Biomedical subjects

T Eki

Publications and source records attributed to T Eki.

At least 37 records · Page 2Linked to original sources

PubMed1996

Sequencing of a 23 kb fragment from Saccharomyces cerevisiae chromosome VI.

Plasmid clone gapB and lambda phage clone 4682, which contain fragments of Saccharomyces cerevisiae chromosome VI, were analysed. A 23 kb sequence was determined and ten open reading frames (ORFs) were revealed. Among them, five ORFs were identical to five yeast genes (SEC4, MSH4, SPB4, DEG1 and NIC96), two were identical to transposable elements (TYA and TYB), one (gapBorfF003) was highly homologous to a yeast expressed sequence tag, and another (4682orfF002) was predicted to be a nuclear protein. Sequence data have been submitted to DDBJ/EMBL/GenBank data library under Accession Number D44604 (clone gapB) and D44600 (clone 4682), respectively.

Amino Acid Sequence↗

PubMed1996

Analysis of a 36.2 kb DNA sequence including the right telomere of chromosome VI from Saccharomyces cerevisiae.

The nucleotide sequence of a 36.2-kb distal region containing the right telomere of chromosome VI was determined. Both strands of DNA cloned into cosmid clone 9965 and plasmid clone pEL174P2 were sequenced with an average redundancy of 7.9 per base pair, by both dye primer and dye terminator cycle sequencing methods. The G+C content of the sequence was found to be 37.9%. Eighteen open reading frames (ORFs) longer than 100 amino acids were detected. Four of these ORFs (9965orfR017, 9965orfF016, 9965orfR009 and 9965orfF003) were found to encode previously identified genes (YMR31, PRE4, NIN1 and HXK1, respectively). Six ORFs (9965orfR013, 9965orfF018, 9965orfF006, 9965orfR014, 9965orfF013 and 9965orfR020) were found to be homologous to hypothetical 121.4-kDa protein in the BCK 5' region, Bacillus subtilis DnaJ protein, hypothetical Trp-Asp repeats containing protein in DBP3-MRPL27, putative mitochondrial carrier YBR291C protein, Salmonella typhimurium nicotinate-nucleotide pyrophosphorylase, and Escherichia coli cystathionine beta-lyase, respectively. The putative proteins encoded by 9965orfF018, 9965orfR014 and 9965orfR020 were found to be, respectively, a new member of the family of DnaJ-like proteins, the mitochondrial carrier protein and cystathionine lyase.

Amino Acid Sequence↗

PubMed1996

Fifteen open reading frames in a 30.8 kb region of the right arm of chromosome VI from Saccharomyces cerevisiae.

The nucleotide sequence of cosmid clone 9765, which contains 30.8 kb of the right arm of chromosome VI, was determined. Both strands were sequenced, with an average redundancy of 8.17 per base pair by both dye primer and dye terminator cycle sequencing methods. The G+C content of the sequence was found to be 40.3%. Fifteen open reading frames (ORFs) greater than 100 amino acids and one tRNA-Tyr gene (SUP6) were detected. Seven of the ORFs were found to encode previously identified genes (HIS2, CDC14, MET10, SMC2, QCR6, PH04 and CDC26). One ORF, 9765orfF010, was found to encode a new member of the Snf2/Rad54 helicase family. Three ORFs (9765orfR002, 9765orfR011 and 9765orfR013) were found to be homologous with Schizosaccharomyces pombe polyadenylate binding protein, Escherichia coli hypothetical 38.1-kDa protein in the BCR 5' region, and transcription regulatory protein Swi3, respectively.

Adenosine Triphosphatases↗

PubMed1996

A long-range physical map of human chromosome 21q22.1 band from the YAC continuum.

The human Chromosome (Chr) 21q22.1 region contains several genes for cytokines and neurotransmitters and the gene for superoxide dismutase (mutant forms of which can cause familial amyotrophic lateral sclerosis). A region of approximately 5.8 Mb encompassing D21S82 and the glycinamide ribonucleotide transformylase (GART) loci was covered by overlapping YAC clones, which were contiguously ordered by clone walking with sequence-tagged site (STSs). A total of 76 markers, including 29 YAC end-specific STSs, were unambiguously ordered in this 5.8-Mb region, and the average interval between markers was 76 kb. Restriction maps of the YAC clones with rare-cutting enzymes were simultaneously prepared, and the restriction sites were aligned to obtain a consensus restriction map of the proximal region of the 21q22.1 band. The restriction map made from 44 overlapping YACs contains 54 physically assigned STSs. By integrating the consensus map of the adjacent 1.8-Mb region, we obtained a fine physical map spanning 6.5 Mb of human Chr 21q22.1. This map contains 24 precisely positioned end-specific STSs and 12 NotI-linking markers. More than 39 potential CpG islands were identified in this region and were found to be unevenly distributed. This physical map and the YACs should be useful as a reference map and as a resource for further structural analysis of the Giemsa-negative band (R-band) of Chr 21q22.1.

Base Sequence↗

PubMed1996

Neurally mediated cardiac effects of forskolin in conscious dogs.

Because major cardiovascular disease states are characterized by defects in adenylyl cyclase regulation, it becomes important to understand the mechanisms by which adenylyl cyclase activators affect inotropy and chronotropy in intact conscious animals. Accordingly, we examined the inotropic and chronotropic responses to forskolin in 11 normal conscious, chronically instrumented dogs and 3 dogs with ventricular denervation (VD). Left ventricular first derivative of pressure (LV dP/dt) increased by 96 +/- 7%, P < 0.05, in response to forskolin (50 nmol.kg-1.min-1) in normal dogs and by significantly less, 52 +/- 14%, in VD dogs. Circulating norepinephrine (NE) levels increased similarly in both groups (from 226 +/- 18 to 389 +/- 33 pg/ml in normal dogs, from 177 +/- 23 to 329 +/- 71 pg/ml in VD dogs). In the presence of ganglionic blockade, the increase in LV dP/dt in response to forskolin was reduced (+62 +/- 4%) in normal dogs but was unchanged in VD dogs (+52 +/- 12%). Ganglionic blockade abolished the increase in circulating NE levels in both groups. Increases in heart rate in the presence of ganglionic blockade (+54 +/- 6 beats/min) were less than in the presence of atropine alone (+92 +/- 10 beats/min). Notably, the LV dP/dt and heart rate responses to forskolin were further attenuated by beta-adrenergic receptor blockade in the presence and absence of ganglionic blockade. Morphine also attenuated the increases in both LV dP/dt and plasma NE in response to forskolin. Increases in LV dP/dt in response to NKH-477 (30 micrograms/kg), a water-soluble forskolin derivative, were similar before and after ganglionic blockade (+63 +/- 8 and +51 +/- 10%, respectively). However, in vitro experiments in LV sarcolemmal membrane preparations demonstrated that stimulation of adenylyl cyclase by forskolin and NKH-477 was not affected by beta-adrenergic receptor blockade. These results indicate that in conscious dogs, inotropic and chronotropic effects of forskolin are not only due to direct activation of adenylyl cyclase, but the effects also are mediated by neural mechanisms and potentiated by the prevailing level of sympathetic tone.

Adenylyl Cyclases↗

PubMed1996

1.8-megabases fine physical map encompassing IFNAR and AML1 loci on human chromosome 21q22.1.

A long-range restriction map of the 1.8-megabases (mb) region encompassing the area between the interferon-alpha receptor and the acute myelogenous leukemia loci on human chromosome 21q22.1 was constructed after analysis of both the contiguous yeast artificial chromosome (YAC) clones and genomic DNA. Analysis of pulsed-field gel electrophoresis of lymphoblastoid DNA digested with three rare-cutting enzymes, Not I, Mlu I, and Nru I, revealed the positions of 17 markers on each restriction map. The 1.8-mb YAC contig that covers this region was obtained through YAC walking mediated by sequence-tagged sites (STSs), with 29 STSs including 12 newly generated YAC end-specific STSs. The consensus restriction map from 15 overlapping YACs and the positioning of the STS markers on each clone allowed 24 markers including 4 Not I-linking STSs to be ordered and mapped physically. Comparison of the maps revealed that the proximal region contains more unmethylated CpG islands than the distal region, which suggests that many expressed genes are in the proximal region. This fine consensus physical map will be informative and useful for construction of contigs of cosmid, P1, or BAC clones for further large-scale sequencing in this gene-rich region.

Base Sequence↗

PubMed1995

Identification of the coding region of Saccharomyces cerevisiae chromosome VI using the computer program GenMark.

We searched the nucleotide sequence of budding yeast Saccharomyces cerevisiae chromosome VI (270 kb) for candidate coding regions, using the computer program GenMark. One hundred and twenty-nine putative genes were identified, which is almost the same as the number of ORFs on this chromosome. Nineteen new putative genes were identified through the GenMark analysis. Most large ORFs were also correctly identified (87% of the predicted putative genes identified by the GenMark (110 of 127) matched the reported ORFs). The new coding regions were mostly small but they were distinguished from the more than 2000 ORFs identified by Genetyx. GenMark did not predict 17 ORFs that were over 300 bp long. As these ORFs include known genes, their sequence context may differ somewhat from that of typical yeast genes. These analyses revealed the high potential of GenMark to identify putative genes from numerous short ORFs and will produce information on the likelihood of their being actual genes.

Base Sequence↗

PubMed1995

Efficient replication of polyomavirus DNA in a cell-free system supplemented with Escherichia coli single-stranded DNA binding protein, which exhibits species-specificity in the requirement for DNA polymerase alpha-primase.

We established a modified cell-free system for polyomavirus (PyV) DNA replication, which was supplemented with Escherichia coli single-stranded DNA binding protein (SSB). DNA synthesis in this system was enhanced by 1.4- to over 15-fold depending upon the amount of cell extracts contained in the reaction mixture. By supplementing with E. coli SSB, we were able to reduce the amount of cell extracts in the reaction mixture, and to lower the concentrations of creatine phosphate and Tris, rendering this system more resistant to salts than the conventional PyV DNA replication system. The modified system was characterized using mutant cell extracts which had heat-inactivated DNA polymerase alpha. DNA synthesis in the system was dependent on PyV T antigen, the PyV origin of DNA replication, mutant cell extracts, and DNA polymerase alpha-primase complex purified from wild-type cells. The DNA polymerase alpha-primase complex was not replaced by DNA polymerase alpha, indicating that this system requires a functional DNA polymerase alpha-primase complex. This system exhibited species-specificity in the requirement for DNA polymerase alpha-primase; only mouse DNA polymerase alpha-primase but not human DNA polymerase alpha-primase functioned in this system.

Animals↗

PubMed1995

Characterization of DNA synthesis and DNA-dependent ATPase activity at a restrictive temperature in temperature-sensitive tsFT848 cells with thermolabile DNA helicase B.

A temperature-sensitive mutant defective in DNA replication, tsFT848, was isolated from the mouse mammary carcinoma cell line FM3A. In mutant cells, the DNA-dependent ATPase activity of DNA helicase B, which is a major DNA-dependent ATPase in wild-type cells, decreased at the nonpermissive temperature of 39 degrees C. DNA synthesis in tsFT848 cells at the nonpermissive temperature was analyzed in detail. DNA synthesis measured by incorporation of [3H]thymidine decreased to about 50% and less than 10% of the initial level at 8 and 12 h, respectively. The decrease in the level of thymidine incorporation correlated with a decrease in the number of silver grains in individual nuclei but not with the number of cells with labeled nuclei. DNA fiber autoradiography revealed that the DNA chain elongation rate did not decrease even after an incubation for 10 h at 39 degrees C, suggesting that initiation of DNA replication at the origin of replicons is impaired in the mutant cells. The decrease in DNA-synthesizing ability coincided with a decrease in the level of the DNA-dependent ATPase activity of DNA helicase B. Partially purified DNA helicase B from tsFT848 cells was more heat sensitive than that from wild-type cells. Inactivation of DNA-dependent ATPase activity of DNA helicase B from mutant cells was considerably reduced by adding DNA to the medium used for preincubation, indicating that the DNA helicase of mutant cells is stabilized by binding to DNA.

Animals↗

PubMed1994

Poly (ADP-ribose) polymerase inhibits DNA replication by human replicative DNA polymerase alpha, delta and epsilon in vitro.

The influence of poly (ADP-ribose) polymerase (PARP) and poly ADP-ribosylation on DNA synthesis supported by human replicative DNA polymerase (DNA pol) alpha, delta, and epsilon has been examined using the replication system containing poly(dA)4500-oligo(dT)12-18 as the template primer. PARP alone inhibited the pol activities in a dose-dependent manner even in the presence of the accessory factors for DNA pol delta, proliferating cell nuclear antigen (PCNA) and activator 1 (Al; RF-C). Both DNA pol alpha and epsilon activities were decreased approximately 10-fold under the poly ADP-ribosylating condition. In contrast, DNA synthesis by DNA pol delta holoenzyme was not affected by poly ADP-ribosylation like prokaryotic DNA pol's. The analysis of poly(dT) formed by DNA pol alpha and epsilon indicated that poly ADP-ribosylation mainly reduced the frequency of replication. These observations suggest a possibility that PARP acts as a negative regulator for the initiation of DNA replication upon cellular DNA damage.

DNA Polymerase II↗

PubMed1994

Molecular cloning of cDNA encoding human DNA helicase Q1 which has homology to Escherichia coli Rec Q helicase and localization of the gene at chromosome 12p12.

A complementary DNA encoding DNA-dependent ATPase Q1 possessing DNA helicase activity, which is the major DNA-dependent ATPase in human cell extracts, was cloned from a cDNA library of human KB cells. The predicted amino acid sequence has seven consecutive motifs conserved in the RNA and DNA helicase super family and DNA helicase Q1 belongs to DEXH helicase family. A homology search indicated that helicase Q1 had 47% homology in the seven conserved regions with Escherichia coli RecQ protein. Three RNA bands of 4.0, 3.3, and 2.2 kilobases were detected in HeLa cells by Northern blotting. Analysis of the genomic DNA indicated the presence of a homologous gene in mouse cells. The DNA helicase Q1 gene was localized on the short arm of human chromosome 12 at 12p12.

Adenosine Triphosphatases↗

PubMed1994

Cloning of a new kinesin-related gene located at the centromeric end of the human MHC region.

We previously reported the presence of a new gene (HSET) with an unknown function, in the centromeric side of the class II gene region of the human major histocompatibility complex (MHC). cDNA clones corresponding to the HSET gene were isolated from a human testis cDNA library. A 2.4 kilobase transcript from the HSET gene was abundantly expressed in testis, B-cell, T-cell, and ovary cell lines but was not detected in lung or stomach. Analysis of the nucleotide sequence of the HSET cDNA clones revealed significant similarity to kinesin-related proteins in yeast, Drosophila, and human. Its predicted amino acid sequence contains a domain with strong sequence similarity to the ATP-binding and motor domains of a plus end-directed microtubule motor protein, kinesin, which might be involved in mitotic chromosome segregation, suggesting that the HSET gene encodes a novel kinesin-related protein.

Amino Acid Sequence↗

PubMed1994

Homologous recombination of monkey alpha-satellite repeats in an in vitro simian virus 40 replication system: possible association of recombination with DNA replication.

To study homologous recombination between repeated sequences in an in vitro simian virus 40 (SV40) replication system, we constructed a series of substrate DNAs that contain two identical fragments of monkey alpha-satellite repeats. Together with the SV40-pBR322 composite vector encoding Apr and Kmr, the DNAs also contain the Escherichia coli galactokinase gene (galK) positioned between two alpha-satellite fragments. The alpha-satellite sequence used consists of multiple units of tandem 172-bp sequences which differ by microheterogeneity. The substrate DNAs were incubated in an in vitro SV40 DNA replication system and used to transform the E. coli galK strain DH10B after digestion with DpnI. The number of E. coli galK Apr Kmr colonies which contain recombinant DNAs were determined, and their structures were analyzed. Products of equal and unequal crossovers between identical 172-bp sequences and between similar but not identical (homeologous) 172-bp sequences, respectively, were detected, although those of the equal crossover were predominant among all of the galK mutant recombinants. Similar products were also observed in the in vivo experiments with COS1 cells. The in vitro experiments showed that these recombinations were dependent on the presence of both the SV40 origin of DNA replication and SV40 large T antigen. Most of the recombinant DNAs were generated from newly synthesized DpnI-resistant DNAs. These results suggest that the homologous recombination observed in this SV40 system is associated with DNA replication and is suppressed by mismatches in heteroduplexes formed between similar but not identical sequences.

Animals↗

PubMed1993

Characterization and chromosomal mapping of the human thromboxane A2 receptor gene.

The human thromboxane A2 gene, present as a single copy, spans over 15 kilobases (kb) and contains 3 exons divided by 2 introns. The first intron, intron 1, exists in the 5'-noncoding region, 83 base pairs upstream from the ATG start site and is 6.3 kb long. Intron 2 with a length of 4.3 kb is located at the end of the sixth transmembrane region, thereby separating it from the downstream coding sequences including the seventh transmembrane region and the 3'-untranslated region. By rapid amplification of 5'-cDNA ends, transcription initiation sites starting in two different putative promoter regions were determined. In the 5'-flanking region of these transcription initiation sites, no typical TATA box exists. The major promoter, the promoter region I, contains four potential SP-1 binding sites and several potential binding sites for other transcription factors. By polymerase chain reaction analysis, a small portion of the RNA transcribed from this gene was shown to contain an additional 115-base pair long noncoding exon, exon 1b, which is located in intron 1. No additional exon in intron 2 was detectable, indicating that a single type of thromboxane A2 receptor protein is encoded by this gene. Chromosomal localization was carried out by fluorescence in situ hybridization of cloned genomic DNA to the metaphase chromosome. The gene was assigned to 19p13.3 of human chromosome.

Base Sequence↗

PubMed1993

Characterization of DNA synthesis at a restrictive temperature in the temperature-sensitive mutants, tsFT5 cells, that belong to the complementation group of ts85 cells containing a thermolabile ubiquitin-activating enzyme E1. Involvement of the ubiquitin-conjugating system in DNA replication.

A temperature-sensitive mutant defective in DNA replication, tsFT5, has been isolated from the mouse mammary carcinoma cell line FM3A. DNA synthesis in tsFT5 cells at a restrictive temperature (39 degrees C) has been characterized in detail. Incorporation of [3H]thymidine decreased rapidly after an increase in temperature to 39 degrees C and the incorporation was less than 20% and 10% of the initial level after 4 and 8 h, respectively. Analysis by DNA fiber autoradiography revealed that the initiation of DNA replication at the origin of the replicons was impaired in tsFT5 cells but that the DNA chain elongation rate of the mutant cells did not decrease at the nonpermissive temperature. tsFT5 cells were confirmed to belong to the complementation group which includes ts85 cells arrested mainly in the G2 phase at the nonpermissive temperature. It has been observed that the amount of ubiquintin-conjugated histone H2A (uH2A) in ts85 cells decreases at the nonpermissive temperature (Marunouchi, T., Yasuda, H., Matsumoto, Y., and Yamada, M. (1980) Biochem. Biophys. Res. Commun. 95, 126-131). The amount of uH2A in tsFT5 cells also decreased rapidly at 39 degrees C. This decrease occurred at the same time as or slightly preceding to reduction in DNA synthesis, and the reappearance of uH2A was followed by the restoration of DNA synthesis after the temperature was reduced. A similar temporal relationship between decrease in the amount of uH2A and reduction in DNA synthesis was observed in ts85 cells cultured at 39 degrees C. However, the rates of the decrease of uH2A and of the reduction in DNA synthesis in ts85 cells were slower than those observed in tsFT5 cells. A comparison of the thermolability of purified ubiquitin-activating enzyme E1s revealed that the E1 from ts85 cells had a thermolability intermediate between those of the E1 from tsFT5 cells and of the wild-type cells. A reduction in the phosphorylation of histone H1 was observed in tsFT5 cells cultured at 39 degrees C, but the reduction occurred several hours after the decrease in uH2A and the reduction in DNA synthesis.

Animals↗

PubMed1993

Molecular cloning and chromosomal localization of the key subunit of the human N-methyl-D-aspartate receptor.

A complementary DNA encoding the key subunit of the human N-methyl-D-aspartate (NMDA) receptor (NMDAR1) has been cloned using a probe derived from the rat NMDAR1 cDNA. The cDNA encodes a 938-amino acid protein, which shows 99% amino acid homology with the rat counterpart. Of the 7 of 938 amino acids which are different, three occur in the region of the signal peptide and the others in the extracellular amino-terminal domain preceding the 4 putative transmembrane segments. Expression in Xenopus oocytes demonstrated that the single protein encoded by the cloned cDNA possesses the electrophysiological and pharmacological properties characteristic of the NMDA receptor, including Ca2+ permeability, voltage-dependent Mg2+ block, and inhibition by selective antagonists such as Zn2+ and channel blockers. The high evolutionary conservation in the structure and properties of NMDAR1 argues strongly for the importance of this receptor in functions of glutamate neurotransmission. RNA blot analysis showed abundant expression of mRNA whose size is about 4.5 and 4.8 kilonucleotides. The human gene encoding the NMDAR1 subunit has been mapped to chromosome 9q34.3 by the analyses of blot hybridization of a DNA panel of human/hamster somatic cell hybrids and fluorescence in situ hybridization of human chromosomes.

2-Amino-5-phosphonovalerate↗

PubMed1993

Characterization of factors that suppress linear DNA replication in SV40 in vitro replication system.

The in vitro simian virus 40 (SV40) replication system has been developed as a model system of cellular DNA replication, because the replication initiated from the replication origin of SV40 and replication fork proceeds bidirectionally. In this system, SV40 T-antigen (TAg) is the only factor provided by viral genes, while all other factors are supplied by the host cells. A suppression of replication has been observed in the linear template containing SV40 replication origin, compared with the closed circular template in the SV40 in vitro replication system using a crude extract of HeLa cells. However in the in vitro replication system reconstituted from partially purified factors, less preference was observed for the replication of the closed circular DNA over the linear DNA. In a mono-polymerase system supplemented by crude extracts, a suppression of replication in a linear template was also observed, when compared with a closed circular template. This suppression effect of crude extract was abolished by heat treatment, suggesting that the suppression was induced by some protein factors. A crude extract of HeLa cells was fractionated by stepwise elution with buffers containing 0.2 M, 0.4 M, 0.6 M and 1 M NaCl on a phosphocellulose column, and characterization of factors that suppress linear DNA replication has been done. Both fractions that were eluted at 0.4 M and 0.6 M from phosphocellulose were necessary to suppress linear DNA replication efficiently. The factors in the 0.6 M fraction that suppressed linear DNA replication synergistically with the 0.4 M fraction were partially purified by successive chromatography with heparin-sepharose and dsDNA-cellulose followed by glycerol gradient centrifugation. These results suggested that multiple factors are required to suppress DNA replication of the linear template.

Cell Fractionation↗

PubMed1993

Mapping of the 70 kDa, 34 kDa, and 11 kDa subunit genes of the human multimeric single-stranded DNA binding protein (hSSB/RPA) to chromosome bands 17p13, 1p35-p36.1, and 7p21-p22.

Human single-stranded DNA binding protein (hSSB/RPA) is a multimeric single-stranded DNA binding protein consisting of three subunits of 70 kDa, 34 kDa, and 11 kDa. Human SSB was isolated from HeLa cells as an essential factor for the in vitro replication of simian virus 40 DNA. We and others have isolated and sequenced cDNAs for each subunit of the SSB. The chromosome on which each gene is located was determined through the analysis of a panel of human/hamster somatic cell hybrids using the polymerase chain reaction with pairs of synthetic oligonucleotide primers from the 3'-untranslated sequences of the genes. Genomic clones for each gene were isolated from a genomic cosmid library prepared from human lymphoblastoid cells. Using those clones as probes, we have carried out fluorescence in situ hybridization to human metaphase chromosomes and have mapped the 70 kDa subunit gene to 17p13, the 34 kDa subunit gene to 1p35-p36.1, and the 11 kDa subunit gene to 7p21-p22. Since hSSB participates in replication, recombination and repair of DNA, the physical mapping of hSSB genes may aid in the identification of human hereditary diseases associated with aberrant DNA reactions caused by genetic alterations of the hSSB.

Animals↗