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Y Shimura

Publications and source records attributed to Y Shimura.

At least 109 records · Page 6Linked to original sources
PubMed1986

Cloning and nucleotide sequence of the aspartase gene of Pseudomonas fluorescens.

The aspartase gene (aspA) of Pseudomonas fluorescens was cloned and the nucleotide sequence of the 2,066-base-pair DNA fragment containing the aspA gene was determined. The amino acid sequence of the protein deduced from the nucleotide sequence was confirmed by N- and C-terminal sequence analysis of the purified enzyme protein. The deduced amino acid composition also fitted the previous amino acid analysis results well (Takagi et al. (1984) J. Biochem. 96, 545-552). These results indicate that aspartase of P. fluorescens consists of four identical subunits with a molecular weight of 50,859, composed of 472 amino acid residues. The coding sequence of the gene was preceded by a potential Shine-Dalgarno sequence and by a few promoter-like structures. Following the stop codon there was a structure which is reminiscent of the Escherichia coli rho-independent terminator. The G + C content of the coding sequence was found to be 62.3%. Inspection of the codon usage for the aspA gene revealed as high as 80.0% preference for G or C at the third codon position. The deduced amino acid sequence was 56.3% homologous with that of the enzyme of E. coli W (Takagi et al. (1985) Nucl. Acids Res. 13, 2063-2074). Cys-140 and Cys-430 of the E. coli enzyme, which had been assigned as functionally essential (Ida & Tokushige (1985) J. Biochem. 98, 793-797), were substituted by Ala-140 and Ala-431, respectively, in the P. fluorescens enzyme.

Amino Acid Sequence↗
PubMed1985

Cloning and nucleotide sequence of the aspartase gene of Escherichia coli W.

The aspA gene of Escherichia coli W which encodes aspartase was cloned into the plasmid vector pBR322. The nucleotide sequences of aspA and its flanking regions were determined. The aspA gene encodes a protein with a molecular weight of 52,224 consisted of 477 amino acid residues. The amino acid sequence of the protein predicted from the nucleotide sequence was consistent with those of the NH2- and COOH-terminal regions and also with the amino acid composition of the purified aspartase determined previously. Potential promoter and terminator sequences for aspA were also found in the determined sequence.

Amino Acid Sequence↗
PubMed1985

Nucleotide sequence of a chicken delta-crystallin gene.

We have determined the complete nucleotide sequence of one of the two non-allelic delta-crystallin genes in the chicken, arbitrarily designated delta-gene 1, using a genomic clone (lambda g delta 106) containing the entire gene sequence. By comparison of the genomic sequence and the delta-crystallin cDNA sequence previously determined, we have identified exon sequences in the genomic sequence. Thus, the presence of 17 exons and 16 introns in the gene has been clarified. The delta-crystallin polypeptide deduced from the exon sequences consists of 465 amino acids which is larger, by 19 amino acid residues, than the polypeptide deduced from the cDNA sequence previously reported. Re-examination of the cDNA sequence using the same cDNA clone previously used shows that the present exon sequences are correct and the molecular weight of the deduced delta-crystallin polypeptide is 50,615 daltons instead of the previously reported value of 48,447 daltons. In addition, some structural features of the delta-crystallin gene including putative expression signals are discussed.

Alleles↗
PubMed1984

The nucleotide sequence of a complete chicken delta-crystallin cDNA.

The nucleotide sequence of a full length cDNA of delta-crystallin mRNA from chicken lens has been determined using a delta-crystallin cDNA clone (pB delta 11), which represents the mRNA sequence of 1530 nucleotides from the poly(A) junction but does not contain the 5'-terminal sequence of 44 nucleotides of the mRNA. The 5'-terminal sequence of the mRNA, absent in the cDNA clone, has been determined with a stretch of cDNA sequence by the primer extension procedure. The amino acid sequence deduced from the nucleotide sequence is consistent with the amino acid sequences of several tryptic peptides, the total amino acid composition, and the mol. wt. of delta-crystallin estimated by SDS-polyacrylamide gel electrophoresis. The computer-assisted analysis predicts high alpha-helical content throughout the polypeptide. Sequence analyses have revealed that gene 1 encodes the mRNA from which the cDNA clone was derived.

Amino Acid Sequence↗
PubMed1983

Nucleotide sequence and stability of the RNA component of RNase P from a temperature-sensitive mutant of E. coli.

The gene coding for the RNA component of RNase P was cloned from a temperature-sensitive mutant of Escherichia coli defective in RNase P activity (ts709) and its parental wild-type strain (4273), and the complete nucleotide sequences of the gene and its flanking regions were determined. The 5'- and 3'-terminal sequences of the RNA component were determined and mapped on the DNA sequence. The mutant gene has GC-to-AT substitutions at positions corresponding to 89 and 365 nucleotides downstream from the 5' terminus of the RNA sequence. Comparing to the wild-type RNA, the mutant RNA is less stable and rapidly degraded in vivo and in vitro.

Base Sequence↗
PubMed1983

Characterization of messenger RNA for chick-embryo DNA polymerase beta and its translation product in vitro.

A specific immunoprecipitation method, using rabbit anti-(chick DNA polymerase beta) IgG was applied to detect the polypeptide of DNA polymerase beta among translation products obtained in vitro with mRNA extracted from chick embryos. A polypeptide of Mr = 40 000 was specifically immunoprecipitated from [35S]methionine-labeled translation products and was competitive with the purified DNA polymerase beta for the antibody. Furthermore, the 40 000-Mr translation product obtained in vitro had DNA polymerase activity, which was detected by assay in situ after electrophoresis in a polyacrylamide gel containing DNA. The mRNA for DNA polymerase beta was polyadenylated and its content was estimated as the range of 0.001% of total poly(A)-rich RNA on the basis of [35S]methionine incorporation in the translation in vitro. The size of this mRNA was determined to be about 1800 nucleotides by zone sedimentation and agarose gel electrophoresis under denaturating conditions.

Animals↗
PubMed1983

Processing of transcription products of the gene encoding the RNA component of RNase P.

The gene coding for the RNA component of RNase P from Escherichia coli was transcribed in vitro by using a restriction fragment carrying the gene as template. The terminal sequences of the transcription products were determined and mapped on the DNA sequence of the gene. The signals for transcription initiation and termination of the gene were thus identified. Transcription termination occurs within a region of two bases at positions 413 and 414 from the transcription start site. The transcripts carry extra stretches of 36 and 37 nucleotides at the 3' end of the RNA molecule isolated from the enzyme. The extra sequences were removed in vitro when the transcripts were incubated with a crude cell extract.

Base Sequence↗
PubMed1983

Construction of plasmid vectors for cloning of promoters using the dihydrofolate reductase gene of Escherichia coli K-12.

Vectors for cloning promoter-DNA fragments were derived from pTP 30-5 which was constructed in our previous work (M. Iwakura et al. (1982) J. Biochem. 91, 1205). The selection was based on the expression of trimethoprim resistance of transformed bacteria in which the enhancement of dihydrofolate reductase production was directed by the cloned promoter. A linear relationship between the content of dihydrofolate reductase and the strength of trimethoprim resistance was observed. It is suggested that the promoter activities can be estimated by trimethoprim resistance without measuring the enzyme activities.

Cloning, Molecular↗
PubMed1983

Purification of dihydrofolate reductase amplified in Escherichia coli K-12.

The Escherichia coli strain carrying pTP 6-10 which was constructed in our previous work (Iwakura, M., et al. (1983) J. Biochem. 93, 927-930) produces more than 400-fold dihydrofolate reductase as compared with the strain without the plasmid. Dihydrofolate reductase was highly purified from the cell-free extract of the plasmid strain simply by two steps; ammonium sulfate fractionation and ion-exchange chromatography. By 10-fold purification, the enzyme was essentially homogeneous as judged by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. The restriction map of pTP 6-10 was also determined and the plasmid was shown to have an Ava I, an EcoR I, a Pst I, a Pvu I, and a Pvu II site. Our results indicate that the plasmid strain is suitable as a source of the enzyme and that plasmid pTP 6-10 is promising as a versatile plasmid vector for efficiently yielding the product of the cloned gene.

Base Composition↗
PubMed1983

Synthesis of N-protected deoxynucleosides via 3',5'-cyclic silyl derivatives.

Treatment of deoxynucleosides with dichlorosilanes in pyridine gives 3',5'-cyclic silyl derivatives. Dimethylsilanediyl derivatives and tetramethyldisiloxanediyl derivatives are not stable solvolytically and cleavage of these silyl ethers to the parent deoxynucleosides occurs readily on addition of water. These solvolytically labile bifunctional silyl groups serve as simultaneous transient protecting 3'- and 5'-hydroxyl functions. Acylation and successive hydrolysis of 3',5'-cyclic silyl derivatives gives the corresponding N-protected deoxynucleosides. Some N-acylated deoxy-adenosines and N-anisoyldeoxycytidine were synthesized easily by this N-protection method.

Chemical Phenomena↗
PubMed1982

In vitro transcription of the supB-E tRNA operon of Escherichia coli. Characterization of transcription products.

The seven tRNA genes clustered in the supB-E region of the Escherichia coli chromosome were transcribed in vitro with purified RNA polymerase, using a restriction fragment from lambda psu degrees 2, a transducing phage carrying the chromosome region, as template. A single major transcript was synthesized, which was about 770 nucleotides long and contained all seven tRNA sequences. The terminal sequences of the transcript were determined and mapped on the DNA sequence of the supB-E region previously determined. The transcription start site is seven base pairs downstream from the Pribnow box sequence, as expected from the DNA sequence analysis and consistent with the findings on the trimeric tRNA precursor (pppG--tRNAMETM-tRNALeu-tRNAGln1) which was detected in an RNase P mutant and shown to be coded for by the supB-E region. Cleavage of the restriction fragment at the -35 region with another restriction endonuclease abolished the template activity of the fragment. Transcription of the supB-E tRNA operon was relatively unaffected by the presence of rho factor. Transcription termination occurs within a region of three bases between positions 770 and 772 from the transcription start site. Immediately upstream from the termination sites, there is a region of 26 nucleotides that could form a stem structure, thereby consistent with the general feature of rho-independent termination sites.

Bacteriophage lambda↗
PubMed1982

Organization of delta-crystallin genes in the chicken.

Double-stranded DNA was synthesized from delta-crystallin mRNA prepared from lens fibers of 15-day-old chick embryos and cloned at the Pst I site of the plasmid pBR322. Using the cloned cDNA and single-stranded cDNA as hybridization probes, a number of genomic DNA fragments containing delta-crystallin gene sequences have been cloned from the partial and complete EcoRI digests of chick brain DNA. One of the clones from the partial digests contains a DNA fragment that consists of four EcoRI fragments of 7.6 kb, 4.0 kb, 2.6 kb, and 0.8 kb. The gene sequences reside in the (5')7.6 kb - 0.8 kb - 4.0 kb (3') fragments. Electron microscopy has provided evidence that the cloned DNA fragment includes the entire gene sequences complementary to delta-crystallin mRNA except for the 3' terminal poly(A) tail, and that the delta-crystallin gene is interrupted by at least 13 intervening sequences. Another clone contains a genomic fragment that consists of two EcoRI fragments of 3.0 kb and 11 kb. The DNA fragment in the latter clone represents a different delta-crystallin gene, as judged by restriction endonuclease mapping and by electron microscopy.

Animals↗
PubMed1982

Cloning of dihydrofolate reductase gene of Escherichia coli K12.

Resistant strains for trimethoprim, a potent inhibitor of dihydrofolate reductase, were obtained by transforming the ligated products of Escherichia coli K12 DNA and plasmid pBR322 BamH I fragments. The strains carry a 13.6 kbp plasmid, pTP1, which contains the trimethoprim- and ampicillin-resistance determinant genes. The trimethoprim-resistance determinant gene was estimated to consist of more than 500 nucleotides and less than 1,500 nucleotides and was restricted by EcoR I and Sal I. Trimethoprim-, ampicillin-, and tetracycline-resistant plasmids were made in the following way, and the resultant plasmids contained a unique EcoR I "insertional inactivation" site for trimethoprim resistance: the DNA sequences extraneous to the determinant gene of the trimethoprim resistance on BamH I fragment of pTP 1 were eliminated by digestion with a double-strand-specific exonuclease BAL 31, and the resultant fragments were ligated with pBR 322 which had been digested by EcoR I and a single-strand-specific nuclease S1. The strains carrying pTP 1 or trimethoprim-resistant plasmids produced about 10 times more dihydrofolate reductase than control strains. The enhancement of the enzyme production, which is due to an increase in the copy number of the enzyme gene, seems to be responsible for the trimethoprim resistance of the transformed cells.

Cloning, Molecular↗
PubMed1982

Isolation of DNA fragment containing phoS gene of Escherichia coli K-12.

The DNA fragment containing the phoS gene, a regulatory gene for alkaline phosphatase, has been isolated from Escherichia coli K-12 chromosomal DNA by cutting off the DNA with Hind III restriction enzyme and by cloning the gene with plasmid vector pTP 4 which was constructed in this study. The isolated fragment was of about 12.3 kbp and seemed to contain the phoT, glmS, and bgl genes. The 12.3 kbp Hind III fragment was subjected to restriction enzymes EcoR I, BamH I, Sal I, and Pst I, and was found to possess two EcoR I, no BamH I, a Sal I, and four Pst I sites. Partial deletion using these restriction enzymes suggested that the about 6 kbp Hind III-Pst I fragment contained the phoS and phoT genes. Further analysis with other restriction enzymes revealed that the 6 kbp Hind III-Pst I fragment contained a BstE II, two Mlu I and four Hpa I sites. The deletion of these restriction sites using single-strand-specific nuclease S1 suggested that the BstE II and one of Mlu I sites were in the phoT gene, and the BstE II and two Mlu I sites were not in the phoS gene.

Culture Media↗
PubMed1981

Organization and structure of an E. coli tRNA operon containing seven tRNA genes.

The structure and organization on the Escherichia coli chromosome of the gene cluster coding for two methionine tRNAs (tRNAmMet), four glutamine tRNAs (two tRNA1Gln and two tRNA2Gln), and a previously unidentified tRNA (called tRNAx) have been studied by restriction enzyme analysis and DNA sequencing, utilizing a specialized transducing bacteriophage (lambda psu degrees 2) carrying the supB-supE region. From the sequence analysis, the previously unidentified tRNA has been shown to have an anticodon sequence (5'-UAG-3') corresponding to a leucine codon. The organization of this tRNA gene cluster on the E. coli chromosome is tRNAmMet-9 base pairs-tRNAx-23 base pairs-tRNA1Gln-34 base pairs-tRNA1Gln-15 base pairs-tRNAmMet-47 base pairs-tRNA2Gln-37 base pairs-tRNA2Gln. The duplicated genes coding for tRNAmMet, tRNA,Gln, and tRNA2Gln have identical sequences, which are the same as the sequences determined previously with tRNA molecules. These tRNA sequences are preceded by a single promoter region where a "Pribnow box" sequence is present seven base pairs upstream from the transcription start site. The spacer regions separating the seven tRNA sequences are different from each other both in size and in nucleotide sequence. The possible implication of these sequences for precursor processing is discussed. A restriction fragment that has been originally identified in lambda psu degrees 2 DNA and shown to contain the seven tRNA genes has been detected in the E. coli chromosome, thereby suggesting that this tRNA gene cluster is present in the bacterial genome with the same organization as in the transducing phage genome.

Base Sequence↗
PubMed1980

[A study of caerulein action on secretory cells, especially in the islets of Langerhans in the rat pancreas (author's transl)].

Although it is known that caerulein exerts an action on the secretory activity of the islets of Langerhans in the pancreas, the mechanism of this hormone has not yet been ascertained. The present investigation was undertaken to observe the ultramicroscopic changes of the pancreatic islets and the peripheral blood levels of insulin, glucagon, glucose and electrolites after caerulein administration. The animals were divided into four groups, and three were injected intraperitoneally with caerulein at 25 micrograms/kg, 2 micrograms/kg and 0.2 microgram/kg body weight, respectively. The fourth group served as the control. In the first group (25 micrograms caerulein), the endocrine cells of the pancreatic islets showed accelerated functioning immediately and up to about 2 hours after injection. Then these cells degenerated due to cytoplasmic edema and evidenced decreased secretory activity. In the second group (2 micrograms) depression in the secretory activity occurred for about 2 hours immediately after the injection, but there was no destruction of cells and they gradually recovered their functioning. The third group (0.2 microgram) displayed an acceleration of secretory activity immediately after the injection and then recovered to the normal state. There were some changes of electrolites in the peripheral blood in each of the three groups, suggesting that caerulein causes acceleration and depression of the secretory activities in the islets of Langerhans in the pancreas depending on the dosage. Moreover, the cell alterations may well depend on the changes of electrolites in the inner and outer atmospheres of the cells.

Animals↗
PubMed1980

Arrangement of the single-stranded fragments in E. coli bacteriophage BF23 DNA.

Bacteriophage BF23st(0) DNA was denatured with alkali and fractionated by agarose gel electrophoresis. Seven single-stranded fragments (designated Fragments I--VII) were identified as the major constituents of the phage DNA. The presence of several minor fragments which represent minor populations of the phage genome was also observed. The largest fragment (Fragment I) represents the intact strand of phage DNA, whereas the other fragments form the complementary strand. Thus, BF23st(0) DNA carries single-strand interruptions in only one strand. The arrangement of the major fragments in the nicked strand was determined by use of gamma-exonuclease and agarose gel electrophoresis. From the mode of action of this nuclease, and from the kinetics of release or disappearance of the fragments, the polarity of the fragments in BF23st(0) DNA was specified. In addition, the presence of two types of major phage populations differing in their composition of the fragments was demonstrated. One type has an additional nick (yielding Fragment IV and Fragment V) in a specific fragment (Fragment II) of other type.

Chromosome Mapping↗