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T Ueda

Publications and source records attributed to T Ueda.

At least 703 records · Page 39Linked to original sources
PubMed1995

[Experimental study on embolic materials for simultaneous segmental embolization through transarterial route].

To determine suitable embolic materials for simultaneous arterioportal embolization through the arterial route, transcatheter arterial embolization (TAE) using iodized oil (Lipiodol) mixed with monomeric n-butyl-2-cyanoacrylate, with absolute ethanol, or mixed with Gelfoam powder was carried out in 14 dogs. Following TAE, the distribution of Lipiodol in hepatic artery, peribiliary plexus, and portal vein was analyzed by soft tissue x-ray radiography and en bloc silver impregnation. As a result, Lipiodol mixed with absolute ethanol, and Gelfoam powder was considered to be the most reasonable embolic materials for this purpose.

Animals↗
PubMed1995

Interaction of mitochondrial elongation factors Tu.Ts with aminoacyl-tRNA.

The interaction between the bovine mitochondrial translational elongation factor Tu.Ts complex (EF-Tu.Tsmt) and aminoacyl-tRNA has been investigated using a nuclease protection assay and fluorescence enhancement of [AEDANS-s2C]Tyr-tRNA(Tyr). The equilibrium dissociation constant, Kd, for the EF-Tu.Tsmt:GTP:E. coli Phe-tRNA complex is approximately 50 nM. A similar binding constant (30 nM) is obtained using bovine mitochondrial Phe-tRNA. The equilibrium binding constant for the EF-Tu.Tsmt:GTP:yeast [AEDANS-s2C]Tyr-tRNA(Tyr) complex is approximately 4 nM when determined using the fluorescence enhancement assay.

Animals↗
PubMed1994

A UGU sequence in the anticodon loop is a minimum requirement for recognition by Escherichia coli tRNA-guanine transglycosylase.

Escherichia coli tRNA-guanine transglycosylase is an enzyme which catalyzes replacement of guanine (G34) of tRNA(Asp), tRNA(Asn), tRNA(His) and tRNA(Tyr) by free guanine or free preQ1 base by a base exchange reaction in the biosynthesis of queuosine (Q) (Okada, N., and Nishimura, S. (1979) J. Biol. Chem. 254, 3061-3066). The gene encoding for this enzyme was amplified from the E. coli genome by polymerase chain reaction and inserted into an overexpression vector, pJLA503. The enzyme was overexpressed by heat induction in E. coli transformed by this recombinant plasmid and purified to homogeneity by two column chromatographies. The sequence requirement in tRNA for recognition by this enzyme was investigated using minihelices corresponding to the anti-codon arm of E. coli tRNA(His). Two uridine residues (U33, U35) were found to be prerequisite for such recognition by this enzyme. Position 32 required pyrimidines, because the enzyme activity toward the minihelices was markedly reduced or entirely lost when this residue was replaced by purines or was deleted. Adenosine at position 37 and the G30-C40 base pair were not essential despite their conservation. Our results suggest that the enzyme recognizes the U33-G34-U35 sequence in the anti-codon loop and not the tertiary structure of tRNA itself.

Anticodon↗
PubMed1994

Higher-order structure of bovine mitochondrial tRNA(SerUGA): chemical modification and computer modeling.

On the basis of enzymatic probing and phylogenetic comparison, we have previously proposed that mammalian mitochondrial tRNA(sSer) (anticodon UGA) possess a slightly altered cloverleaf structure in which only one nucleotide exists between the acceptor stem and D stem (usually two nucleotides) and the anticodon stem consists of six base pairs (usually five base pairs) [Yokogawa et al. (1991) Nucleic Acids Res. 19, 6101-6105]. To ascertain whether such tRNA(sSer) can be folded into a normal L-shaped tertiary structure, the higher-order structure of bovine mitochondrial tRNA(SerUGA) was examined by chemical probing using dimethylsulfate and diethylpyrocarbonate, and on the basis of the results a tertiary structure model was obtained by computer modeling. It was found that a one-base-pair elongation in the anticodon stem was compensated for by multiple-base deletions in the D and extra loop regions of the tRNA(SerUGA), which resulted in preservation of an L-shaped tertiary structure similar to that of conventional tRNAs. By summarizing the findings, the general structural requirements of mitochondrial tRNAs necessary for their functioning in the mitochondrial translation system are considered.

Alkylating Agents↗
PubMed1994

Identification of the complement iC3b binding site in the beta 2 integrin CR3 (CD11b/CD18).

The divalent cation-dependent interaction of the beta 2 integrin CR3 (CD11b/CD18) with the major complement opsonic C3 fragment iC3b is an important component of the central role of CR3 in inflammation and immune clearance. In this investigation we have identified the iC3b binding site in CR3. A recombinant fragment representing the CR3 A-domain, a 200-amino acid region in the ectodomain of the CD11b subunit, bound to iC3b directly and in a divalent cation-dependent manner. The iC3b binding site was further localized to a short linear peptide that also bound iC3b directly and inhibited iC3b binding to the A-domain as well as to CR3 expressed by human neutrophils. These data establish a major recognition function for the integrin A-domain and have important implications for development of novel antiinflammatory therapeutics.

Amino Acid Sequence↗
PubMed1994

Primary and higher order structures of nematode (Ascaris suum) mitochondrial tRNAs lacking either the T or D stem.

By fractionation using polyacrylamide gel electrophoresis and/or a preparative hybrid selection method employing solid-phase DNA probes, we prepared and characterized mitochondrial tRNAs from the body wall muscle of Ascaris suum, all of which are thought to lack either the T stem or the D stem from their gene sequences (Okimoto, R., and Wolstenholme, D. R. (1990) EMBO J. 10, 3405-3411). Some of the partially purified tRNAs were appreciably aminoacylated with an extract of A. suum mitochondria. The three species sequenced had CCA sequence at their 3'-ends, and tRNA(Met) had 5-formylcytidine at the anticodon first position, a new modified nucleoside found at the same position of bovine mitochondrial tRNA(Met) (Moriya, J., Yokogawa, T., Wakita, K., Ueda, T., Nishikawa, K., Crain, P. F., Hashizume, T., Pomerantz, S. C., McCloskey, J. A., Kawai, G., Hayashi, N., Yokoyama, S., and Watanabe, K. (1994) Biochemistry 33, 2234-2239). Enzymatic probing of these tRNAs supported the secondary structural model proposed by Okimoto and Wolstenholme in the reference cited above. Chemical probing of tRNA(Phe) demonstrated the existence of tertiary interactions between the (T arm-variable loop)-replacement loop and the D arm. The results suggest that these tertiary interactions enable the bizarre tRNAs of nematode mitochondria to maintain an L-shape-like structure in order to function in the nematode mitochondrial translation system.

Animals↗
PubMed1994

Isolation and characterization of 101-succinimide lysozyme that possesses the cyclic imide at Asp101-Gly102.

Lytic activity of lysozyme solution gradually increased on incubation at pH 4, 40 degrees C. When the solution was analyzed by use of cation-exchange HPLC at pH 5, a new peak appeared with increased incubation time. The derivative in the new peak was identified to be 101-succinimide lysozyme in which cyclic imide formed at Asp101-Gly102. The formation of 101-succinimide lysozyme increased with increases in concentration of acetate buffer. Kinetic analysis of the formation of 101-succinimide lysozyme indicated that the cyclic imide was stable below pH 5 due to suppression of the hydrolysis of cyclic imide. Its lytic activity against M. luteus, which has a negative charge, was 165% at pH 7, whereas its activity against glycol chitin, which has no charge, was 90%. Since the lytic activity of Asn101 lysozyme, where one negative charge is eliminated, reached a maximum of 125%, it was suggested that the increase of lytic activity against bacterial cells in 101-succinimide lysozyme was due not only to the disappearance of the negative charge at Asp101 but also to the removal of steric hindrance at the upper part of the active site cleft.

Acetates↗
PubMed1994

Nuclease resistance of an extraordinarily thermostable mini-hairpin DNA fragment, d(GCGAAGC) and its application to in vitro protein synthesis.

The nuclease resistance of a short, thermostable mini-hairpin, d(GCGAAGC), and other related hairpins was examined. Hairpins possessing a purine-rich (GAA) or (GAAA) loop appeared to be more resistant against nucleases than those with a pyrimidine-rich loop or single-stranded oligomers. Among 8 kinds of oligodeoxyribonucleotides examined, the fragment most resistant against nucleases was a hairpin with the sequence of d(CGCGAAGCG). This hairpin was then utilized for the stabilization of mRNA in an in vitro translation system; the 3'-terminal region of an mRNA was hybridized with an oligodeoxyribonucleotide including the sequence complementary to the 3'-terminus of the mRNA tagged with the nuclease-resistant d(CGCGAAGCG) hairpin sequence. By using this method, dihydrofolate reductase (DHFR) mRNA was stabilized against nucleases contaminating a cell-free translation system of E.coli, with a consequent increase in protein synthesis efficiency of 200%.

Base Sequence↗
PubMed1994

Efficient expression of E. coli dihydrofolate reductase gene by an in vitro translation system using phosphorothioate mRNA.

Dihydrofolate reductase (DHFR) of Escherichia coli (E. coli) was synthesized in a cell-free translation system of E. coli directed by phosphorothioate-containing mRNA (thio-mRNA) which was polymerized by an in vitro transcription of the DHFR gene in the presence of SP diastereomers of ribonucleoside 5'-O-(1-thiotriphosphates). The molecular weights of the products thus obtained were identical to those with the unsubstituted mRNA. Furthermore, the thio-mRNA for DHFR showed higher translational activities than the corresponding unsubstituted mRNA. It is suggested that this effectiveness resulted from the higher stability of thio-mRNA in the cell-free translation system. Amongst the various types of thio-mRNAs, the single substitution of adenosine residues was most effective in translational activity. This higher translational activity of thio-mRNA compared with the unsubstituted mRNA was also demonstrated in a continuous flow cell-free system originally developed by Spirin et al. (1988). Therefore, introduction of sulfur atoms into phosphodiester bonds of mRNA appears to be a useful strategy for the stabilization of mRNA in large-scale protein production in vitro.

Base Sequence↗
PubMed1994

A double-blind controlled study of granulocyte colony-stimulating factor started two days before induction chemotherapy in refractory acute myeloid leukemia. Kohseisho Leukemia Study Group.

We conducted a prospective, double-blind controlled study to determine the efficacy of a recombinant granulocyte colony-stimulating factor (G-CSF, 200 microgram/m2) starting daily from 2 days before an induction therapy until neutrophils recovered to above 1,500/microL or until 35 days after the therapy in 58 patients with relapsed or refractory acute myeloid leukemia (AML). Twenty-eight patients in the G-CSF group showed significantly faster recovery of neutrophils (P < .001) than 30 patients in the placebo group. The incidence of febrile episodes and of documented infections was almost the same in both groups. However, among 39 patients who did not show any infectious episodes during the 2-week period after the start of chemotherapy, the incidence of documented infections after the third week tended to be lower in the G-CSF group, but not statistically significantly. There was no evidence that G-CSF stimulated the growth of AML cells in the bone marrow during the 2-day period before the chemotherapy, nor that G-CSF accelerated the regrowth of AML cells during the 5-week period after the therapy. Fifty percent of patients in the G-CSF group and 37% in the placebo group had complete remission (CR). Although the rate was higher in the G-CSF group, the difference was not statistically significant (P = .306). There was no difference between the two groups in event-free survival of all patients and in disease-free survival of patients who had achieved CR.

Adolescent↗
PubMed1994

A novel modified nucleoside found at the first position of the anticodon of methionine tRNA from bovine liver mitochondria.

Methionine tRNA was purified from bovine liver mitochondria, and its nucleotide sequence was determined. The tRNA possesses only three posttranscriptionally modified nucleosides, two pseudouridines in the anticodon and T stems and a previously unknown nucleoside specified by the gene sequence as cytidine, in the first position of the anticodon. Structure analysis of the anticodon nucleoside by mass spectrometry revealed a molecular mass 28 Da greater than that of cytidine, and unmodified ribose, with substitution at C-5 implied by hydrogen-deuterium exchange experiments. Proton NMR of the intact tRNA showed presence of a formyl moiety, thus leading to the candidate structure 5-formylcytidine (f5C), not a previously known compound. The structure assignment was confirmed by chemical synthesis and comparison of data from combined HPLC/mass spectrometry and proton NMR for the natural and synthetic nucleosides. The potential function of f5C in the tRNA(Met) anticodon is discussed with regard to codon-anticodon interactions.

Animals↗
PubMed1994

Higher-order structure of bovine mitochondrial tRNA(Phe) lacking the 'conserved' GG and T psi CG sequences as inferred by enzymatic and chemical probing.

Bovine mitochondrial (mt) phenylalanine tRNA (tRNA(Phe)), which lacks the 'conserved' GG and T psi YCG sequences, was efficiently purified by the selective hybridization method using a solid phase DNA probe. The entire nucleotide sequence of the tRNA, including modified nucleotides, was determined and its higher-order structure was investigated using RNaseT2 and chemical reagents as structural probes. The D and T loop regions as well as the anticodon loop region were accessible to RNaseT2, and the N-3 positions of cytidines present in the D and T loops were easily modified under the native conditions in the presence of 10mM Mg2+. On the other hand, the nucleotides present in the extra loop were protected from the chemical modification under the native conditions. From the results of these probing analyses and a comparison of the sequences of mitochondrial tRNA(Phe) genes from various organisms, it was inferred that bovine mt tRNA(Phe) lacks the D loop/T loop tertiary interactions, but does have the canonical extra loop/D stem interactions, which seem to be the main factor for bovine mt tRNA(Phe) to preserve its L-shaped higher-order structure.

Animals↗
PubMed1994

Existence of nuclear-encoded 5S-rRNA in bovine mitochondria.

A number of proteins functioning in mitochondria are synthesized in the cytoplasm and imported into the mitochondria via specific transport systems. In mammals, on the contrary, mitochondrial membranes have generally been considered to be impermeable to nucleic acids. However, here we show that an RNA with 120 nucleotides, the sequence of which is identical to that of the nuclear-encoded 5S RNA, exists in bovine mitochondria, although the mitochondrial genome encodes no 5S RNA gene. This RNA molecule was found to be retained in purified bovine mitochondria as well as in the mitoplasts, even after extensive treatment with an RNase, demonstrating that the 5S RNA is actually located inside the mitochondrial inner membrane. The 5S rRNA molecule was also shown to exist in mitochondria from rabbit and chicken.

Animals↗
PubMed1994

Formation of alpha-helix 88-98 is essential in the establishment of higher-order structure from reduced lysozyme.

Lys96 and Lys97 in lysozyme are located at the C terminus of alpha-helix 88-98. The positive charges of these residues are supposed to stabilize the helical structure, and these residues are conserved as the basic amino acids among c-type lysozymes. The renaturation rate of reduced mutant lysozyme, where both Lys96 and Lys97 were mutated together to Ala, was slower than that of native lysozyme at pH 8.0 and 37 degrees C by SH-SS interchange reactions. In order to investigate the reason, the peptide fragment 36-105 (where we can obtain information of the interaction between helix 88-98 and Trp62 and Trp63 residues) was prepared. CD spectra were compared between peptide fragment 36-105 and its acetylated form, where the positive charges of Lys96 and Lys97 were eliminated, and it was elucidated that the displacement of positive charges at the C terminus of the helix caused the shift of the advantageous structure of the fragment from alpha-helix to coil. Moreover, we obtained evidence that there was interaction of the helix with Trp62 and/or Trp63, which maintained a thermodynamically stable higher-order structure. Therefore, these results suggest that the formation of alpha-helical structure in 88-98 is a significant factor in the establishment of native structure from reduced lysozyme.

Amino Acid Sequence↗
PubMed1994

Characterization of serine and leucine tRNAs in an asporogenic yeast Candida cylindracea and evolutionary implications of genes for tRNA(Ser)CAG responsible for translation of a non-universal genetic code.

Five serine and three leucine isoaceptor tRNAs were purified from the asporogenic yeast Candida cylindracea, in which codon CUG is translated as serine instead of leucine, and their primary structures were determined. From the wobble hypothesis, it was assumed that one of the tRNA(Leu) species (Leu1), with the anticodon CmAA, corresponded to the UUG leucine codon, and that the remaining two leucine tRNAs (Leu2 and Leu3), with the same IAG anticodon sequence would decode the CUU, CUC and CUA codons as leucine, but not the CUG codon; this was clarified by an in vitro translation experiment with C.cylindracea using synthetic mRNAs containing the CUA or CUG codons. One of the serine tRNAs (Ser1) has already been demonstrated to have the anticodon CAG and to be responsible for translation of the codon CUG in C.cylindracea. Three of the other species of tRNA(Ser) (Ser2,3 and 4), with the anticodon sequences cm5UGA, IGA and CGA, can translate all four codons in the UCN codon box, while the remaining species (Ser5), with the anticodon GCU, corresponds to AGU and AGC serine codons. The gene sequences for these five serine and three leucine tRNAs were also determined, with the finding that only tRNA(Ser)CAG (Ser1) has an intron. At least five different types of tRNA(Ser)CAG genes exist in the genome of C.cylindracea. The nucleotide sequences of the flanking regions of these tRNA(Ser)CAG genes indicated that the tRNA(Ser)CAG gene has duplicated at least three times on the genome. The existence of multiple genes for tRNA(Ser)CAG on the genome may account for the observation that codon CUG is used very frequently in C.cylindracea. All of these tRNASerCAG genes contain the CCA sequence in their 3' termini, suggesting the possibility that during their multiplication process in the evolution of the C.cylindracea genome, the tRNA(Ser)CAG molecule was integrated into DNA via reverse transcription.

Base Sequence↗
PubMed1994

Unusual anticodon loop structure found in E.coli lysine tRNA.

Although both tRNA(Lys) and tRNA(Glu) of E. coli possess similar anticodon loop sequences, with the same hypermodified nucleoside 5-methylaminomethyl-2-thiouridine (mnm5s2U) at the first position of their anticodons, the anticodon loop structures of these two tRNAs containing the modified nucleoside appear to be quite different as judged from the following observations. (1) The CD band derived from the mnm5s2U residue is negative for tRNA(Glu), but positive for tRNA(Lys). (2) The mnm5s2U monomer itself and the mnm5s2U-containing anticodon loop fragment of tRNA(Lys) show the same negative CD bands as that of tRNA(Glu). (3) The positive CD band of tRNA(Lys) changes to negative when the temperature is raised. (4) The reactivity of the mnm5s2U residue toward H2O2 is much lower for tRNA(Lys) than for tRNA(Glu). These features suggest that tRNA(Lys) has an unusual anticodon loop structure, in which the mnm5s2U residue takes a different conformation from that of tRNA(Glu); whereas the mnm5s2U base of tRNA(Glu) has no direct bonding with other bases and is accessible to a solvent, that of tRNA(Lys) exists as if in some way buried in its anticodon loop. The limited hydrolysis of both tRNAs by various RNases suggests that some differences exist in the higher order structures of tRNA(Lys) and tRNA(Glu). The influence of the unusual anticodon loop structure observed for tRNA(Lys) on its function in the translational process is also discussed.

Anticodon↗