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Biomedical subjects

N Shimamoto

Publications and source records attributed to N Shimamoto.

At least 19 recordsLinked to original sources

Structure of a replication-terminator protein complexed with DNA.

The crystal structure of the Escherichia coli replication-terminator protein (Tus) bound to terminus-site (Ter) DNA has been determined at 2.7 A resolution. The Tus protein folds into a previously undescribed architecture divided into two domains by a central basic cleft. This cleft accommodates locally deformed B-form Ter DNA and makes extensive contacts with the major groove, mainly through two interdomain beta-strands. The unusual structural features of this complex may explain how the replication fork is halted in only one direction.

Amino Acid Sequence

Kinetics of transcription in a minute column.

Immobilized enzymes or nucleic acids are widely used to analyze association and dissociation reactions. A pseudo-rapid kinetic method for studying transcription was developed by using an immobilized template DNA packed in a minute column, in a micro-scale liquid chromatography system. This method, which has a dead-time of only several seconds, is quick enough to allow analysis of the release of product RNA in transcription by Escherichia coli RNA polymerase. The method could be applied to most enzymes that interact with DNA.

Base Sequence

Contribution of sustained Ca2+ elevation for nitric oxide production in endothelial cells and subsequent modulation of Ca2+ transient in vascular smooth muscle cells in coculture.

To elucidate the intracellular Ca2+ (Ca2+i ) transient responsible for nitric oxide (NO) production in endothelial cells (ECs) and the subsequent Ca2+i reduction in vascular smooth muscle cells (VSMCs), we administrated four agonists with different Ca2+i-mobilizing mechanisms for both cells in iso- or coculture. We monitored the Ca2+i of both cells by two-dimensional fura-2 imaging, simultaneously measuring NO production as NO2-. The order of potency of the agonists in terms of the peak Ca2+i in ECs was bradykinin (100 nM) > ATP (10 microM) > ionomycin (50 nM) > thapsigargin (1 microM). In contrast, the order in reference to both the extent of Ca2+i reduction in cocultured VSMCs and the elevation in NO production over the level of basal release in ECs completely matched and was ranked as thapsigargin > ionomycin > ATP > bradykinin. Treatment by NG-monomethyl-L-arginine monoacetate but not indomethacin or glybenclamide restored the Ca2+i response in cocultured VSMCs to the isoculture level. In ECs, when the Ca2+ influx was blocked by Ni2+ or by chelating extracellular Ca2+, all four agonists markedly decreased NO production, the half decay time of the Ca2+i degenerating phase, and the area under the Ca2+i curve. The amount of produced NO hyperbolically correlated to the half decay time and the area under the Ca2+i curve but not to the Ca2+i peak level. Thus, the sustained elevation of Ca2+i in ECs, mainly a result of Ca2+ influx, determines the active NO production and subsequent Ca2+i reduction in adjacent VSMCs. Furthermore, L-arginine but not D-arginine or L-lysine at high dose (5 mM) without agonist enhanced the NO production, weakly reduced the Ca2+i in ECs, and markedly decreased the Ca2+i in VSMCs, demonstrating the autocrine and paracrine effects of NO (Shin, W. S., Sasaki, T., Kato, M., Hara, K., Seko, A., Yang, W. D., Shimamoto, N., Sugimoto, T., and Toyo-oka, T. (1992) J. Biol. Chem. 267, 20377-20382).

Animals

A branched pathway in the early stage of transcription by Escherichia coli RNA polymerase.

The time-course of synthesis of long and short (abortive) transcripts by Escherichia coli RNA polymerase was investigated under single round conditions in vitro. The synthesis of long RNA initiated at the lambda PR (with an altered leader sequence) or at the lacUV5 promoter was completed within five minutes, but abortive transcripts were continuously synthesized for at least 20 minutes. The results indicate the presence of transcription complexes that are capable only of abortive synthesis, and not of productive elongation. Consistently, only one in four of the RNA polymerase molecules that initially associated with the lambda PR promoter synthesized long RNA. The enzyme reisolated from productive complexes synthesized both long and abortive transcripts, behaving just like the original enzyme. This suggests that RNA polymerase is homogeneous with respect to its ability to synthesize the two types of product. Overall, the results indicate that many transcription complexes can be irreversibly trapped in vitro in an abortive cycle.

Base Sequence

Crystallization and preliminary X-ray analysis of the Escherichia coli replication terminator protein complexed with DNA.

Crystals of the Escherichia coli replication terminator protein (Tus) complexed with its binding site DNA were obtained by a microdialysis method using PEG 4000. They belong to the tetragonal space group P4(1)2(1)2 or P4(3)2(1)2 with the unit cell parameter: a = 68.1 A, c = 230.7 A and contain one protein-DNA complex in an asymmetric unit. The native data set has been collected to 2.7 A resolution.

Bacterial Proteins

Effects of a potent, non-selective endothelin receptor antagonist, [Thr18, gamma-MeLeu19]-endothelin-1, on the isolated blood vessels.

The endothelin (ET) receptor has been classified as the ETA1, ETA2, ETB1 and ETB2 subtypes. BQ-123 and RES-701-1 are the ETA1 and ETB1 antagonists, respectively, whereas BQ-788 is the ETB1/ETB2 antagonist. To find the ETA2 antagonist, the effects of [Thr18, gamma-MeLeu19]-ET-1 (TM-ET-1) were examined. In the rabbit saphenous vein, contraction induced by ET-1 is due to simultaneous activation of the ETA1, ETA2, ETB1 and ETB2 receptors whereas contraction induced by sarafotoxin S6c is mediated by the ETB1 and ETB2 receptors. Neither BQ-123 nor RES-701-1 inhibited these contractions. TM-ET-1 antagonized the effects of ET-1 and sarafotoxin S6c. In the vein in which the ETB1/ETB2 receptors were desensitized and the ETA1 receptor was inhibited by BQ-123, ET-1 still induced contraction. This contraction was inhibited by TM-ET-1. In the rat aorta with endothelium, ET-3 induced endothelium-dependent relaxation by activating the endothelial ETB1 receptor. TM-ET-1 inhibited the effect of ET-3 without changing the relaxation induced by carbachol. In the rat aorta without endothelium, ET-1 induced contraction by activating the smooth muscle ETA1 receptor. TM-ET-1 inhibited this contraction. These results suggest that TM-ET-1 is a novel antagonist against the ETA2 receptor that also inhibits other types of the ET receptors.

Animals

Purification and characterization of a cam repressor (CamR) for the cytochrome P-450cam hydroxylase operon on the Pseudomonas putida CAM plasmid.

The cytochrome P-450cam hydroxylase operon of Pseudomonas putida PpG1 (ATCC 17543) encodes proteins responsible for early steps of the degradation of D-camphor. Transcription of this operon is negatively controlled by the cam repressor (CamR), and the expression of camR is autoregulated. CamR was purified from Escherichia coli harboring an overproducing plasmid. The repressor forms a homodimer with a molecular mass of 40 kDa, as judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis and gel filtration. CamR protected a specific DNA region from attack by DNase I. This region contains a palindromic operator of the cytochrome P-450cam hydroxylase operon and of the camR gene. Protection was inhibited by the addition of 60 microM D-camphor and also by certain camphor analogs and degradation products, including D-3-bromocamphor, adamantane, 2-adamantanone, 5-exo-hydroxycamphor, and 2,5-diketocamphane. These analogs and degradation products induced cytochrome P-450cam hydroxylase operon expression in vivo.

Base Sequence

PACAP stimulates catecholamine release from adrenal medulla: a novel noncholinergic secretagogue.

The secretory response of the adrenal medulla to pituitary adenylate cyclase-activating polypeptide (PACAP), a novel polypeptide with 68% structural homology to vasoactive intestinal polypeptide (VIP), was investigated in anesthetized rats by in vivo microdialysis. The injection of PACAP (1.5 nmol) caused a greater amount of increase in catecholamine concentration than carbachol (30 nmol) or VIP (30 nmol) in the dialysate for a period of 60 min. The ratios of norepinephrine to epinephrine in the dialysate after stimulation with these compounds showed no change from resting conditions. The simultaneous application of both nicotinic and muscarinic antagonists (10 mM mecamylamine and 1 mM atropine) eliminated the increase in catecholamine secretion induced by carbachol. In contrast, PACAP-induced catecholamine secretion was not inhibited by these cholinergic antagonists. These data led to the following conclusions: 1) PACAP was more potent than either carbachol or VIP in enhancing the secretion of catecholamine from the adrenal medulla, and 2) PACAP-induced catecholamine secretion was due to the direct action of PACAP on the adrenal medulla rather than an indirect action mediated by acetylcholine release. These results strongly suggest that PACAP is a noncholinergic secretagogue of the adrenal medulla in rats.

Adrenal Medulla

Ontogeny of pituitary adenylate cyclase-activating polypeptide (PACAP) and its binding sites in the rat brain.

Endogenous levels of pituitary adenylate cyclase-activating polypeptide (PACAP) and its binding site densities were measured in eight brain regions in rats of different ages (2-240 days) by sandwich-enzyme immunoassay and autoradiography. PACAP levels were quite low at day 2, peaked in 30-60 days, and then remained constant in most regions. Such ontogenetic changes are similar to those of vasoactive intestinal polypeptide (VIP) and classical neurotransmitters. PACAP-binding sites were already dense at day 2 and varied only slightly up to day 240. These results suggest that PACAP may have modulatory effects on brain development.

Animals

Effect of high pressure on EcoRI reactions.

The effect of pressure on reactions of restriction endonucleases was investigated. No obvious irreversible (after) effect was observed for EcoRI, while a considerable irreversible inactivation was found for BamHI. Thus the EcoRI reactions against lambda DNA, pBR322 and pBluescript were studied under high pressure and little effect was observed on the overall reactions. The DNA concentration dependence of the kinetic data apparently fits the Michaelis-Menten type equation and the evaluated rate parameters were: Vmax = 6.2 +/- 0.24 and 7.0 +/- 0.22 (x 10(-2) nM/min) at 0.1 and 200 MPa, respectively; Km = 19 +/- 1.8 and 28 +/- 1.7 nM at 0.1 and 200 MPa, respectively. The apparent activation volume corresponding to kcat/Km was ca +1 mL/mol. A characteristic effect of pressure on the sequence specificity of these enzymes was seen in their star activity. Relaxed specificity was tightened by increasing pressure (200 MPa) with respect to that induced by low salt concentration or by the presence of organic solvent.

Bacteriophage lambda

Endothelin-1 analogues substituted at both position 18 and 19: highly potent endothelin antagonists with no selectivity for either receptor subtype ETA or ETB.

Novel endothelin-1 (ET-1) analogues which are highly potent endothelin antagonists at both receptor subtype ETA and ETB are reported. The replacement of Asp18 with the Thr18 and of Ile19 with a hydrophobic amino acid whose side-chain branches on the gamma-carbon such as Leu, cyclohexylalanine, and gamma-methylleucine (gamma-MeLeu) resulted in loss of or significantly decreased the biological activity of ET-1, while high affinity for the ETA (IC50 = 0.42-0.70 nM) and ETB (IC50 = 0.17-0.43 nM) receptor was retained. These compounds were shown to have high antagonist activities in ET-1-induced vasoconstriction of porcine coronary artery (pA2 7.4-7.7) and in Sarafotoxin S6c-induced vasoconstriction of rabbit pulmonary artery ([Thr18, gamma-MeLeu19]ET-1: pA2 8.4). Among these compounds, [Thr18, gamma-MeLeu19]ET-1 has the desirable characteristic of possessing no agonist activity at either receptor subtype.

Amino Acid Sequence

Visualization of single molecules of RNA polymerase sliding along DNA.

Transcription requires that RNA polymerase binds to promoters buried in nonspecific sites on DNA. The search for promoters may be facilitated if the polymerase slides along the molecule of DNA. Single molecules of Escherichia coli RNA polymerase were visualized, and their movements on immobilized bacteriophage lambda and T7 DNAs were examined. Deviating from drifts by bulk flow, about 40 percent of the enzyme molecules moved along the extended DNA. The results provide direct evidence for sliding as a mechanism for relocation of the enzyme on DNA.

Bacteriophage T7

Pharmacologic profile of endothelinA/B antagonist, [Thr18, gamma methyl Leu19]endothelin-1.

The pharmacologic profile of [Thr18,gamma methyl Leu19]endothelin-1 (TM ET-1) was investigated in several in vitro and in vivo studies. We found that TM ET-1 inhibited 125I-ET-1 binding in porcine cardiac membrane (ETA receptor) and in bovine brain membrane (ETB receptor), with IC50 values of 0.7 and 0.25 nM, respectively. These values were almost comparable to those for ET-1. TM ET-1 had no effect on intracellular Ca2+ concentration ([Ca]i) in A10 cells mediated by ETA receptors, even at 10(-5) M, or in mouse peritoneal macrophages (MPMs) mediated by ETB receptors, even at 10(-6) M. Increases in [CA]i in A10 cells by ET-1 and in MPMs by ET-3 were completely blocked by pretreatment with 10(-7) M of TM ET-1. In porcine right coronary arteries (PCAs) and in great cardiac veins (PCVs), TM ET-1 caused no contraction at concentrations < or = 10(-6) and 10(-7) M, respectively, although it competitively inhibited ET-1-induced contraction of PCAs and Ala1,3,11,15-ET-1-induced constriction of PCVs with pA2 values of 7.0 and 9.2, respectively. Furthermore, TM ET-1 was more potent than BQ123, an ETA-specific antagonist, in inhibiting the rise in perfusion pressure in a hind-limb preparation in vitro and the increase in blood pressure in rats. These results suggest that TM ET-1 is a potent ETA and ETB antagonist without agonistic effects and can be used in future studies to help clarify the physiological role of ET.

Animals

Autocrine and paracrine effects of endothelium-derived relaxing factor on intracellular Ca2+ of endothelial cells and vascular smooth muscle cells. Identification by two-dimensional image analysis in coculture.

To elucidate the effects of endothelium-derived relaxing factor (EDRF) released from vascular endothelial cells (ECs) on handling of intracellular calcium ion (Ca2+i) in ECs themselves and vascular smooth muscle cells (VSMCs), we measured the Ca2+i by two-dimensional digital image analysis of fura-2-loaded ECs and VSMCs in tissue culture. In isoculture of one cell type, adenosine triphosphate (ATP, 1 microM) transiently increased the Ca2+i of both ECs and VSMCs. High-K+ depolarization or angiotensin II also elevated the Ca2+i of VSMCs, whereas neither stimulants changed the Ca2+i of ECs. In coculture of ECs with VSMCs, the same dose of ATP rapidly increased the Ca2+i of ECs and then transiently decreased the Ca2+i of VSMCs to below the resting level. The maximal Ca2+i-modulating effects of ATP on both cell types were reproducible after the second application of ATP. Three kinds of EDRF blockers (L-NG-monomethylarginine, methemoglobin, or methylene blue) potentiated the ATP-induced Ca2+i rise in ECs and attenuated the Ca2+i reduction in VSMCs, suggesting the autocrine and paracrine effects of EDRF on ECs and VSMCs, respectively. However, neither indomethacin, superoxide dismutase, nor neutralizing monoclonal antibody to endothelin-1 altered the second responses. Thus, two-dimensional Ca2+i image analysis of ECs and VSMCs in coculture enabled direct visualization of the EDRF actions in ECs and VSMCs and their modifications.

Adenosine Triphosphate

Morphological pathway of flagellar assembly in Salmonella typhimurium.

The process of flagellar assembly was investigated in Salmonella typhimurium. Seven types of flagellar precursors produced by various flagellar mutants were purified by CsCl density gradient protocol. They were characterized morphologically by electron microscopy, and biochemically by two-dimensional gel electrophoresis. The MS ring is formed in the absence of any other flagellar components, including the switch complex and the putative export apparatus. Four proteins previously identified as rod components, FlgB, FlgC, FlgF, FlgG, and another protein, FliE, assemble co-operatively into a stable structure. The hook is formed in two distinct steps; formation of its proximal part and elongation. Proximal part formation occurs, but elongation does not occur, in the absence of the LP ring. FlgD is necessary for hook formation, but not for LP-ring formation. A revised pathway of flagellar assembly is proposed based on these and other results.

Bacterial Proteins

Requirement for the beta,gamma-pyrophosphate bond of ATP in a stage between transcription initiation and elongation by Escherichia coli RNA polymerase.

A linear fragment of DNA was fixed to acrylamide or agarose beads by its ends. When a fragment containing the lambda PR promoter is immobilized and transcribed, the RNA products are unchanged from those obtained on the unfixed DNA. Transcription from the immobilized fragment can be interrupted by diluting the reaction mixture into a large volume of the same buffer. Brief centrifugation allows isolation of the transcription complex with the immobilized DNA. If interruption occurs during elongation, the elongation can be resumed upon a second addition of substrates. If ATP is replaced by a beta, gamma-unhydrolyzable analogue in the second addition, the elongated products are similar to those obtained when the substrate contain ATP. When ATP is replaced by the analogue at the initiation step, however, the yield of elongated products is decreased to less than one-sixth and that of short abortive products is increased. Thus the ATP analogues are good substrates once elongation has been established in the presence of ATP, but not good enough to get past a stage just after initiation in the absence of ATP. We conclude that the beta, gamma-pyrophosphate bond of ATP is important for preparation of efficient elongation.

Adenosine Triphosphate