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A Taketo

Publications and source records attributed to A Taketo.

At least 37 records · Page 2Linked to original sources

Initial stage of DNA-electrotransfer into E. coli cells.

The mechanism of electrotransfer of DNA into Escherichia coli cells was investigated under conditions optimal for genetic transformation or transfection. Simple mixing in 10% polyethylene glycol 6000 did not cause binding of DNA to the recipient bacteria. When subjected to a high electric field, however, 90-98% of the input plasmid or phage DNAs were complexed with the cells. By application of the electric field, a significant amount of biotin-labeled DNA was bound onto the recipient surface, as detected by fluorescein isothiocyanate coupled avidin. When subjected to a high voltage pulse, DNA molecules were rapidly attracted toward the anode. Concurrently, the electric field induced the orientation of bacterial cells, along the field lines and their movement toward the anode. Since the bacterial movement was relatively slow, a substantial fraction of DNA molecules must strike the cathode-facing end or side of the recipient cells. Irrespective of the high efficiency of DNA transformation, the voltage pulse did not induce release of alkaline phosphate and beta-galactosidase. The electrotransferred DNA first remained sensitive to Tris-EDTA treatment, and became refractory to spheroplasting only after incubation at 37 degrees C. These results indicate that the infecting DNA is electrophoretically plugged to the outer membrane loosened by the voltage pulse.

Cell Membrane Permeability↗

Cloning, sequence analysis, and expression of the genes encoding lytic functions of Bacteriophage phi g1e.

The lysis genes of a Lactobacillus phage phi g1e were cloned, sequenced, and expressed in Escherichia coli. Nucleotide sequencing of a 3813-bp phi g1e DNA revealed five successive open reading frames (ORF), Rorf50, Rorf118, hol, and lys and Rorf175, in the same DNA strand. By comparative analysis of the DNA sequence, the putative hol product (holin) has an estimated molecular weight is 14.2 kDa, and contains two potential transmembrane helices and highly charged N- and C-termini, resembling predicted holins (which are thought to be a cytoplasmic membrane-disrupting protein) encoded by other phages such as mv1 from Lactobacillus bulgaricus, phi adh from Lactobacillus gasseri, as well as monocins from Listeria. On the other hand, the putative phi g1e lys product (lysin) of 48.4 kDa shows significant similarity with presumed muramidase, known as a cell wall peptidoglycandegrading enzyme, encoded by the Lactobacillus phage mv1 and phi adh, the Lactococcus lactis phage phi LC3, and the Streptococcus pneumoniae phages Cp-1, Cp-7 and Cp-9. When expressed in E. coli, the phi g1e lysin and/or holin decreased the cell turbidity significantly, suggesting that the phi g1e hol-lys system is involved in cytolytic process.

Amino Acid Sequence↗

Cloning and nucleotide sequence of the major capsid proteins of Lactobacillus bacteriophage phi gle.

Bacteriophage phi gle was induced from a lysogenic Lactobacillus strain Gle. phi gle genome is double-stranded DNA of approximately 42.5 kilo-base (kb) pairs. SDS poly-acrylamide gel electrophoresis demonstrated that the phage particles contain 4 major structural (capsid) proteins, gpB, gpG, gpO, and gpP, whose molecular weights (MW) are estimated to be 64, 43, 29 and 26 kilodaltons (kDa), respectively. More than 16 minor proteins ranging from 113 to 9.6 kDa were also detected. The genes for the major capsid proteins were cloned and each DNA sequence was determined. N-terminal amino acid alignments determined by protein sequencing completely coincided with those deduced from the nucleotide sequences.

Amino Acid Sequence↗

Studies on electrotransfer of DNA into Escherichia coli: effect of molecular form of DNA.

Effects of several molecular forms of DNA were examined on voltage-pulse-mediated transfection or transformation. Among circular DNAs, the single-stranded microvirid DNA was less infective than the double-stranded replicative form, whereas transfectivity of the relaxed or nicked molecule was nearly equal to or slightly lower than that of the supercoiled DNA. The linearized double-stranded DNA derived from phage or plasmid electrotransfects Escherichia coli, albeit at a reduced efficiency. Alkaline denaturation of the linearized DNA resulted in complete loss of the infectivity. Relationship between terminal structure of the linearized DNA and efficiency of the transfection was investigated. Host recombination function did not significantly affect the infectivity of the linearized DNA.

DNA↗

The virion proteins encoded by bacteriophage phi K and its host-range mutant phi KhT: host-range determination and DNA binding properties.

The microvirid phage phi K, specific for Escherichia coli K12, contains a circular single-stranded (SS) DNA in the icosahedral virion, which comprises four phage gene products, F (capsid), G (major spike), H (minor spike), and J (core). phi KhT, a host-range mutant of phi K, can grow on E. coli C and B, besides K12, and is more thermosensitive than the parental phage phi K. Sequencing analysis revealed that the genome of phi K and phi KhT consists of 6,089 nucleotides (nt), and codes for eleven genes, whose sequences are similar to those of alpha 3, phi X174, and G4 infective to strain C. In phi KhT, two nt had changed: one is in the gene G, resulting in replacement of the 75th codon Ala with Ser, and the other is at 67th codon of the gene H: Val to Ala. Chemically synthesized gene J protein composed of 23 amino acids (aa) binds to phi K SS DNA more tightly than and preferentially over the host E. coli SS-DNA-binding protein (SSB). These results indicate that the two spike proteins G and H are involved in the determination of phi K host-range, and support a model in which the gene J protein functions in packaging the viral SS DNA into the virion vesicle.

Amino Acid Sequence↗

A new and efficient method for gene transfer into mouse FM3A cells using metaphase chromosomes by electroporation.

We introduced chromosome-mediated genes into mouse thymidine kinase-deficient FM3A (FM3Atk-) cells, by electroporation. The effects of some parameters on the electric shock-mediated transfection of FM3Atk- cells were investigated. Gene transfer of mouse L929 metaphase chromosome DNA into FM3Atk- resulted in a maximum frequency of (3.0 +/- 0.3) x 10(-5) at a cell density of 2.0 x 10(8)/ml and chromosome dosage of 5.0 x 10(7) cell equivalents/ml in a buffer containing 0.25 M mannitol, 0.5 mM MgCl2, 0.1mM CaCl2, and 1 mM Tris-HCl (pH 7.1). The highest yield of the transformants was obtained at an electric field strength of 1 kV/cm and a capacitance of 35 microF, with a single exponentially decaying pulse at 0 degrees C was optimal for post-shock incubation after electroporation. The tk gene was detected in the transformants by in situ hybridization analysis.

Animals↗

Identification of a genetic mutation in a family with fructose-1,6- bisphosphatase deficiency.

Fructose-1,6-bisphosphatase deficiency is an inheritable disorder of gluconeogenesis. Sequence analysis of the cDNA of the fructose-1,6-bisphosphatase mRNA isolated from monocytes from a girl with this disease and her consanguineous parents revealed that the patient and her parents were a homozygote and heterozygotes for an insertion of one G residue at G957GGGG961, respectively. This mutation resulted in translation of a truncated enzyme protein, and the mutant protein showed no fructose-1,6- bisphosphatase activity in an overexpression experiment in Escherichia coli. However, this mutation is located in a region of the amino acid sequence which is not well conserved among mammals. A mutagenized clone was prepared from the normal clone. The extents of substitutions and deletions of the amino acid sequence were predicted to be less in the mutagenized protein than in the mutant protein. This mutagenized clone also expressed no fructose-1,6-bisphosphatase activity, although both of two normal clones from control monocytes and a control liver sample expressed an apparently normal level of fructose-1,6-bisphosphatase activity. Thus, this mutation is concluded to be responsible for fructose-1,6-bisphosphatase deficiency in this patient.

Amino Acid Sequence↗

Determination of the single strand origin of Shigella sonnei plasmid pKYM.

The Shigella sonnei plasmid pKYM replicates by a rolling-circle mechanism in Escherichia coli. A 571 nucleotides HincII restriction fragment of the pKYM DNA harbors two potential hairpin loops (I and II). We cloned the fragment into a -ori defective M13 vector phage, M13 delta lac183. The chimera phage, MDKY5, showed a larger plaque size, and increased phage yield and rate of progeny replicative form DNA (RF) synthesis. Rifampicin reduced rate of conversion of the single- to double-stranded RF DNA. In addition, we introduced nucleotide deletions within the cloned pKYM DNA, by Bal31 nuclease digestion. Each of the deletion mutants thus constructed was lacking in a sequence containing the hairpin loops and formed smaller plaques. The in vivo analyses revealed that a 136 nucleotides sequence containing the two hairpins I and II is the pKYM minus origin for complementary strand synthesis (single strand origin, referred to as SSO) and harbors a recognition site(s) by host E. coli RNA polymerase, for primer RNA synthesis. Moreover, we found a 24 nt sequence, upstream of the SSO domain having 83% homology to the recombination site A (RSA) which functions in plasmid sitespecific recombination and/or transfer.

Base Sequence↗

Comparative studies on the minus origin mutants of Escherichia coli spherical single-stranded DNA phages.

The minus origins for complementary strand DNA synthesis (-ori) of Escherichia coli spherical single-stranded DNA (microvirid) phages G4, phi K, alpha 3, and St-1 closely resemble each other in DNA structure and contain two potential secondary hairpin loops (I and II) that have been implicated as direct recognition sites for host E. coli dnaG protein (primase). We introduced mutations (deletion or insertion) within the -ori regions of phi K and G4 by the nuclease digestion method. Mutants thus constructed produced minute plaques, showed thermosensitivity, and they remarkably reduced the phage yield and rate of viral DNA synthesis. Deletions in the phi K mutants (dTa) were ranging from 1 nucleotide (nt) to 102 nt centered at the hairpin II; a dTa8 mutant was entirely lacking in the two hairpins besides the starting point for primer RNA synthesis. On the other hand, the G4 mutants (dSa) had deletions centered at hairpin I; two mutants dSa35 and dXN completely lost the hairpin I and the primer RNA starting point. In addition, progeny phage populations of several phi K and G4 mutants contained revertant-like phages. DNA sequencing analysis revealed that these secondary phages had been generated by spontaneous DNA rearrangement with additional insertion or deletion near the parental mutation sites, via an unknown recA-independent pathway.

Base Sequence↗

cDNA sequences encoding human fructose 1,6-bisphosphatase from monocytes, liver and kidney: application of monocytes to molecular analysis of human fructose 1,6-bisphosphatase deficiency.

Fructose 1,6-bisphosphatase deficiency is an autosomal recessive inherited disorder of gluconeogenesis. We could isolate cDNAs encoding human fructose 1,6-bisphosphatase from normal monocytes, liver and kidney, but not from normal lymphocytes. The cDNAs contained an open reading frame coding for 338 amino acids, and their nucleotide sequences in monocytes and liver were identical. G644C645 nucleotides in this sequence were the same as those of cDNA from HL-60 cells, although our result differed from a previous report (M. El-Maghrabi et al. (1993) J. Biol. Chem. 268, 9466-9472) on an alteration to C644G645 nucleotides in human liver cDNA resulting in a change of Gly-214 to Ala-214 in the enzyme. The Gly-214 (GGC) residue was therefore conserved in the enzymes hitherto isolated from humans and other animals. Analysis of monocytes in seven patients with fructose 1,6-bisphosphatase deficiency showed a DNA fragment with apparent normal size in two sisters but no detectable DNA fragment in the other five patients. Monocytes were thus useful as an alternative source for mRNA from human liver for the molecular analysis of fructose 1,6-bisphosphatase deficiency.

Alanine↗

Nucleotide sequence of the genome of the bacteriophage alpha 3: interrelationship of the genome structure and the gene products with those of the phages, phi X174, G4 and phi K.

The complete nucleotide sequence of the genome of the circular single-stranded DNA (isometric) phage alpha 3 has been determined and compared with that of the related phages phi X174 and G4. The alpha 3 genome consists of 6087 nucleotides, which is 701 nucleotides longer than the nucleotide sequence of the phi X174 genome and 510 nucleotides more than that of the G4 genome. The results demonstrated that the three phage species have 11 homologous genes (A, A*, B, C, K, D, E, J, F, G and H), the order of which is fundamentally identical, suggesting that they have evolved from a common ancestor. The sequence of some genes and untranslated intergenic regions, however, differs significantly from phage to phage: for example, the degree of amino acid sequence homology of the gene product is averaged at 47.7% between alpha 3 and phi X174 and 46.9% between alpha 3 and G4, and alpha 3 has a remarkable longer intergenic region composed of 758 nucleotides between the genes H and A compared with the counterparts of phi X174 and G4. Meanwhile, in vivo experiments of genetic complementation showed that alpha 3 can use none of the gene products of phi X174 and G4, whereas the related phage phi K can rescue alpha 3 nonsense mutants of the genes B, C, D and J. These sequencing and in vivo rescue results indicated that alpha 3 is closely related to phi K, but distantly remote from phi X174 or G4, and supported an evolutional hypothesis which has been so far proposed that the isometric phages are classified into three main groups: the generic representatives are phi X174, G4 and alpha 3.

Amino Acid Sequence↗

The unc-18 gene encodes a novel protein affecting the kinetics of acetylcholine metabolism in the nematode Caenorhabditis elegans.

Genes affecting acetylcholine (ACh) levels without influencing choline acetyltransferase activity have been identified in Caenorhabditis elegans. We have examined one such gene, unc-18. We isolated a transposon-insertion allele for unc-18 and used it to clone a genomic region containing the unc-18 locus. The unc-18 location within this region was determined by rescuing the unc-18 mutant phenotype in a germ-line transformation experiment and identifying transcripts affected by four independent unc-18 mutations. A single-sized poly(A)+ RNA was synthesized from the gene. Expression of the transcript appears to be stage specific: The transcript is found in abundance at the early larval stage but in decreased amounts at the fourth larval and the adult stages. These results show that the unc-18 gene plays a role in development as well as in the kinetics of ACh metabolism.

Acetylcholine↗

Properties of the bacteriophage alpha 3 mutants with deletion and/or insertion in the complementary strand origin.

Bacteriophage alpha 3 origin of complementary strand DNA synthesis (-ori) contains two potential secondary loop structures (I and II), which have been implicated in direct recognition sites for host Escherichia coli dnaG protein. We have introduced nucleotide deletion or insertion within the -ori region, by nuclease digestion and polymerase treatment of alpha 3 replicative form DNA. Deletion mutants (delo) showing the following in vivo properties were isolated: minute plaque size, longer latent period, and reduction both in phage yield and viral DNA synthesis as compared with the wild-type phage. In addition, several strains among the delo mutants did not grow on host E. coli dnaB cells at 42 degrees C. These results suggest that certain type of deletion in the -ori region converts simple priming of the complementary strand synthesis to a more complicated phi X174-type initiation that depends on the primosome, rather than on dnaG protein alone.

Bacteriophage phi X 174↗

Novel replication mutant of microvirid phage alpha 3 deleted in the complementary strand origin.

The bacteriophage alpha 3 origin of complementary strand DNA synthesis (-ori) contains two potential secondary loop structures (I and II), which have been implicated as direct recognition sites for host Escherichia coli DnaG protein. To elucidate to what extent such structures are essential, we introduced a nucleotide deletion within the -ori region, by nuclease digestion of alpha 3 replicative form DNA. A mutant, delB, thus constructed had a 121 nucleotide deletion within the -ori region and was completely lacking in the two putative hairpin loops, I and II. The delB mutant formed smaller plaques on the host E. coli C and had a longer latent period, but the mean burst size at 37 degrees C was almost the same (400 phages) as that of the wild type. In contrast to the parental phage, growth of the mutant depends on host dnaB and dnaC functions. These results indicate that the prototype secondary structures in the alpha 3 origin of complementary strand synthesis are dispensable for delB and that the alpha 3 mutant has an additional replication origin whose function is dependent on DnaB and DnaC proteins, rather than on DnaG protein alone.

Bacteriophages↗

Possible finger structure in gene A protein of Microviridae.

Microvirid phages alpha 3 and phi K encode for A protein which functions in initiation of the viral DNA synthesis. By nucleotide sequencing analysis, we have found that each gene A protein has 'finger motif structure' which conserves two cysteine and histidine residues similar to the consensus sequence deduced from more than thirty finger motifs reported from many eukaryotic regulatory proteins. In closely related phages, phi X174 and G4, we have detected the same structures in their gene A proteins also.

Amino Acid Sequence↗

Mutational analysis of the bacteriophage alpha 3 origin of complementary DNA synthesis: in vivo properties of mutants.

Bacteriophage alpha 3 origin of complementary strand DNA synthesis contains two potential secondary loop structures, I and II, which have been implicated in direct recognition sites for host Escherichia coli dnaG protein. To elucidate the function of the hairpin loops, we have introduced point mutations within the stem of the hairpin II so as to disturb its base-pairings. A mutant, oriAA, which had two point mutations in the region, formed minute plaques on E. coli host cells and its mean burst size at 37 degrees C was about 50, whereas that of wild-type was 250. In addition, the growth of oriAA at 42 degrees C was thermosensitive and the burst size was reduced to 5. From the oriAA, a revertant-like phage oriGA occurred spontaneously with a high-frequency of about 2.10(-2). It retained one point mutation and the plaque size and phage yield were nearly same as those of wild-type. These results are discussed with respect to the role of secondary structure as well as specific nucleotide sequence in the recognition site for the dnaG protein.

Base Sequence↗

RNA transfection of Escherichia coli by electroporation.

Cells of Escherichia coli were efficiently transfected with Q beta phage RNA by electroporation. A single voltage shock at 6.25 kV/cm with a 25 microF capacitor resulted in an infectivity yield considerably higher than that attained by a lysozyme-EDTA spheroplast method or a CaCl2 procedure. A linear relationship was found between concentration of the input RNA and yield of the transfectants, over a wide range. Efficiency of the electroporation-mediated transfection (electrotransfection) was increased by addition of certain sodium salts but decreased by preincubation in a Tris buffer containing sucrose.

Bacteriophages↗

Properties of electroporation-mediated DNA transfer in Escherichia coli.

Efficient and reproducible DNA-transfection was attained in E. coli, by electroporation. The yield of the transfectants was affected by pretreatment of the recipient cells as well as by the composition of the electroporation medium. Using a single pulse procedure, relationships among the electrical parameters, the transfection efficiency, and the cellular viability were investigated in 10 mM Tris-HCl buffer (pH 7.5) containing 5% sucrose. Certain sodium salts (e.g., citrate, phosphate, and sulfate) were promotive, whereas Mg2+, DEAE-dextran, and polyvinylpyrrolidone were inhibitory to the transfection. Heterologous nucleic acids (native DNA, denatured DNA, and tRNA) exerted only a marginal effect on transfection with a viral replicative-form DNA. The efficiency of DNA transfer was affected by culture conditions, and bacteria grown at a higher temperature were more competent. The electroporation system was more efficient than an improved CaCl2 method, not only in transfection with viral single- and double-stranded DNAs, but also in transformation with plasmid DNAs.

Calcium Chloride↗