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Biomedical subjects

S Kim

Publications and source records attributed to S Kim.

At least 829 records · Page 46Linked to original sources
PubMed1996

Mutational analysis of RNA structures and sequences postulated to affect 3' processing of M1 RNA, the RNA component of Escherichia coli RNase P.

When the rnpB gene encoding M1 RNA, the RNA component of Escherichia coli RNase P, is transcribed, the primary M1 RNA transcript (pM1 RNA) is produced and subsequently processed at the 3' end to generate the mature M1 RNA. To study features of pM1 RNA thought to be involved in RNA processing, systematic mutations were introduced in sequence elements and secondary structures surrounding the processing site using p23 RNA, a truncated pM1 RNA transcribed from the internally deleted rnpB gene, as a model substrate and the processing of its mutant derivatives was analyzed in vivo and in vitro. Neither the alteration of two bases forming the processing site nor the disruption of secondary structures surrounding the site significantly affected the processing efficiency although the secondary structures were required for maintaining RNA stability. In contrast, mutations at the rne-dependent site, GAUUU, immediately 3' to the processing site inhibited the processing and the extent of the inhibition varied with the altered sequences. Furthermore, the processing of the mutants of the rne-dependent site as well as wild-type p23 RNA was inhibited in an E. coli rnets strain at the nonpermissive temperature.

Base Sequence↗
PubMed1996

A mechanism for reducing entropic cost of induced fit in protein--RNA recognition.

Induced fit has been postulated to be an important component of ligand interactions with proteins, including protein-DNA interactions. We imagined that the entropic cost of induced fit might be highly dependent on the local protein sequence context around critical contact residues. To investigate this question, we analyzed the basis for active or inactive phenotypes found in a library of combinatorial sequence variants of a surface-located helix-loop peptide which is essential for the anticodon-binding activity of a class I tRNA synthetase. Molecular dynamics simulations of the domain encompassing the helix-loop peptide of the active variants consistently demonstrated fixation of the local motion of five critical (for function) residues which are highly mobile in inactive variants. Additional experiments with other rationally chosen mutants extended the correlation between phenotype and motion of these vital residues. We propose that the need for fixation of local motion is an important constraint on sequences of surface peptides which form parts of RNA-binding sites. The fixation of motion of critical residues in the unbound protein can significantly reduce the entropic cost of complex formation by induced fit.

Amino Acid Sequence↗
PubMed1996

Induction of 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) activation in rat lung microsomes by chronic ethanol consumption and repeated running exercise.

The effects of both chronic ethanol consumption and repeated exercise on metabolism of the tobacco-specific carcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) by rat lung microsomes were investigated. Keto aldehyde production was significantly enhanced 52% and 98%, respectively, by the ethanol and exercise, as was keto alcohol production (72% and 76%). 4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL) production was significantly enhanced only by the exercise (+32%). The combined treatment enhanced the keto alcohol production by 39%, indicating non-additive effects on cytochrome P450 (CYP) isozymes by the different treatments. Immunoblot and metabolic studies revealed an increased activity and content of CYP1A2 and CYP2B induced by the ethanol and exercise treatments as well as an induction of CYP2E1 proteins by the ethanol and combined treatments. These results indicate that both ethanol consumption and running exercise enhance NNK activation by increasing the expression of the CYP enzymes responsible for NNK activation.

Alcohol Drinking↗
PubMed1996

Pronase-based assay method for O6-methylguanine-DNA methyltransferase.

A new, simple, and rapid assay method for O6-methylguanine-DNA methyltransferase (MGMT) has been developed. When [methyl-3H] DNA radiolabeled with N-[methyl-3H]-N-nitrosourea was incubated together with tissue homogenate, [methyl-3H] group was transferred to the enzyme, forming S-[methyl-3H]cysteine. In contrast to the previous methods which determined the amount of [methyl-3H] group removed from [methyl-3H] DNA, the present method measured the amount of [methyl-3H] transferred to the enzyme. This has been done by hydrolyzing the radiolabeled enzyme with pronase which is a proteolytic enzyme with a broad substrate specificity. On pronase digestion, [methyl-3H]-labeled enzyme becomes soluble in trichloroacetic acid. The method is very simple and rapid, and the only expensive equipment required is a scintillation counter which is a relatively routine piece of equipment at present. More than a dozen samples can be processed within 4-5 h without any difficulty. This new method has been employed in the studies on organ distribution of MGMT of rat and mouse.

Animals↗
PubMed1996

Evidence for the direct interaction of the nifW gene product with the MoFe protein.

The Azotobacter vinelandii nifW gene, under control of the nifH promoter, was subcloned into the broad host range multicopy plasmid pKT230 for overexpression in both wild-type and delta nifW strains of A. vinelandii. Unlike the parent delta nifW strain, which grows slowly relative to wild-type under N2-fixing conditions, both overproduction strains grow at the same rate, showing that the overexpressed nifW product is functional in vivo. The approximately 40-fold overexpressed protein was purified, and sequence analysis confirmed its identity. During purification it was observed that NifW in crude extracts ran above the predicted molecular weight on denaturing gels and that as the purification proceeded lower molecular weight forms appeared. Mass spectrometry and studies with protease inhibitors revealed that this abnormal behavior was due to proteolysis. Native molecular weight determinations demonstrate that NifW is a homomultimer, most likely a trimer. Native gel electrophoresis analysis shows that the behavior of wild-type and overexpressed NifW are identical and that when extracts are prepared anaerobically only the homomultimeric forms of NifW are observed. When extracts are exposed to oxygen, however, NifW becomes part of a very high molecular weight complex. Immunoprecipitation with NifW antibodies demonstrate that under those conditions NifW specifically associates with the MoFe protein. These data are consistent with a model whereby NifW is not involved in the initial assembly of an active MoFe protein but rather is part of a system design to protect the MoFe protein from O2 damage.

Amino Acid Sequence↗
PubMed1996

Characterization of a soluble adrenal phosphatidylinositol 4-kinase reveals wortmannin sensitivity of type III phosphatidylinositol kinases.

Phosphorylation of phosphatidylinositol (PtdIns) by PtdIns 4-kinases is the first step in the synthesis of polyphosphoinositides, the lipid precursors of intracellular signaling molecules. We have recently identified a cytosolic PtdIns 4-kinase (cPI4K) in the bovine adrenal cortex that is distinguished from previously known PtdIns 4-kinases by its sensitivity to the PtdIns 3-kinase inhibitor wortmannin (WT). The present study has further characterized this soluble enzyme and compared its properties to those of the membrane-bound, type II PtdIns 4-kinase activity of the adrenal cortex and the type III enzyme of bovine brain. The enzymatic activity of adrenal cPI4K was inhibited not only by WT (IC50 approximately 50 nM) but also by LY-294002 (IC50 approximately 100 microM), another inhibitor of PtdIns 3-kinase, and neither compound affected type II PtdIns 4-kinase at concentrations that inhibited cPI4K. In contrast to the type II enzyme, cPI4K had a significantly higher Km for ATP, was relatively insensitive to inhibition by adenosine (Ki approximately 800 microM vs approximately 40 microM), had lower affinity for PtdIns, and was not inhibited by Ca2+ ions. These properties identify the WT-sensitive adrenal cPI4K as a type III PtdIns 4-kinase that is distinct from the tightly membrane-bound, Ca2+- and adenosine-sensitive, type II PtdIns 4-kinase. The type III PtdIns 4-kinase prepared from bovine brain exhibited similar kinetic parameters as the adrenal cPI4K, and was also inhibited by WT with an IC50 of 30-50 nM. Since WT inhibits the synthesis of agonist-regulated phosphoinositide pools in intact cells at micromolar concentrations, these findings indicated that type III rather than type II PtdIns 4-kinases are responsible for the maintenance of the precursor phospholipids required for intracellular signaling through the inositol phosphate/Ca2+ pathway.

1-Phosphatidylinositol 4-Kinase↗
PubMed1996

Effect of hypoxia and reoxygenation on regional activity of nitric oxide synthase in brain of newborn piglets.

The activity of nitric oxide synthase (NOS) was measured in homogenates from cortex, striatum, hippocampus, cerebellum, pons, thalamus and midbrain of the brain of newborn piglets and the effects of hypoxia and posthypoxic period on this activity was evaluated. The control activities were 19.7, 31.5, 26.8, 16.7, 33.6, 19.3 and 39.4 pmol/mg protein per min, respectively. A 1 h period of hypoxia (an FiO2 of 7%) resulted in statistically significant decreases in the activity of NOS in every region of the brain except for the cortex, where the activity was not significantly altered compared to control. By 2 h of reoxygenation following such a hypoxic episode, the NOS activities increased to above control levels in all regions of the brain, but this increase was statistically significant compared to control only in thalamus. Since hypoxia induced the greatest decrease in NOS activity in the cerebellum, the kinetic constants of the enzyme were measured in homogenates from this region of brain. The decreased activity following the hypoxic episode was associated with an approximately four-fold increase in the apparent affinity (KM) for arginine with no significant change in the maximal rate of reaction (Vmax). The decrease in NOS activity subsequent to a hypoxic episode may contribute to the disturbances in cellular metabolism in the immature brain induced by episodes of hypoxia-reoxygenation.

Animals↗
PubMed1996

The inhibitory activity of a transdominant c-jun mutant fused to the ligand binding domain of the estrogen receptor.

Tam-67 is an amino-terminal deletion mutant of c-Jun (delta3-122) lacking most of the c-Jun transactivation domain, which has been shown previously to function in a transdominant fashion to inhibit c-Jun-induced transactivation and cellular transformation. In order to create a ligand-dependent dominant negative repressor of AP-1, we have constructed a fusion of the TAM-67 gene with the ligand binding domain of the estrogen receptor. Fusion of TAM-67 with the ligand binding domain of the estrogen receptor produced a 68 kD protein (TAM-67ER) which was immunoprecipitated by c-Jun-specific and estrogen receptor-specific antisera and shown by gel retardation assay to bind oligonucleotides containing an AP-1 sequence. Cotransfection of TAM-67ER and an AP-1-dependent reporter construct into rat embryo cells demonstrated ligand specific inhibition of AP-1 transactivation. In the absence of hormone, TAM-67ER produced complete inhibition of c-Jun-induced AP-I transactivation. This inhibition was relieved by treatment with estradiol but not by treatment with tamoxifen. In addition, TAM-67ER inhibited activated c-Ha-ras- or c-raf-induced transformation of NIH3T3 cells. However, this inhibition of transformation was not relieved by the addition of estrogen. Thus, TAM-67ER inhibits transactivation in a ligand-dependent manner, but inhibits transformation in a ligand-independent manner. The results suggest that the ligand-dependent transactivation domain of the estrogen receptor (TAF-2) can substitute for the c-Jun transactivation domain absent in TAM-67 to stimulate transactivation. However, TAF-2 cannot substitute for the missing c-Jun transactivation domain to induce cellular transformation.

3T3 Cells↗
PubMed1996

Postelectrophoresis capillary scanning method for DNA sequencing.

A postelectrophoresis capillary scanning method for increasing the throughput of DNA sequencing has been developed. The method features a spatially and temporally separated arrangement between capillary gel electrophoresis separation of DNA sequencing fragments and the visualization of the separation pattern. Fluroescently labeled DNA sequencing fragments of pBluescript SK(-) were produced in enzymatic chain-termination reactions and separated by capillary gel electrophoresis using a 110 cm fused silica capillary with a transparent polymer coating. A partial sequence from the DNA was then determined by repeated scanning of the capillary at a rate of 8.39 cm/s, with changing excitation wavelengths and spectral filter sets.

Base Sequence↗
PubMed1996

Coupling of a replicative polymerase and helicase: a tau-DnaB interaction mediates rapid replication fork movement.

The E. coli replication fork synthesizes DNA at the rate of nearly 1000 nt/s. We show here that an interaction between the tau subunit of the replicative polymerase (the DNA polymerase III holoenzyme) and the replication fork DNA helicase (DnaB) is required to mediate this high rate of replication fork movement. In the absence of this interaction, the polymerase follows behind the helicase at a rate equal to the slow (approximately 35 nt/s) unwinding rate of the helicase alone, whereas upon establishing a tau-DnaB contact, DnaB becomes a more effective helicase, increasing its translocation rate by more than 10-fold. This finding establishes the existence of both a physical and communications link between the two major replication machines in the replisome: the DNA polymerase and the primosome.

Bacterial Proteins↗
PubMed1996

Tau protects beta in the leading-strand polymerase complex at the replication fork.

Replication forks formed in the absence of the tau subunit of the DNA polymerase III holoenzyme produce shorter leading and lagging strands than when tau is present. We show that one reason for this is that in the absence of tau, but in the presence of the gamma-complex, leading-strand synthesis is no longer highly processive. In the absence of tau, the size of the leading strand becomes proportional to the concentration of beta and inversely proportional to the concentration of the gamma-complex. In addition, the beta in the leading-strand complex is no longer resistant to challenge by either anti-beta antibodies or poly(dA):oligo(dT). Thus, tau is required to cement a processive leading-strand complex, presumably by preventing removal of beta catalyzed by the gamma-complex.

DNA Polymerase III↗
PubMed1996

Effect of replicative age on transcriptional silencing near telomeres in Saccharomyces cerevisiae.

Individual yeasts have a finite replicative life span in similarity to normal human fibroblasts. Telomere loss is a hallmark of replicative senescence in normal human fibroblasts and has been proposed to play a role in cellular senescence, perhaps by affecting subtelomeric genes. While telomere loss does not occur with replicative age in yeast, subtelomeric genes are subject to transcriptional silencing. It is possible that components of the silencing machinery other than telomeres change with replicative age and that these changes then lead to alterations in gene expression that contribute to aging. In an initial test of this possibility, we have examined the silencing of the URA3 gene at two different telomeres as a function of yeast replicative age. Silencing declined rapidly and significantly at one telomere consistent with the involvement of silencing in aging, but it remained in comparison nearly constant at the other. These changes in silencing raise the possibility that the transcriptional status of genes in the subtelomeric region may be important for the senescence of both dividing cells and postmitotic cells, in which telomeres remain constant in length.

Centromere↗
PubMed1996

Quadruple immunosuppression in a pig model of small bowel transplantation.

Rejection remains a major obstacle to successful small bowel transplantation in humans, irrespective of the immunosuppressants. Previous large animal studies have not used quadruple immunosuppression (with high-dose intravenous cyclosporine A [CSA]) for induction, followed by triple immunosuppression for maintenance therapy. Nor have immunosuppressive doses been comparable to clinical solid organ transplants. We studied, in 78 nonrelated outbred pigs, the effect of quadruple immunosuppression (including horse anti-pig thymocyte globulin [ATG] and high-dose intravenous CSA) on the incidence and severity of rejection in the early, critical posttransplant period. Group A (n = 19) pigs were nonimmunosuppressed. Group B (n = 20) received quadruple immunosuppression: pig ATG (10 mg/kg/day x 10 days), intravenous CSA (3.0 mg/kg/day), prednisolone (2 mg/kg/day), and azathioprine (2.5 mg/kg/day); prednisolone and azathioprine were each reduced by 50% on posttransplant Days 8 and 15. Trough CSA levels were > or = 400 ng/ml for the first 7 days posttransplant, > 200 ng/ml thereafter. Recipient pigs underwent resection of large and small bowel; orthotopic transplants (proximal duodenojejunostomy, distal ileostomy) were done with systemic vein drainage. We developed a scoring system (no, mild, moderate, severe rejection) to grade the extent of both interstitial and vascular rejection: biopsies were obtained daily from the ileostomy. Rejection-free graft survival at posttransplant Days 7, 10, and 14 was 32, 26, and 16% in the nonimmunosuppressed group versus 95, 90, and 85% in the immunosuppressed group (P < 0.0001). Rejection grades were significantly better over the whole observation period in immunosuppressed pigs: interstitial rejection was not present in up to 67% of all daily biopsy specimens. Rejection was present in all specimens of nonimmunosuppressed pigs. Vascular rejection was uncommon (incidence < 10%) in both groups. Isolated vascular rejection without interstitial rejection was not found. Graft-versus-host reaction was noted in both groups in the skin only; liver and native bowel were not involved. We conclude that quadruple immunosuppression with pig ATG and high-dose intravenous CSA for induction effectively prevents moderate and severe rejection in this model. Since clinical transplant complications (rejection, lymphomas) have persisted under FK 506 treatment, our immunosuppressive regimen should be considered an alternative for bowel transplantation in humans to prevent early rejection.

Animals↗
PubMed1996

Structure and expression of the tenecin 3 gene in Tenebrio molitor.

A genomic DNA fragment encoding tenecin 3, an antifungal protein was cloned from the genomic DNA library of Tenebrio molitor. The DNA sequence analysis showed that the coding region is divided into two exons by an intron of 49 bp in the middle of the putative leader peptide coding region. Southern blot analysis suggests that the gene is present as a single copy. The transcription initiation site was determined by primer extension analysis and S1 mapping. The TATA box and CCAAT box sequences were found at -30, and -121, respectively, from the transcription initiation site. Tenecin 3 mRNA is abundantly expressed in larvae and adults, while little was detected in RNAs from pupae, suggesting that the expression of the tenecin 3 gene is developmentally regulated.

Amino Acid Sequence↗
PubMed1996

Regulation of NF-kappa B activation in T helper 1 and T helper 2 cells.

In most cell types, NF-kappa B is activated by release from a cytoplasmic inhibitor protein, I kappa B, followed by its translocation to the nucleus where it binds to the regulatory regions of many genes, including the IL-2 gene in T lymphocytes. We have previously shown by electrophoretic mobility shift assays that nuclear extracts prepared from activated, non-IL-2-producing Th2 cell clones. We show here that Th-1 and Th2 cells have similar levels of cytoplasmic p65(RelA) and p50, but TCR stimulation fails to induce the nuclear translocation of p65(RelA) in Th2 cells. Nuclear translocation of p65(RelA) can be induced by IL-1 stimulation of Th2 cells, indicating that a basic mechanism of NF-Kappa B activation common to many cells is intact in Th2 cells. We demonstrate that IL-1 and TNF induce rapid nuclear translocation of p65(RelA) in T cell clones, whereas TCR-induced NF-Kappa B activation in Th1 cells is delayed and may be longer in duration. This suggests that the TCR pathway of NF-Kappa B activation is different from the cytokine pathway. Furthermore, we show that Th1 and Th2 cells express different levels and/or different forms of I kappa B alpha, and that cytokines, but not TCR stimuli, significantly modulate detectable levels of cytoplasmic I kappa B alpha.

Animals↗