amino acid codon was different. 2. The restriction enzyme map of the inserted part of pBX1 was successfully constructed. 3. The recombinant plasmid pBX1 expressed a 29 kd fusion protein in E. coli XL1-Blue MRF' after induced with IPTG. The recombinant fusion protein could be recongnized by rabbit polyclonal antiserum against Borrelia burgdorferi B31 strain. CONCLUSION: A recombinant plasmid which contains the gene fragment encoding the specific region of the 83 kd antigen protein from Borrelia burgdorferi B31 strain has been successfully constructed. The recombinant plasmid can stably express 29 kd fusion protein in E. coli XL1-Blue MRF'. These results could serve as a base of further studies on the usefulness of the fusion protein in serodiagnosis and vaccine for Lyme disease.

Animals↗
PubMed1996

DNA sequence analysis of hprt mutations in lymphocytes from Sprague-Dawley rats treated with 7,12-dimethylbenz[a]anthracene.

Treatment of female Sprague-Dawley rats with the potent mammary gland carcinogen 7,12-dimethylbenz[a]anthracene (DMBA) results in the formation of DNA adducts with dG and dA and in the induction of 6-thioguanine-resistant (TGr) lymphocyte mutants. In this study, we have examined the types of mutations induced in TGr lymphocytes from DMBA-treated rats. DNA from 263 TGr lymphocyte clones was screened for mutations in exons 2, 3, and 8 of the hprt gene by polymerase chain reaction (PCR) amplification of the exons followed by heteroduplex analysis using denaturing gradient-gel electrophoresis. Twenty-five of the clones produced heteroduplexes in exon 2, 35 produced heteroduplexes in exon 3, and 36 produced heteroduplexes in exon 8. Direct sequence analysis of the heteroduplexes revealed 96 mutations, and at least 74 of these mutations were produced independently. Eighty-five of the total mutations were simple base pair (bp) substitutions, with A --> T and G --> T transversions being the predominant types. Seven mutations were deletions, three were complex bp substitutions, and one was an insertion. The results suggest that the types of mutations produced by DMBA in rat lymphocytes are specific to the DNA adducts produced by this compound.

9,10-Dimethyl-1,2-benzanthracene↗
PubMed2000

DNA sequence analysis of the photosynthesis region of Rhodobacter sphaeroides 2.4.1.

This paper describes the DNA sequence of the photosynthesis region of Rhodobacter sphaeroides 2.4.1 (T). The photosynthesis gene cluster is located within a approximately 73 kb Ase I genomic DNA fragment containing the puf, puhA, cycA and puc operons. A total of 65 open reading frames (ORFs) have been identified, of which 61 showed significant similarity to genes/proteins of other organisms while only four did not reveal any significant sequence similarity to any gene/protein sequences in the database. The data were compared with the corresponding genes/ORFs from a different strain of R.sphaeroides and Rhodobacter capsulatus, a close relative of R. sphaeroides. A detailed analysis of the gene organization in the photosynthesis region revealed a similar gene order in both species with some notable differences located to the pucBAC = cycA region. In addition, photosynthesis gene regulatory protein (PpsR, FNR, IHF) binding motifs in upstream sequences of a number of photosynthesis genes have been identified and shown to differ between these two species. The difference in gene organization relative to pucBAC and cycA suggests that this region originated independently of the photosynthesis gene cluster of R.sphaeroides.

Base Sequence↗
PubMed1993

DNA sequence analysis of serologically detected ELA class II haplotypes at the equine DQ beta locus.

The genetic diversity at the ELA DQ beta locus was investigated using polymerase chain reaction and DNA sequencing. Based upon serological methods 16 class II homozygous animals were selected and their genomic DNA was used. A DQ beta gene from an equine cDNA library was also sequenced. Our methodology and the similarity between the genomic and the cDNA sequences suggest that the studied locus is expressed on equine lymphocytes. In the predicted amino acid sequence the most extensive variation is located at residues 56-60. The pattern of these five amino acids is strongly correlated to the serological ELA class II specificities (W13, W22, W23, Be200). The alleles corresponding to the W23 specificity are the most divergent among the equine DQ beta alleles and also from other mammalian DQ beta sequences.

Alleles↗
PubMed1997

Gene identification and DNA sequence analysis in the GC-poor 20 megabase region of human chromosome 21.

In contrast to the distal half of the long arm of chromosome 21, the proximal half of approximately 20 megabases of DNA, including 21q11-21 bands, is low in GC content, CpG islands, and identified genes. Despite intensive searches, very few genes and cDNAs have been found in this region. Since the 21q11-21 region is associated with certain Down syndrome pathologies like mental retardation, the identification of relevant genes in this region is important. We used a different approach by constructing microdissection libraries specifically for this region and isolating unique sequence microclones for detailed molecular analysis. We found that this region is enriched with middle and low-copy repetitive sequences, and is also heavily methylated. By sequencing and homology analysis, we identified a significant number of genes/cDNAs, most of which appear to belong to gene families. In addition, we used unique sequence microclones in direct screening of cDNA libraries and isolated 12 cDNAs for this region. Thus, although the 21q11-21 region is gene poor, it is not completely devoid of genes/cDNAs. The presence of high proportions of middle and low-copy repetitive sequences in this region may have evolutionary significance in the genome organization and function of this region. Since 21q11-21 is heavily methylated, the expression of genes in this region may be regulated by a delicate balance of methylation and demethylation, and the presence of an additional copy of chromosome 21 may seriously disturb this balance and cause specific Down syndrome anomalies including mental retardation.

Chromosomes, Human, Pair 21↗
PubMed1999

[Analysis of kidney tumors in trichloroethylene exposed workers by comparative genomic hybridization and DNA sequence analysis].

Environmental and occupational mutagens such as chemical agents are suspected to be involved in cancer development. However, a direct link between carcinogen exposure and genetic alterations has been established only in a few examples. Carcinogen involvement in renal cell carcinoma (RCC) was recently supported by reports of an increased frequency of RCC among workers exposed to Trichloroethylene (TRI) in Germany. The aim of this study was to evaluate the phenotype and the genotype of renal tumors in occupationally TRI-exposed patients. Sporadic RCCs from TRI nonexposed patients served as control. Normal and renal tumor tissues from 12 patients with occupational histories of solvents and TRI exposure were histologically analyzed. Comparative Genomic Hybridization (CGH) was used to screen for genomic alterations along all chromosomal arms. Tumor DNA was analyzed for mutations of the von Hippel-Lindau gene (VHL) on 3p25.5 by PCR and sequencing analyses. The histological analysis revealed 9 clear cell (75%), 2 papillary RCC (18%) and 1 oncocytoma (8%). In clear cell RCC, DNA losses were frequently observed on 3p (66%), 6q (56%), 9p and 4q (44% each) and 2q (33%). DNA gains were detected on 9q, 17 (33% each) and 5q (22%). DNA gains were identified on chromosome 7 and 17 in papillary RCC. Four VHL gene mutations were found in three clear cell RCC (33%) with 3p loss. Comparisons of these results with data obtained from sporadic RCC revealed no unique phenotype, genotype or mutation pattern in the VHL gene of renal tumors after TRI exposure. Therefore, further studies on the relevance of dose and exposure time for the nephrocarcinogenic effect of TRI are indicated.

Base Sequence↗
PubMed2002

Expressed sequence tags for the chicken genome from a normalized 10-day-old white leghorn whole-embryo cDNA library. 3. DNA sequence analysis of genetic variation in commercial chicken populations.

Single nucleotide polymorphisms (SNPs) have emerged as a major class of DNA markers with the advantage of permitting the development of high-density genetic maps adequate for quantitative trait loci (QTL) identification by linkage-disequilibrium analysis. Here we describe results of a relatively high-depth survey of chicken broiler and layer populations for SNPs in targeted genomic regions of chicken expressed sequence tag (EST) sites. The sequences scanned, representing the composite sequence of 12 amplified fragments for a total of 6489 bp, were randomly distributed, occurring on six different chromosomes or linkage groups in the chicken genome. Although one of the genomic DNA sequences did not match the reference cDNA sequence, another contained an intron that separated two putative exons. The number of SNPs observed within each of the 12 EST-targeted genomic regions ranged from 0 to 10 for a total of 44 and a frequency of 0.7%. About 70% of the polymorphisms were shared between layer and broiler populations. The average heterozygosity within the populations ranged from 0.15 to 0.48, with the layer populations showing the higher heterozygosity. SNPs and oligonucleotides described will provide a resource for genetic analysis in commercial chicken populations. The data appear to indicate that the relative frequency of SNPs in the targeted regions scanned is higher than the frequency reported for any of the other regions scanned to date in other eukaryotic genomes. Additionally, the results suggest that the use of DNA pools may offer an efficient approach to SNP detection in chickens, as has been shown in other vertebrates.

Animals↗