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At least 469 records · Page 26Linked to original sources
PubMed1988

Sequence analysis of the NgoPII methyltransferase gene from Neisseria gonorrhoeae P9: homologies with other enzymes recognizing the sequence 5'-GGCC-3'.

Recombinant plasmids harbouring the functional M.NgoPII methyltransferase (specificity 5'-GGCC-3') were isolated from amplified gene libraries of gonococcal chromosomal DNA cloned in pBR322 and in Escherichia coli RR1. The M.NgoPII gene was localized by sub-cloning and the nucleotide sequence of a cloned 1.6 kb segment of Neisseria gonorrhoeae DNA harbouring the methylase gene was determined. This data, coupled with sub-cloning experiments and in vitro transcription-translation studies, indicates a theoretical size of 38.5 kd for the methylase protein. The predicted amino acid sequence of the methylase contains significant regions of homology with the projected sequences of other cytosine-modifying methylases, upon which the activity of these enzymes is likely to depend.

Amino Acid Sequence↗
PubMed2004

Host-inducible immunogenic sphingomyelinase-like protein, Lk73.5, of Leptospira interrogans.

Leptospira interrogans causes a variety of clinical syndromes in animals and humans. Although much information has accumulated on the importance of leptospiral lipopolysaccharide in protective antibody responses, relatively little is known about proteins that participate in immune responses. Identification of those proteins induced only in the host is particularly difficult. Using a novel double-antibody screen designed to identify clones in a gene library of L. interrogans serovar Pomona expressing host-inducible proteins, we have characterized a gene (lk75.3) encoding a sphingomyelinase-like preprotein of 648 amino acids with cytotoxic activity for equine pulmonary endothelial cells and weak hemolytic activity for equine and rabbit erythrocytes. lk73.5 was found as a single gene copy in all serovars of L. interrogans but not in other Leptospira spp. except L. inadai. The open reading frame (ORF) for Lk73.5 is followed by another partially homologous sequence containing an ORF (sph-like 2) for a 28.7-kDa peptide. Lk73.5 and Sph-like 2 share 95.1 and 97.7% amino acid identity with putative sphingomyelinases Sph2 and Sph1 (N terminus) from L. interrogans serovar Lai (S.-X. Ren, G. Fu, X.-G. Jiangk, R. Zeng, Y.-G. Miao, H. Xu, Y.-X. Zhang, H. Xiong, G. Lu, L.-F. Lu, H.-Q. Jiang, J. Jia, Y.-F. Tu, J.-X. Jiang, W.-Y. Gu, Y.-Q. Zhang, Z. Cai, H.-H. Sheng, H.-F. Yin, Y. Zhang, G.-F. Zhu, M. Wank, H.-L. Huangk, Z. Qian, S.-Y. Wang, Wei Ma, Z.-J. Yao, Y. Shen, B.-Q. Qiang, Q.-C. Xia, X.-K. Guo, A. Danchinq, I. S. Girons, R. L. Somerville, Y.-M. Wen, M.-H. Shik, Z. Chen, J.-G. Xuk, and G.-P. Zhao, Nature 422:88-893, 2003). Substantial homologies to sphingomyelinases from other leptospiras and other bacteria are also present. Lk73.5 was not detected in leptospiras cultured at 30 or 37 degrees C. The recombinant protein reacted strongly with sera from recently infected mares but not with sera from horses vaccinated with commercial pentavalent bacterin. The host-inducible immunogenic Lk73.5 should have value in distinguishing vaccine from infection immune response.

Amino Acid Sequence↗
PubMed1991

Genetic and molecular analyses of the SUP201 gene: a tRNA(3Arg) nonsense suppressor of yeast cyrl-2.

The temperature-sensitive cyr1-2 mutant in Saccharomyces cerevisiae produces low levels of adenylate cyclase and cyclic AMP at 25 degrees C and is unable to synthesize repressible acid phosphatase at 25 degrees C. Suppressor mutants of cyr1-2 were isolated by detecting acid phosphatase activity. One of the dominant suppressor mutations isolated was designated SUP201 and characterized. The SUP201 mutant gene was isolated from a gene library made from cyr1-2 SUP201 mutant DNA. Nucleotide sequence analysis of the cloned SUP201 gene revealed that the SUP201 gene was a mutated tRNA gene flanking GCN4, which worked as a UGA suppressor.

Base Sequence↗
PubMed2005

A microarray study of MPP+-treated PC12 Cells: Mechanisms of toxicity (MOT) analysis using bioinformatics tools.

BACKGROUND: This paper describes a microarray study including data quality control, data analysis and the analysis of the mechanism of toxicity (MOT) induced by 1-methyl-4-phenylpyridinium (MPP+) in a rat adrenal pheochromocytoma cell line (PC12 cells) using bioinformatics tools. MPP+ depletes dopamine content and elicits cell death in PC12 cells. However, the mechanism of MPP+-induced neurotoxicity is still unclear. RESULTS: In this study, Agilent rat oligo 22K microarrays were used to examine alterations in gene expression of PC12 cells after 500 muM MPP+ treatment. Relative gene expression of control and treated cells represented by spot intensities on the array chips was analyzed using bioinformatics tools. Raw data from each array were input into the NCTR ArrayTrack database, and normalized using a Lowess normalization method. Data quality was monitored in ArrayTrack. The means of the averaged log ratio of the paired samples were used to identify the fold changes of gene expression in PC12 cells after MPP+ treatment. Our data showed that 106 genes and ESTs (Expressed Sequence Tags) were changed 2-fold and above with MPP+ treatment; among these, 75 genes had gene symbols and 59 genes had known functions according to the Agilent gene Refguide and ArrayTrack-linked gene library. The mechanism of MPP+-induced toxicity in PC12 cells was analyzed based on their genes functions, biological process, pathways and previous published literatures. CONCLUSION: Multiple pathways were suggested to be involved in the mechanism of MPP+-induced toxicity, including oxidative stress, DNA and protein damage, cell cycling arrest, and apoptosis.

1-Methyl-4-phenylpyridinium↗
PubMed2002

[The cloning and functional analysis of Sinorhizobium fredii 042BS regulatory modulation genes].

The total DNA of Sinorhizobium fredii 042BS was digested by EcoRI for Southern blotting with probes of nodD1 and nodD2 from S. fredii USDA257. The 3 kb positive band hybrided with nodD1 probe and 6 kb positive band with nodD2 probe were found, respectively. Partial gene library were constructed using pUC18 as vector, and the clones with the nodD1 and nodD2 genes were obtained. The sequence of nodD1 and nodD2 of 042B showed that they are highly homologous with nodD1 and nodD2 of S. fredii. The fragment with nodD1 was cloned into the vector pBBRIMCS-5 and introduced into R. leguminosarum bv. viciae LPR5054 to study the function of the nodD1. The results showed that nodD1 of 042B can be induced by genistein and luteolin secreted by the seedlings of soybean and alfalfa respectively.

Amino Acid Sequence↗
PubMed1989

Molecular cloning and characterization of a chromosomal gene for human eosinophil peroxidase.

Using human myeloperoxidase cDNA as a probe, a chromosomal gene related to myeloperoxidase was isolated from a human gene library. Comparison of the amino acid sequence deduced from the nucleotide sequence of the cloned gene with that of human eosinophil peroxidase purified from buffy coats has indicated that the isolated gene is the chromosomal gene for human eosinophil peroxidase. Like human myeloperoxidase gene, human eosinophil peroxidase gene consists of 12 exons and 11 introns spanning about 12 kilobases. The gene can code for a protein of 715 amino acids with a calculated Mr of 81,036. The heavy chain and the light chain of eosinophil peroxidase were located on the COOH and NH2 terminus of the protein, respectively. The coding sequences of eosinophil peroxidase and myeloperoxidase show homologies of 72.4% at the nucleotide and 69.8% at the amino acid level, while little homology was found in the 5'-flanking region. Northern hybridization and S1 mapping analysis of RNA from human leukemic cells have indicated that the eosinophil peroxidase gene is expressed in the eosinophilic subline of human HL-60 cells but not in the neutrophilic subline or in parental HL-60 cells.

Amino Acid Sequence↗
PubMed2001

Screening of environmental DNA libraries for the presence of genes conferring Na(+)(Li(+))/H(+) antiporter activity on Escherichia coli: characterization of the recovered genes and the corresponding gene products.

Environmental DNA libraries prepared from three different soils were screened for genes conferring Na(+)(Li(+))/H(+) antiporter activity on the antiporter-deficient Escherichia coli strain KNabc. The presence of those genes was verified on selective LK agar containing 7.5 mM LiCl. Two positive E. coli clones were obtained during the initial screening of 1,480,000 recombinant E. coli strains. Both clones harbored a plasmid (pAM1 and pAM3) that conferred a stable Li(+)-resistant phenotype. The insert of pAM2 (1,886 bp) derived from pAM1 contained a gene (1,185 bp) which encodes a novel Na(+)/H(+) antiporter belonging to the NhaA family. The insert of pAM3 harbored the DNA region of E. coli K-12 containing nhaA, nhaR, and gef. This region is flanked by highly conserved insertion elements. The sequence identity with E. coli decreased significantly outside of the insertion sequence elements, indicating that the unknown organism from which the insert of pAM3 was cloned is different from E. coli. The products of the antiporter genes located on pAM2 and pAM3 revealed functional homology to NhaA of E. coli and enabled the antiporter-deficient E. coli mutant to grow on solid media in the presence of up to 450 mM NaCl or 250 mM LiCl at pH 8.0. The Na(+)/H(+) antiporter activity in everted membrane vesicles that were derived from the E. coli strains KNabc/pAM2 and KNabc/pAM3 showed a substantial increase between pHs 7 and 8.5. The maximal activity was observed at pHs 8.3 and 8.6, respectively. The K(m) values of both antiporters for Na(+) were approximately 10-fold higher than the values for Li(+).

Amino Acid Sequence↗
PubMed2001

Expression of homeobox-containing genes in cDNA libraries derived from cattle oocytes and preimplantation stage embryo.

The homeobox-containing gene family plays a pivotal role in regulating, patterning, and axial morphogenesis in the developing embryo. But there is still very little known about the expression and function of these genes in mammalian oocytes and preimplantation stage embryos. In this study we have used degenerate primers corresponding to the highly conserved regions of Antennapedia class homeodomains as a rapid and an efficient method to survey bovine cDNA libraries derived from unfertilised oocytes, single 2-cell, 4-cell, 8-cell, morula, and blastocyst stage embryos for the presence of homeobox sequences. Our results provide, for the first time, evidence for the transcription of Hoxa3 and Hoxd1 in oocytes; Cdx1 and Cdx2 in the 2-cell; Cdx1, Hoxa1, Hoxd1, and Hoxd4 in the 4-cell; Cdx1, Hoxa1, and Hoxc9 in the 8-cell; Cdx2, Hoxb9, and Hoxc9 in the morula; Cdx2, Hoxb7, Hoxb9, and Hoxc9 in blastocyst stage cattle embryos. These are candidate genes for the developmental capacity of in vivo and in vitro produced bovine embryos.

Amino Acid Sequence↗
PubMed1984

Polypeptide chain elongation factor 1 alpha (EF-1 alpha) from yeast: nucleotide sequence of one of the two genes for EF-1 alpha from Saccharomyces cerevisiae.

Messenger RNA for yeast cytosolic polypeptide chain elongation factor 1 alpha (EF-1 alpha) was partially purified from Saccharomyces cerevisiae. Double-stranded complementary DNA (cDNA) was synthesized and cloned in Escherichia coli with pBR327 as a vector. Recombinant plasmid carrying yEF-1 alpha cDNA was identified by cross-hybridization with the E. coli tufB gene and the yeast mitochondrial EF-Tu gene (tufM) under non-stringent conditions. A yeast gene library was then screened with the EF-1 alpha cDNA and several clones containing the chromosomal gene for EF-1 alpha were isolated. Restriction analysis of DNA fragments of these clones as well as the Southern hybridization of yeast genomic DNA with labelled EF-1 alpha cDNA indicated that there are two EF-1 alpha genes in S. cerevisiae. The nucleotide sequence of one of the two EF-1 alpha genes (designated as EF1 alpha A) was established together with its 5'- and 3'-flanking sequences. The sequence contained 1374 nucleotides coding for a protein of 458 amino acids with a calculated mol. wt. of 50 300. The derived amino acid sequence showed homologies of 31% and 32% with yeast mitochondrial EF-Tu and E. coli EF-Tu, respectively.

Amino Acid Sequence↗
PubMed1990

Genomic DNA 5' to the mouse and human angiotensin-converting enzyme genes contains two distinct regions of conserved sequence.

Genomic DNA 5' to the mouse and human genes encoding angiotensin-converting enzyme has been isolated and analyzed. A sequence comparison identifies two discrete regions of genomic DNA that are highly conserved. One region, found immediately 5' to the mouse and human ACE genes, is a GC rich segment that contains a "TATA box" and several potential Spl binding sites. The second conserved region is found further 5' and contains several potential regulatory cis elements including a possible glucocorticoid responsive element. These two regions of genomic DNA may influence the rate of mRNA transcription from the angiotensin-converting enzyme gene.

Animals↗
PubMed1983

Cloning and characterization of the ornithine carbamoyltransferase gene from Aspergillus nidulans.

An Aspergillus nidulans DNA fragment composed of two adjacent SalI subfragments (1.8 and 0.85 kb) that carries an argB gene complementing the yeast arg3 mutation has been isolated from two different gene libraries. Hybridization results and immunological tests indicate that the cloned fragment contains the A. nidulans structural gene coding for ornithine carbamoyltransferase (OTCase). Using the cloned gene as a probe, the specific mRNA was identified. The level of this RNA observed in A. nidulans strains grown under various conditions correlated with the level of the OTCase activity, suggesting transcriptional control of OTCase synthesis. Expression of the cloned gene in Saccharomyces cerevisiae does not depend on its orientation in the vector. In Escherichia coli, the cloned gene does not function; however arg- transformants revert to prototrophy with high frequency possibly due to DNA rearrangements within the recombinant plasmid.

Aspergillus nidulans↗
PubMed1981

Structure of a chromosomal gene for human interferon beta.

We have cloned and analyzed a chromosomal DNA segment containing the human interferon beta(1) gene from a human gene library. The nucleotide sequence of the protein-coding and the noncoding regions of the chromosomal gene was identical to the cDNA sequence reported previously. In the region upstream from the putative transcription initiation site, significant nucleotide sequence homology was observed between interferon beta(1) and alpha(1) genes. This region thus may play a role in expression of the interferon genes. From the sequence data and the result of nuclease S1 mapping experiments, we conclude that, like the interferon alpha(1) gene, the interferon beta(1) gene is devoid of intervening sequences.

Journal Article↗
PubMed1990

Human interleukin 2 receptor beta-chain gene: chromosomal localization and identification of 5' regulatory sequences.

Interleukin 2 (IL-2) binds to and stimulates activated T cells through high-affinity IL-2 receptors (IL-2Rs). Such receptors represent a complex consisting of at least two proteins, the 55-kDa IL-2R alpha chain and the 70-kDa IL-2R beta chain. The low-affinity, IL-2R alpha chain cannot by itself transduce a mitogenic signal, whereas IL-2 stimulates resting lymphocytes through the intermediate-affinity, IL-2R beta receptor. We report here identification of the genomic locus for IL-2R beta. The exons are contained on four EcoRI fragments of 1.1, 9.2, 7.2, and 13.7 kilobases. The 1.1-kilobase EcoRI fragment lies at the 5'-most end of the genomic locus and contains promoter sequences. The promoter contains no TATA box-like elements but does contain the d(GT)n class of middle repetitive elements, which may play an interesting regulatory role. The IL-2R beta gene is localized to chromosome 22q11.2-q12, a region that is the locus for several lymphoid neoplasias.

Base Sequence↗
PubMed1994

Direct isolation of genes encoded within a homogeneously staining region by chromosome microdissection.

Identification of genes involved in recurring chromosome rearrangements has provided significant insight into the molecular basis of malignancy. We describe here a strategy combining chromosome microdissection and hybrid selection for the direct isolation of chromosome region-specific genes. We modeled this strategy by using sequences recovered from the microdissection of a homogeneously staining region to allow isolation of genes that were overexpressed and present at high copy number within the homogeneously staining region, including the direct isolation of two genes encoded within a 12q homogeneously staining region found in the osteosarcoma cell line OsA-CL. Although first applied to amplified genes, this strategy should be applicable to the isolation of cDNAs from any chromosomal region.

Base Sequence↗
PubMed1997

The human p167 gene encodes a unique structural protein that contains centrosomin A homology and associates with a multicomponent complex.

The characterization of novel cytoplasmic, structural, and enzymatic proteins has been enhanced by a panel of monoclonal antibodies specific for protein substrates of transforming and nontransforming c-Src mutants. These protein substrates have included the focal adhesion kinase (FAK), cortactin, AFAP-110, p120CAS, and p130CAS. The monoclonal antibody 4G8 was generated as part of this panel of antibodies and was used to isolate the human gene for a 167-kD polypeptide. The cDNA sequence is 5,238 nucleotides in length with a predicted open reading frame consisting of 1,382 amino acids. The polypeptide is largely hydrophilic and highly charged. The central region of p167 has 88% identity with the entire 278-amino-acid encoded sequence of the murine centrosomin A gene. The carboxyl third of p167 contains a unique cluster of 10 amino acid repeats with the consensus sequence (A/M)DDDRGPRRG. The p167 protein was found primarily in the cytoplasm of lymphocytes and is part of a multicomponent protein complex with prominent members of 167, 120, 64, 45, 40, 38, and 25 kD. Finally, we illustrate the conservation of p167 and its associated complex, and demonstrate its expression in different human tissues and cell types. The data suggest that p167 is novel and has an important cellular function as a cytoplasmic structural protein.

Amino Acid Sequence↗
PubMed1994

Interaction of the yeast RAD7 and SIR3 proteins: implications for DNA repair and chromatin structure.

We have used the two-hybrid system to identify proteins that interact with the product of RAD7, a gene involved in DNA repair. A screen of a yeast genomic DNA-GAL4 activation domain (GAD) fusion gene library allowed the isolation of plasmids containing sequences corresponding to the 3' end of the SIR3 gene. This gene is known to be involved in the production of transcriptionally silent DNA at the cryptic mating-type cassettes and at telomeres. The cloned sequences coded for amino acids 307-979 of the Sir3 protein. A sir3 deletion allele, constructed in an isogenic rad7-deletion strain, rescued approximately one-quarter of the UV sensitivity associated with the rad7 deletion, indicating that the two genes interact genetically. Radiolabeled fusion proteins, made with the glutathione S-transferase (GST) gene in the vector pGEX-2T, were purified from Escherichia coli and shown to interact in vitro. This evidence suggests that the Sir3 protein interacts with the Rad7 protein to allow the nucleotide excision repair complex access to transcriptionally inactive chromatin. The proportions of 5-FOA-resistant cells in cultures from isogenic RAD+ and rad7-delta strains containing a telomeric URA3 gene were similar, suggesting that the RAD7 gene is not involved in the production or structure of transcriptionally silent chromatin at the telomeres. RAD7-dependent DNA repair of transcriptionally silent chromatin was shown not to induce expression of a telomeric copy of the URA3 gene, suggesting that repair of transcriptionally silent chromatin differs from transcriptionally active chromatin. Expression of a telomeric copy of the URA3 gene was stimulated in a rad7-delta mutant, suggesting that repair of lesions in the absence of Rad7 can result in the activation of transcriptionally silenced genes.

Base Sequence↗
PubMed1992

A putative anaerobic coproporphyrinogen III oxidase in Rhodobacter sphaeroides. I. Molecular cloning, transposon mutagenesis and sequence analysis of the gene.

A mutant of Rhodobacter sphaeroides, N1, has been isolated which is incapable of photosynthetic growth and, instead of synthesizing bacteriochlorophyll, N1 excretes coproporphyrin III into the growth medium. Using conjugative gene transfer, several clones were isolated from a R. sphaeroides gene library which restored normal pigment synthesis and photosynthetic growth to N1. Using transposon Tn5 mutagenesis, the gene was located to a 1.05 kb EcoRI fragment. Sequence and transcription analysis defined the position and expression of an open reading frame of approximately 920 bp, which is proposed as the anaerobic coproporphyrinogen III oxidase dedicated to bacteriochlorophyll biosynthesis.

Amino Acid Sequence↗
PubMed1987

The genes of the Paracoccus denitrificans bc1 complex. Nucleotide sequence and homologies between bacterial and mitochondrial subunits.

The genes for the three subunits of the cytochrome bc1 complex from the bacterium Paracoccus denitrificans were identified by screening a gene library constructed in pBR 322 for expression using a cytochrome c1-specific antibody. These three genes coding for the FeS subunit, cytochrome b, and cytochrome c1 were located on contiguous sites on the genome in a presumed operon arrangement. The DNA-deduced amino acid sequence shows that all three subunits are homologous to corresponding polypeptides of the mitochondrial cytochrome bc1 complex. Cytochrome c1 of Paracoccus is much larger than its mitochondrial counterpart due to an extra 150 amino acids of unique, highly acidic composition; in addition, it is most likely synthesized as a precursor polypeptide.

Amino Acid Sequence↗