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K Taira

Publications and source records attributed to K Taira.

At least 73 records · Page 4Linked to original sources
PubMed2000

Novel sugar-binding specificity of the type XIII xylan-binding domain of a family F/10 xylanase from Streptomyces olivaceoviridis E-86.

The type XIII xylan-binding domain (XBD) of a family F/10 xylanase (FXYN) from Streptomyces olivaceoviridis E-86 was found to be structurally similar to the ricin B chain which recognizes the non-reducing end of galactose and specifically binds to galactose containing sugars. The crystal structure of XBD [Fujimoto, Z. et al. (2000) J. Mol. Biol. 300, 575-585] indicated that the whole structure of XBD is very similar to the ricin B chain and the amino acids which form the galactose-binding sites are highly conserved between the XBD and the ricin B chain. However, our investigation of the binding abilities of wt FXYN and its truncated mutants towards xylan demonstrated that the XBD bound xylose-based polysaccharides. Moreover, it was found that the sugar-binding unit of the XBD was a trimer, which was demonstrated in a releasing assay using sugar ranging in size from xylose to xyloheptaose. These results indicated that the binding specificity of the XBD was different from those of the same family lectins such as the ricin B chain. Somewhat surprisingly, it was found that lactose could release the XBD from insoluble xylan to a level half of that observed for xylobiose, indicating that the XBD also possessed the same galactose recognition site as the ricin B chain. It appears that the sugar-binding pocket of the XBD has evolved from the ancient ricin super family lectins to bind additional sugar targets, resulting in the differences observed in the sugar-binding specificities between the lectin group (containing the ricin B chain) and the enzyme group.

Binding Sites↗
PubMed2000

ATF-2 has intrinsic histone acetyltransferase activity which is modulated by phosphorylation.

Transcription factors carry functional domains, which are often physically distinct, for sequence-specific DNA binding, transcriptional activation and regulatory functions. The transcription factor ATF-2 is a DNA-binding protein that binds to cyclic AMP-response elements (CREs), forms a homodimer or heterodimer with c-Jun, and stimulates CRE-dependent transcription. Here we report that ATF-2 is a histone acetyltransferase (HAT), which specifically acetylates histones H2B and H4 in vitro. Motif A, which is located in the HAT domain, is responsible for the stimulation of CRE-dependent transcription; moreover, in response to ultraviolet irradiation, phosphorylation of ATF-2 is accompanied by enhanced HAT activity of ATF-2 and CRE-dependent transcription. These results indicate that phosphorylation of ATF-2 controls its intrinsic HAT activity and its action on CRE-dependent transcription. ATF-2 may represent a new class of sequence-specific factors, which are able to activate transcription by direct effects on chromatin components.

Acetyltransferases↗
PubMed2000

Significant change in the structure of a ribozyme upon introduction of a phosphorothioate linkage at P9: NMR reveals a conformational fluctuation in the core region of a hammerhead ribozyme.

A modified hammerhead ribozyme (R32S) with a phosphorothioate linkage between G(8) and A(9), a site that is considered to play a crucial role in catalysis, was examined by high-resolution 1H and (31)P nuclear magnetic resonance (NMR) spectroscopy. Signals due to imino protons that corresponded to stems were observed, but the anticipated signals due to imino protons adjacent to the phosphorothioate linkage were not detected and the (31)P signal due to the phosphorothioate linkage was also absent irrespective of the presence or absence of the substrate. (31)P NMR is known to reflect backbone mobility, and thus the absence of signals indicated that the introduction of sulfur at P9 had increased the mobility of the backbone near the phosphorothioate linkage. The addition of metal ions did not regenerate the signals that had disappeared, a result that implied that the structure of the core region of the hammerhead ribozyme had fluctuated even in the presence of metal ions. Furthermore, kinetic analysis suggested that most of the R32S-substrate complexes generated in the absence of Mg(2+) ions were still in an inactive form and that Mg(2+) ions induced a further conformational change that converted such complexes to an activated state. Finally, according to available NMR studies, signals due to the imino protons of the central core region that includes the P9 metal binding site were broadened or not observed, suggesting that this catalytically important region might be intrinsically flexible. Our present analysis revealed a significant change in the structure of the ribozyme upon the introduction of the single phosphorothioate linkage at P9 that is in general considered to be a conservative modification.

Base Sequence↗
PubMed2000

A simple and efficient method to determine the terminal sequences of restriction fragments containing known sequences.

We present an improvement of the inverse PCR method for the determination of end sequences of restriction fragments containing unknown DNA sequences flanked by known segments. In this approach, a short "bridge" DNA is inserted during the self-ligation step of the inverse PCR technique. This bridge DNA acts as primer annealing sites for amplification and subsequent direct sequencing. Successive PCR amplifications enable selective amplification of the unknown sequences from a complex mixture. Unlike previously described methods, our method does not require special materials, such as synthetic adapters or biotinylated primers that must be prepared each time to adapt the target. Furthermore, no complex steps such as dephosphorylation or purification are needed. Our method can save time and reduce the cost of cloning unknown sequences; it is ideal for routine, rapid gene walking. We applied this method to a GC-rich bacterial genome and succeeded in determining the end sequences of a 4.5-kb fragment.

Chromosome Walking↗
PubMed2000

A further investigation and reappraisal of the thio effect in the cleavage reaction catalyzed by a hammerhead ribozyme.

We synthesized three types of 11mer substrate, namely the natural substrate S11O and the thio-substituted substrates S11 S pS and S11 R pS, in which the respective pro-S p and pro-R p oxygen atoms were replaced by sulfur, and subjected them to detailed kinetic analysis in the cleavage reaction catalyzed by a hammerhead ribozyme. In agreement with previous findings, in the presence of Mg(2+)or Ca(2+)ions the rate of ribozyme-catalyzed cleavage of S11 S pS was as high as that of S11O, whereas the corresponding rate for S11 R pS was nearly four orders of magnitude lower than that for either S11O or S11 S pS. However, the rate of the ribozyme-catalyzed reaction with each of the three substrates was enhanced by Cd(2+)ions. Such results have generally been taken as evidence that supports the direct interaction of the sulfur atom at the R p position of the cleavage site with the added Cd(2+)ion. However, our present analysis demonstrates that (i) the added Cd(2+)ion binds at the P9 site; (ii) the bound Cd(2+)ion at the P9 site replaces two Mg(2+)or two Ca(2+)ions, an observation that suggests a different mode of interaction with the added Cd(2+)ion; and, most importantly and in contrast to the conclusion reached by other investigators, (iii) the Cd(2+)ion does not interact with the sulfur atom at the R p position of the scissile phosphate either in the ground state or in the transition state.

Anions↗
PubMed2000

Control of the functional activity of an antisense RNA by a tetracycline-responsive derivative of the human U6 snRNA promoter.

In an effort to develop a regulatable derivative of the promoter of the human gene for U6 snRNA, we generated several constructs composed of the human U6 snRNA promoter and sequences derived from the gene for the tetracycline operator of a prokaryotic tetracycline resistance transposon. One of the constructs had strong transcriptional activity in the presence of tetracycline that was equivalent to 80% of the activity of the wild-type promoter. Furthermore, the transcriptional activity was almost completely repressed in the absence of tetracycline. Transcriptional activity became detectable within 4 hr after the addition of tetracycline to the culture medium. We used this system to control the functional activity of an antisense RNA for a chimeric gene derived from genes for the epidermal growth factor receptor (EGFR) and green fluorescent protein (GFP). A plasmid that expressed the chimeric gene and a plasmid that expressed the antisense RNA under the control of the inducible U6 promoter were used to cotransfect HeLa cells that were producing the tetracycline repressor protein (Tet R). Addition of tetracycline to the culture medium 12 hr after transfection resulted in the almost complete disappearance of the fluorescent signal due to the chimeric protein within 24 hr. Our results suggest that this expression system might be a useful tool for controlling the expression of functional RNAs, such as aptamers and antisense RNAs, both in basic research and in gene therapy.

Base Sequence↗
PubMed2000

Effects of cetyltrimethylammonium bromide on reactions catalyzed by maxizymes, a novel class of metalloenzymes.

We demonstrated previously that some shortened forms of hammerhead ribozymes had high cleavage activity that was similar to that of the wild-type parental hammerhead ribozyme. Moreover, the active species appeared to form dimeric structures with a common stem II (in order to distinguish monomeric forms of conventional minizymes that have low activity from our novel dimers with high-level activity, the latter very active short ribozymes were designated 'maxizymes'). The dimers can be homodimeric (with two identical binding sequences) or heterodimeric (with two different binding sequences). In the case of heterodimers, they are in equilibrium with inactive homodimers. In this study, we investigated the effects of cationic detergent, cetyltrimethylammonium bromide (CTAB), on reactions catalyzed by a variety of maxizymes. The slope of close to unity in profiles of pH versus rate demonstrated that the deprotonation was important in catalysis and that the rate-limiting chemical step was followed in these reactions. Addition of appropriate amounts of CTAB enhanced the activity of a variety of maxizymes. The activity of our least stable, least active maxizyme was enhanced 100-fold by CTAB. Thus, CTAB effectively enhanced the conversion of kinetically trapped inactive conformations to active forms. Moreover, we suggest that the activity and specificity of catalytic RNAs in vivo might be better estimated if their reactions are monitored in vitro in the presence of appropriate amounts of CTAB.

Base Pairing↗
PubMed2000

Limitations of exogenous L-arginine in exerting a cytoprotective effect on hepatic ischemia/reperfusion injury.

To test whether or not the L-arginine/nitric oxide (NO) pathway induces a protective effect, we investigated the effect of exogenous L-arginine on hepatic ischemia/reperfusion (I/R) injury, using ex vivo perfusion of the isolated rat liver. The rat liver was removed and preserved in cold saline for 60 min, followed by 120 min of reperfusion with oxygenated perfusate at 37 degrees C. Either 600 mg/kg of L-arginine (groups 1 and 4), D-arginine (group 2), N(G)-nitro-L-arginine methyl ester (L-NAME) (group 3), or saline (group 5) were administered through the portal vein starting from 5 min before reperfusion to 5 min after reperfusion. In group 4, 600 mg/kg of L-NAME was preadministered at 10 min prior to the administration of L-arginine. The intrahepatic nitric oxide (NO) levels showed only a temporal elevation (227% +/- 70% of the pre-reperfusion levels at 5 min) after reperfusion in group 1. Pretreatment with L-NAME suppressed the elevation of the NO levels immediately after reperfusion in group 4. The lactate dehydrogenase release to the effluent perfusate significantly decreased and the histological findings showed that the sinusoidal damage observed after reperfusion was mitigated in group 1 more than in the other groups. These results thus suggest that exogenous L-arginine produced a relatively small amount of NO and therefore resulted in a slight decrease of hepatic I/R injury.

Animals↗
PubMed2000

Surgical treatment of a sigmoid volvulus associated with megacolon: report of a case.

Sigmoid volvulus occurring concomitantly with megacolon is an uncommon cause of bowel obstruction, and various approaches to treatment have been proposed. We report herein a case of sigmoid volvulus with megacolon that was successfully treated by elective surgery following endoscopic reduction during the same hospital stay. A 70-year-old woman was admitted to our hospital with abdominal pain, distension, and severe constipation. Physical examination, plain abdominal X-ray, and barium enema confirmed a sigmoid volvulus and further examinations revealed concomitant megacolon. An elective sigmoid colectomy was performed following successful endoscopic decompression. The postoperative course was uneventful and there was no residual colonic dysmotility. Histologically, no aganglionic tissue was observed in the resected specimen.

Abdominal Pain↗
PubMed2000

Marked elevation in serum apolipoprotein E in a case of heterozygous cholesteryl ester transfer protein deficiency.

The subject was a 57-year-old Japanese woman with a body mass index of 21.2 kgm(-2). Her serum total cholesterol (TC), triglycerides (TG) and HDL-cholesterol levels were 7.11 mmoll(-1), 0.53 mmoll(-1) and 2.05 mmoll(-1), respectively. She had a marked increase of serum apolipoprotein (Apo) E concentration of 25 mgdl(-1) with normal concentrations of serum Apo A-I, A-II, B, C-II and C-III. Polymerase chain reaction-restriction fragments length polymorphism analysis of the cholesteryl ester transfer protein (CETP) gene from this subject revealed the heterozygous nucleotide change causing a Asp442 to Gly substitution (D442G) in the CETP protein. For comparison, 11 unrelated female subjects with this mutation (age, 57+/-5.1 years; BMI, 22+/-1.5 kgm(-2); TC, 7.23+/-1.16 mmoll(-1); TG, 1.44+/-0.80 mmoll(-1); HDL-C, 2.47+/-0.53 mmoll(-1)) were found to have a serum Apo E concentration of 7+/-1.5 mgdl(-1), about a third of the patient's concentration. The lipoprotein profile of the proband's serum analyzed by disk polyacrylamide gel electrophoresis showed a trace amount of VLDL. A vitamin A fat-loading test showed little increase in serum triglycerides and retinyl palmitate levels compared with control subjects at 2, 4 and 6 h after fat loading. Ultracentrifugation analysis of her serum revealed no detectable Apo E in the VLDL fraction but showed a large amount of Apo E in the HDL fraction, in contrast to a normal control, who had Apo E in the VLDL fraction as well as in the HDL fraction. Sequence analysis of the Apo E gene from the subject showed no nucleotide changes in exon 3 and exon 4, which code the mature Apo E protein, indicating there is no structural abnormality in the Apo E protein. Direct sequence analysis of the LDL receptor gene also did not show any nucleotide change. Based on these findings, it was hypothesized that the marked increase of Apo E in the patient's serum was caused by a decreased transfer of Apo E from HDL particles to TG-rich lipoproteins or impaired uptake of Apo E-containing HDL by LDL receptor or remnant receptor, due presumably to a dysfunction of these receptors in the patient.

Apolipoproteins E↗
PubMed2000

Chemical and enzymatic probing of effector-mediated changes in the conformation of a maxizyme.

The protein encoded by chimeric BCR-ABL mRNA causes chronic myelogenous leukemia (CML). We showed previously that a novel allosterically controllable ribozyme, of the type known as a maxizyme, can cleave this mRNA, with high specificity and high-level activity in vivo. We designed the maxizyme in such a way that it was able to form an active core with which to capture the catalytically indispensable Mg2+ ions only in the presence of the BCR-ABL mRNA junction. In order to probe the putative conformational changes, we used a weakly alkaline solution (pH 9.2) in the presence of 25 mM Mg2+ ions to hydrolyze differentially phosphodiester bonds that were located in different environments. Phosphodiester bonds in single-stranded regions were clearly more susceptible to attack by alkali than those within a double-stranded helix. As indicated by earlier data obtained in vivo, our results demonstrated that the active conformation was achieved only in the presence of the junction within the chimeric BCR-ABL mRNA. Moreover, we demonstrated that the use of mild alkaline solutions to probe RNA structures is very informative.

Base Sequence↗
PubMed2000

Allosterically controllable maxizymes cleave mRNA with high efficiency and specificity.

Ribozymes are small and versatile nucleic acids that can cleave RNA molecules at specific sites. However, because of the limited number of cleavable sequences on the target mRNA, in some cases conventional ribozymes do not have precise cleavage specificity. To overcome this problem, an allosteric version (a maxizyme) was developed that displayed activity and specificity in vivo. More than five custom-designed maxizymes have demonstrated sensor functions, which indicates that the technology might be broadly applicable in molecular biology and possibly in the clinic.

Allosteric Regulation↗
PubMed2000

Differences among mechanisms of ribozyme-catalyzed reactions.

The catalytic properties of ribozymes depend on the sophisticated structures of the respective ribozyme-substrate complexes. Although it has been suggested that ribozyme-mediated cleavage of RNA occurs via a rather strictly defined mechanism, recent findings have clearly demonstrated the diversity of reaction mechanisms.

Acids↗