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Biomedical subjects

T Oshima

Publications and source records attributed to T Oshima.

At least 235 records · Page 13Linked to original sources
PubMed1996

A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 28.0-40.1 min region on the linkage map.

The 569,750 base pair sequence corresponding to the 28.0-40.1 min region on the genetic map of Escherichia coli K-12 (W3110) was determined. This region includes the replication terminus region and contained at least 549 potential open reading frames. Among them, 160 (29%) were previously reported, 174 (32%) were homologous to other known genes, 102 (18%) were identical or similar to hypothetical genes registered in databases, and the remaining 113 (21%) did not show a significant similarity to any other gene. Of interest was the finding of a large number of genes and gene clusters in and near the replication termination region which had been thought to be genetically silent. Those included a cluster of genes for fatty acid beta-oxidation, the third copy of the pot (spermidine/putrescine transport system) gene cluster, the second dpp (dipeptide transport system) operon, the second dsm (anaerobic dimethyl sulfoxide reductase) operon, a cluster of fim (fimbrial) genes and a DNA helicase-like gene with a high molecular weight. In addition, we found the dnaC- and dnaT-like genes in the cryptic prophage, Rac, and a number of genes originated probably from plasmids.

Chromosome Mapping↗
PubMed1996

A 460-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 40.1-50.0 min region on the linkage map.

The 465,813 base pair sequence corresponding to the 40.1-50.0 min region on the genetic map of Escherichia coli K-12 (W3110) was determined. Analysis of the sequence revealed that this region contained at least 466 potential open reading frames, of which 187 (40%) were previously reported, 105 (23%) were homologous to other known genes, 103 (22%) were identical or similar to hypothetical genes registered in databases, and the remaining 71 (15%) did not show a significant similarity to any other gene. At the 45.2-46.0 min region, we found a very large cluster of about 30 genes, whose functions are involved in the biosynthesis of polysaccharides as the components of outer membranes. In addition, we identified a new asn-tRNA gene, designated asnW, between the asnT and asnU genes and a new lysogenic phage attachment site as the cis-element.

Attachment Sites, Microbiological↗
PubMed1996

Electrostatic interaction between two domains of isocitrate dehydrogenase from Thermus thermophilus is important for the catalytic function and protein stability.

The role of electrostatic interaction between Lys96 and Glu147 of isocitrate dehydrogenase from Thermus thermophilus was investigated by site-directed mutagenesis. These two residues are located near the active site and involved in the interdomain interaction. Analyses of the catalytic properties and thermostability of the Glu147Gln mutant revealed that this interaction plays important roles in catalytic function and protein stability.

Amino Acid Sequence↗
PubMed1996

Eubacteria-type isocitrate dehydrogenase from an archaeon: cloning, sequencing, and expression of a gene encoding isocitrate dehydrogenase from a hyperthermophilic archaebacterium, Caldococcus noboribetus.

A gene coding for isocitrate dehydrogenase (ICDH) was cloned from a hyperthermophilic archaebacterium, Caldococcus noboribetus, and sequenced. The gene was preceded by a promoter-like sequence and was followed by a terminator-like sequence. The deduced amino acid sequence of C. noboribetus ICDH showed high similarities to eubacterial ICDH. In particular, extremely high identity scores were found for ICDHs from Vibrio sp. (48.2%) and Escherichia coli (47.9%). The gene was expressed in E. coli by connecting it with the T7 promoter. The molecular weight of the gene product was estimated to be 48,000, which is consistent with that calculated from the deduced amino acid sequence. The gene product showed NADP-dependent ICDH activity at 80 degrees C. While the host-derived ICDH was completely inactivated by treatment at 70 degrees C for 10 min, the ICDH from C. noboribetus showed much higher thermostability.

Amino Acid Sequence↗
PubMed1996

Cloning and sequencing of a gene encoding 16S ribosomal RNA from a novel hyperthermophilic archaebacterium NC12.

A hyperthermophile NC12 was newly isolated from Noboribetsu hot spring. To characterize this organism, a gene coding for 16S rRNA was cloned and sequenced. The 16S rRNA sequence from NC12 shows the highest similarity with those from Pyrodictium occultum and Desulfurococcus mobilis among the sequences in the database, indicating that NC12 belongs to a cluster of extreme thermophiles (Crenarchaeota) in the archaeal domain. However, since the highest identity score was only 91.2%, it is suggested that NC12 may constitute a new genus.

Archaea↗
PubMed1996

Redox-linked ionization of sulredoxin, an archaeal Rieske-type [2Fe-2S] protein from Sulfolobus sp. strain 7.

"Sulredoxin" of Sulfolobus sp. strain 7 is an archaeal soluble Rieske-type [2Fe-2S] protein and was initially characterized by several spectroscopic techniques (Iwasaki, T., Isogai, T., Iizuka, T. , and Oshima, T. (1995) J. Bacteriol. 177, 2576-2582). It appears to have tightly linked ionization affecting the redox properties of the protein, which is characteristic of the Rieske FeS proteins found as part of the respiratory chain. Sulredoxin had an Em(low pH) value of +188 +/- 9 mV, and the slope of pH dependence of the midpoint redox potential indicated two ionization equilibria in the oxidized form with pKa(ox1) of 6.23 +/- 0.22 and pKa(ox2) of 8.57 +/- 0.20. The absorption, CD, and resonance Raman spectra of oxidized sulredoxin are consistent with the proposed St2FeSb2Fe[N(His)]t2 core structure, and deprotonation of one of the two putative coordinated histidine imidazoles, having the pKa(ox2) of 8.57 +/- 0.20, causes a decrease in the midpoint redox potential, the change in the optical and CD spectra, and the appearance of a new Raman transition at 278 cm-1, without major structural rearrangement of the [2Fe-2S] cluster as well as the overall protein conformation. The redox-linked ionization of sulredoxin is also contributed by local changes involving another ionizable group having the pKa(ox1) of 6.23 +/- 0. 22, which is probably attributed to a certain positively charged amino acid residue that may not be a ligand by itself but located very close to the cluster. We suggest that sulredoxin provides a new tractable model of the membrane-bound homologue of the respiratory chain, the Rieske FeS proteins of the cytochrome bc1-b6f complexes.

Circular Dichroism↗
PubMed1996

Role of cytochrome b562 in the archaeal aerobic respiratory chain of Sulfolobus sp. strain 7.

The role of cytochrome b562, a fragile constituent of the respiratory terminal oxidase supercomplex of the thermoacidophilic archaeon, Sulfolobus sp. strain 7, was investigated spectroscopically in the membrane-bound state. Cytochrome b562 did not react with CO or cyanide in the membrane-bound state, while it was irreversibly modified to a CO-reactive form (b59) upon solubilization in the presence of cholate and LiCl. Cyanide titration analyses with the succinate-reduced membrane suggested that cytochrome b562 was upstream of both the "gy = 1.89' Rieske FeS cluster and the a-type cytochromes. These results show that the b-type cytochrome functions as an intermediate electron transmitter in the terminal oxidase supercomplex.

Aerobiosis↗
PubMed1996

Molecular cloning, sequencing, and heterologous expression of a novel zinc-containing ferredoxin gene from a thermoacidophilic Archaeon Sulfolobus sp. strain 7.

The gene encoding a novel zinc-containing ferredoxin from a hyperthermophilic and acidophilic archaeon (archaebacterium) Sulfolobus sp. strain 7 was cloned and sequenced. The DNA sequence predicts a 103 residue protein after removal of N-terminal methionine, which is in good agreement with the results of the protein analysis. Surprisingly, the residues responsible for binding a zinc atom were conserved among three other thermoacidophilic archaea. A common sequence stretch VXGXHXGHX8-17PXXLGXHGTX38-56KXDPV is proposed as a new zinc-binding motif, where three histidines and an aspartic acid are ligated to a zinc atom. The ferredoxin gene was expressed in Eschericia coli. The recombinant ferredoxin was indistinguishable from the protein purified from Sulfolobus sp. strain 7 cells by several criteria so far investigated except that the methylation of the 29th lysine was suppressed.

Amino Acid Sequence↗
PubMed1996

Na+,K(+)-ATPase activity in the cochlear lateral wall of the gerbil.

We examined Na+,K(+)-ATPase activity in four regions of the gerbil cochlear lateral wall by measuring intracellular Na+ concentration ([Na+]i). The application of 1 mM ouabain and removal of external K+ caused a most striking increase in [Na+]i of the suprastrial fibrocytes, followed by the stria vascularis and the type II fibrocytes, but no detectable response in the type I fibrocytes. These results may imply the potency of the Na+,K(+)-ATPase activity. The high values of the resting [Na+]i in these cells under perilymph-like solution returned to the [Na+]i within physiological values after exposure to low-Na+ conditions similar to endolymph. Our results are interpreted in the light of recent morphological findings with regard to the roles in the secretion of K+ into endolymph of several cell types within the lateral wall.

Animals↗
PubMed1996

Cryocrystallography of 3-Isopropylmalate dehydrogenase from Thermus thermophilus and its chimeric enzyme.

The crystal structures of thermostable enzyme, 3-isopropylmalate dehydrogenase of Thermus thermophilus (10T) and a chimeric enzyme between T. thermophilus and Bacillus subtilus with one point mutation (cS82R), were determined at both 100 and 150 K. At the cryogenic condition, the volume of the unit cell decreased by 5% as a result of a contraction in the solvent region. Although the overall structures of both enzymes at low temperature were the same as that of 10T at room temperature, interactions between two domains and between two subunits in a functional dimer of cS82R were significantly altered. The decrease in the average temperature factor of 10T at low temperature and no significant decrease for cS82R suggested that the structure of the engineered enzyme (cS82R) may have many conformational substates even at low temperature, while the native enzyme (10T) at low temperature has a more definite conformation than that at room temperature. The location of water molecules around the enzyme molecule and the calculation of the radii of gyration suggested that cS82R had a weaker hydration than 10T.

Journal Article↗
PubMed1996

A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map.

The 718,122 base pair sequence of the Escherichia coli K-12 genome corresponding to the region from 12.7 to 28.0 minutes on the genetic map is described. This region contains at least 681 potential open reading frames, of which 277 (41%) have been previously identified, 147 (22%) are homologous to other known genes, 139 (20%) are identical or similar to the hypothetical genes registered in databases, and the remaining 118 (17%) do not show a significant similarity to any other gene. In this region, we assigned a cluster of cit genes encoding multienzyme citrate lyase, two clusters of fimbrial genes and a set of lysogenic phage genes encoding integrase, excisionase and repressor in the e14 genetic element. In addition, a new valine tRNA gene, designated valZ, and a family of long directly repeated sequences, LDR-A, -B and -C, were found.

DNA, Bacterial↗
PubMed1996

Potentiation of the intracellular Ca2+ response to arginine vasopressin by increased cytosolic-free Mg2+ in rat vascular smooth muscle cells.

Although the inhibitory effects of extracellular Mg2+ on Ca2+ influx are well established, little is known about the effects of intracellular Mg2+ on Ca2+ handling. In the present study, the effects of cytosolic-free Mg2+ concentration in the physiological (submillimolar) range on Ca2+ handling were investigated after stimulation of rat vascular smooth muscle cells with arginine vasopressin. Cytosolic Mg2+ was manipulated by culturing cells in medium containing different Mg2+ concentrations. Peak cytosolic-free Ca2+ concentration responses to arginine vasopressin (1 mumol/1) were measured in the presence and absence of external Ca2+. The results suggest that an increase in cytosolic-free Mg2+ concentration increases both Ca2+ discharge from intracellular stores and Ca2+ influx, whereas a decrease in intracellular Mg2+ attenuates Ca2+ influx.

Animals↗
PubMed1996

The Na-K-Cl cotransporters in the rat cochlea: RT-PCR and partial sequence analysis.

Nonsensory epithelial cells of the mammalian cochlea contribute to the production of the endolymph. The presence as well as the function of the Na-K-Cl cotransporter has been suggested, but not yet been proved. To identify the Na-K-Cl cotransporter isoforms expressed in the cochlea, mRNA was extracted from the cochlear lateral wall. After reverse transcription, resulting cDNA was amplified by polymerase chain reaction (PCR) with primers specific for Na-K-Cl cotransporter isoforms. In the rat cochlear lateral wall, mRNA homologous to the mouse bumetanide-sensitive Na-K-Cl cotransporter (mBSC2) was detected. These results suggest that the basolateral localization of the cotransporter in the marginal cell is involved in the secretory process of the endolymph.

Animals↗
PubMed1996

Structure of a loop-deleted variant of 3-isopropylmalate dehydrogenase from Thermus thermophilus: an internal reprieve tolerance mechanism.

A loop-deleted mutant form of 3-isopropylmalate dehydrogenase from Thermus thermophilus was constructed to investigate the relationship between the flexibility of the structure and the thermostability of the enzyme. The structure of the mutant enzyme was determined by X-ray crystallography and was found to be almost the same as that of the native enzyme with a reduced temperature factor. Although the mutant protein had lost the flexible loop, its function and thermostability had remained unchanged. This phenomenon can be explained by an internal reprieve tolerance mechanism.

Journal Article↗