Biomedical subjects

K Nishikawa

Publications and source records attributed to K Nishikawa.

At least 307 records · Page 17Linked to original sources

PubMed1994

Michael addition-type 4-hydroxy-2-nonenal adducts in modified low-density lipoproteins: markers for atherosclerosis.

It has been proposed that plasma low-density lipoprotein (LDL) undergoes oxidative modification before it can give rise to foam cells in atherosclerosis. Oxidation of LDL generates a variety of reactive aldehyde products including 4-hydroxy-2-nonenal (HNE), which may covalently attach to the LDL apolipoproteins. We here present direct evidence that HNE derivatization of LDL forms Michael addition-type adducts of HNE with histidine and lysine residues of apolipoprotein B-100 (apoB) and also demonstrate the utility of an antibody specific to the HNE adducts generated in the LDL treated with HNE or oxidatively modified by Cu2+ or cultured endothelial cells. HNE adducts present in the LDL that had been treated with HNE were attested to be Michael addition-type adducts on the basis of the fact that incubation of LDL with 1 mM HNE (2 h, 37 degrees C) resulted primarily in the formation of Michael addition-type HNE-histidine (39.9 mol/mol of LDL) and HNE-lysine (19.3 mol/mol of LDL) adducts. An enzyme-linked immunosorbent assay (ELISA) and an SDS-polyacrylamide gel electrophoresis (SDS-PAGE)/immunoblot analysis of HNE-modified LDL demonstrated that these HNE adducts were detectable with the HNE-specific antibody affinity-purified with the Michael adduct (HNE-histidine) as a ligand. The following lines of evidence indicated the presence of Michael addition-type HNE adducts in the oxidatively modified LDL in vitro: (i) Amino acid analysis of LDL that had been treated with Cu2+ (24 h, 37 degrees C) demonstrated the presence of a Michael addition-type HNE-histidine adduct (7-9 mol/mol of LDL).(ABSTRACT TRUNCATED AT 250 WORDS)

Aldehydes↗

PubMed1994

A tRNA-like structure is present in 10Sa RNA, a small stable RNA from Escherichia coli.

We have determined that 10Sa RNA (one of the small stable RNAs found in Escherichia coli) has an interesting structural feature: the 5' end and the 3' end of 10Sa RNA can be arranged in a structure that is equivalent to a half-molecule (acceptor stem and TFC stem-loop) of alanine tRNA of E. coli. Primer-extension analysis of 10Sa RNA extracted from a bacterial mutant with temperature-sensitive RNase P function revealed that the precursor to 10Sa RNA (pre-10Sa RNA) is folded into a pre-tRNA-like structure in vivo such that it can be cleaved by RNase P to generate the 5' end of the mature 10Sa RNA. The purified 10Sa RNA can be charged with alanine in vitro. Disruption of the gene encoding 10Sa RNA (ssrA) caused a reduction in the rate of cell growth, which was especially apparent at 45 degrees C, and a reduction in motility on semisolid agar. These phenotypic characteristics of the deletion strain (delta ssrA) allowed us to investigate the effects of some mutations in 10Sa RNA in vivo, although the exact function of 10Sa RNA still remains unclear. When the G.U pair (G3.U357) in 10Sa RNA, which may be equivalent to the determinant G.U pair of alanine tRNA, was changed to a G.A or G.C pair, the ability to complement the phenotypic mutations of the delta ssrA strain was lost. Furthermore, this inability to complement the mutant phenotypes that was caused by the substitution of the determinant bases by a G.A pair could be overcome by the introduction of a gene encoding alanyl-tRNA synthetase (alaS) on a multicopy plasmid. The evidence suggests that the proposed structural features of 10Sa RNA are indeed manifested in vivo.

Base 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

Structural model of the ATP-binding domain of the F1-beta subunit based on analogy to the RecA protein.

In contrast to the previous topological model of the ATP binding domain of the F1-ATPase beta subunit based on analogies to those of ras p21 and adenylate kinase, a more consistent model can be constructed with the known structure of the recA protein as a reference. The secondary structure of the F1-ATPase beta subunit predicted from the primary structure agrees well with that of the recA protein. The topology includes a repetitive beta alpha c beta alpha beta alpha beta alpha beta structure where all beta strands are parallel and surround the central alpha c helix above which bound ATP is located. Several residues thought to be located at catalytic site as reported in genetic and chemical labeling work can be consistently positioned in this model.

Adenosine Triphosphate↗

PubMed1994

Prediction of the structural similarity between spermidine/putrescine-binding protein and maltose-binding protein.

A structural similarity between spermidine/putrescine-binding protein and maltose-binding protein has been predicted by a sequence-structure compatibility method. The sequence alignment obtained by this method revealed a consensus sequence motif located on the surface loop between the first alpha-helix and the second beta-strand, and the further analysis identified a similar motif in iron-binding protein. The conservation of this motif among certain bacterial periplasmic binding proteins suggests a common functional role for this region as well as an evolutionary relationship between them.

ATP-Binding Cassette Transporters↗

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

Discrimination of intracellular and extracellular proteins using amino acid composition and residue-pair frequencies.

Sequences of intracellular and extracellular soluble proteins were analyzed statistically in terms of amino acid composition and residue-pair frequencies. Residue-pair frequencies were calculated for sequential separations from (n, n + 1) to (n, n + 5), and converted into scoring parameters. Then, for each test protein, the single-residue and residue-pair parameters were applied to calculate a total score. According to our definition, a protein which yields a positive score is indicative of an intracellular protein, whereas a negative score implies an extracellular one. The parameter set was derived from 894 sequences constituting different protein families in the PIR database, and assessed by application to a test of 379 proteins. The results showed that 88% of intracellular and 84% of extracellular proteins were correctly assigned. The discrimination power was improved by about 8% in comparison with the previous study, which used composition data alone. Segregation of intra/extracellular proteins is also observed by other criteria, such as structural class (intracellular proteins prefer alpha and alpha/beta types and extracellular proteins prefer beta and alpha + beta types). Segregation by sequence was found to be a more reliable procedure for distinguishing intra/extracellular proteins than methods using structural class. Possible causes for this segregation by sequence are discussed.

Amino Acids↗

PubMed1994

Interleukin-8 production by CD16-CD56bright natural killer cells in the human early pregnancy decidua.

Decidual CD16-CD56bright natural killer (NK) cells were sorted from the decidual mononuclear cells (MNC) at the early pregnancy using a fluorescence activated cell sortor. The CD16-CD56bright NK cell population occupies a major population in the decidual MNC, in contrast to a very small population (< 1%) in the peripheral blood MNC. These decidual CD16-CD56bright NK cells produced a large amount of IL-8, i. e., mean of 96.7 +/- 19.8 ng/ml in the 24 hr-cultured supernatants without any stimulant, which was comparable to the IL-8 production by LPS-stimulated peripheral blood MNC. Most of the IL-8 was ascribable to the production from decidual CD16-CD56bright NK cells. Intracytoplasmic IL-8 in the decidual CD56bright NK cells was also detected by flow cytometry. RT-PCR methods confirmed IL-8 mRNA expression in this population, while no or very scarce expression of IL-1 alpha and IL-1 beta mRNA was observed. The present study is a first observation revealing that decidual CD16-CD56bright NK cells express IL-8 mRNA and produce IL-8.

Antigens, CD↗

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

Effect of an angiotensin II receptor antagonist, CV-11974, and its prodrug, TCV-116, on production of aldosterone.

In dispersed rabbit adrenocortical glomerulosa cells, a non-peptide angiotensin II (AT1) receptor antagonist, CV-11974 (10(-10)-10(-5) M), competitively inhibited angiotensin II- or angiotensin III-stimulated aldosterone production, whereas PD123177, an angiotensin AT2 receptor antagonist, did not. CV-11974 inhibited aldosterone production induced by 4 mM K+ but not by 12 mM K+. CV-11974 had no effect on adrenocorticotropic hormone-stimulated aldosterone or corticosterone production, but inhibited angiotensin II-stimulated corticosterone production. In the rat, TCV-116, the prodrug of CV-11974, (0.1 and 1 mg/kg, p.o.) markedly reduced the elevation of both plasma aldosterone concentration and blood pressure induced by i.v. infusion of angiotensin II. In spontaneously hypertensive rats, TCV-116 at daily p.o. doses of 0.1, 1 and 10 mg/kg for 2 weeks caused a dose-dependent reduction of blood pressure and plasma aldosterone concentration without affecting plasma corticosterone. Thus, TCV-116 inhibited the induction of aldosterone production by not only exogenous but also endogenous angiotensin II.

Administration, Oral↗

PubMed1994

Expression of nerve growth factor family neurotrophins in a mouse osteoblastic cell line.

With cultured osteoblastic cells, clone MC3T3-E1 derived from newborn mouse calvaria, the mRNAs encoding three representative neurotrophins, namely, nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF) and neurotrophin-3 (NT-3), were proved in estimation by the polymerase chain reaction (PCR) method. The increase and then subsequent decrease of all three mRNAs within the proliferation phase were followed by their gradual increase in the differentiation phase, with a tendency of enhancement by exogenous TGF-beta as was particularly evident in the case of NGF. These findings were further substantiated by identification of NGF-like neutrophils in the conditioned medium of the osteoblastic cells by an immunoblotting and neurite extension assay.

Animals↗

PubMed1994

Cell adhesion activity of a 30-kDa major secreted protein from human bladder carcinoma cells.

Human bladder carcinoma cell line EJ-1 secreted a protein of 30 kDa as a major component. This protein was purified from the serum-free conditioned medium of EJ-1. Its N-terminal amino acid sequence was identical to that of fibroblast-derived endothelial cell growth factor (f-ECGF), but there were differences in their amino acid compositions and isoelectric points. The 30-kDa protein showed no effect on the growth of bovine capillary endothelial cells, but it promoted the attachment and spreading of rat liver cell line BRL and human umbilical vein endothelial cell line ECV-304. These results suggest that the 30-kDa protein, tentatively named "tumor-derived adhesion factor (TAF)", may be related with the aberrant cell adhesion of cancer cells.

Amino Acid Sequence↗

PubMed1994

Mapping of antigenic sites involved in serotype-cross-reactive neutralization on group A rotavirus outercapsid glycoprotein VP7.

Two neutralizing monoclonal antibodies (N-mAbs) were utilized to locate amino acid (aa) residues involved in the formation of serotype-cross-reactive epitopes on the VP7 of selected group A rotaviruses. N-mAb 954/159/13 neutralized G serotype 3 as well as porcine G serotype 4 rotaviruses, whereas N-mAb 57/8 neutralized G serotype 3, 4, 6, 9, and 10 strains. Neutralization-resistant variants of each serotype were selected in the presence of these two monoclonal antibodies. Sequence analysis of the gene encoding VP7 of such variants revealed: (i) variable regions VR-5 (aa 88-100), VR-8 (aa 209-223), and VR-9 (aa 235-242) are involved in cross-reactive neutralization; (ii) an aa substitution can occur at the same position on the VP7 of different serotypes selected by a given N-mAb; (iii) the location of an aa substitution on the variant VP7 selected by a given N-mAb can vary depending on the rotavirus serotype; (iv) a substituted single aa species at a specific position on the variant VP7 selected by a single N-mAb can vary, resulting in variants which exhibit antigenic differences; and (v) the VP7 of a porcine rotavirus Gottfried strain has a unique antigenic mosaic of serotype 3 and serotype 4.

Amino Acid Sequence↗

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

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↗

PubMed1994

Effect of CTLA-4 chimeric protein on rat autoimmune anti-glomerular basement membrane glomerulonephritis.

The interaction of the T cell receptor with the antigen/major histocompatibility class II complex is insufficient to induce optimal T cell activation. Co-stimulatory signals, including those provided by CD28/CTLA-4 on T cells and B7 molecules (B7-1, -2, and -3) on antigen-presenting cells, are also required. CD28-B7 interactions can be blocked by a soluble human CTLA-4 chimeric protein (CTLA4Ig). We tested the effect of administration of CTLA4Ig on experimental anti-glomerular basement membrane (GBM) autoimmune glomerulonephritis in Wistar-Kyoto rats induced by immunization with bovine GBM. The disease is characterized by development of antibody to the alpha 3 chain of type IV collagen (Goodpasture's antigen), deposition of rat IgG in GBM, infiltration of the kidney by T cells and macrophages, severe crescent formation and renal failure leading to death in 5-6 weeks. Animals injected with human CTLA4Ig from day 0 to day 14 or to day 35 had reduced disease severity. Beneficial effects were observed even when injections were begun after the onset of glomerulonephritis on day 14. However, the rats developed antibody to the human CTLA4Ig, associated with reduction in levels of circulating CTLA4Ig. The results provide evidence for CD28/CTLA-4 signaling in rat autoimmune glomerulonephritis, and suggest that more effective inhibition of B7-dependent T cell activation, such as might be achieved with homologous CTLA4Ig, could be useful in the treatment of autoimmune diseases.

Abatacept↗