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[Molecular biology of protein C-thrombomodulin pathway. Structure and function, and basic studies on its clinical application].

Vascular endothelial cells have several mechanisms which play an active role in preventing blood clot formation in vivo. One of the mechanisms by which prevention is achieved involves a cell surface thrombin receptor, thrombomodulin, which converts thrombin from a procoagulant into an anticoagulant due to accelerating thrombin-catalyzed activation of an anticoagulant protease zymogen, protein C. Activated protein C then proteolytically inactivates coagulation cofactors, Factors Va and VIIIa, in concert with another anticoagulant protein S. Activated protein C is finally neutralized by protein C inhibitor. The physiological relevance of the anticoagulant protein C-thrombomodulin pathway is demonstrated by the identification of hereditary deficiency of protein C or protein S with severe thrombotic complications. The recombinant protein C or thrombomodulin would be useful for treatment of the thrombotic diseases.

Amino Acid Sequence↗

Paired human fibrosarcoma cell lines that possess or lack endogenous mutant N-ras alleles as experimental model for Ras signaling pathways.

We present here a human cell model for examination of mutant N-ras function. The HT1080 human fibrosarcoma cell line is pseudodiploid and contains a single endogenous mutant N-ras allele. MCH603c8 cells are a variant of HT1080 cells, in which the mutant allele has been deleted. The two cell lines differ dramatically in the constitutive levels of activation of downstream members of the Ras signaling pathways, and in biological features of transformation and tumorigenicity. Downregulation or activation of individual Ras-dependent pathways can be accomplished via transfection of dominant negatives or activated mutant cDNAs into HT1080 and MCH603c8 cells, respectively. The biochemical and biological consequences of expression of these mutant cDNAs can be assessed. There are dramatic effects on both the transformed and tumorigenic phenotype, depending on the cell line and mutant cDNA that is transfected.

Actins↗

VisANT: an online visualization and analysis tool for biological interaction data.

BACKGROUND: New techniques for determining relationships between biomolecules of all types--genes, proteins, noncoding DNA, metabolites and small molecules--are now making a substantial contribution to the widely discussed explosion of facts about the cell. The data generated by these techniques promote a picture of the cell as an interconnected information network, with molecular components linked with one another in topologies that can encode and represent many features of cellular function. This networked view of biology brings the potential for systematic understanding of living molecular systems. RESULTS: We present VisANT, an application for integrating biomolecular interaction data into a cohesive, graphical interface. This software features a multi-tiered architecture for data flexibility, separating back-end modules for data retrieval from a front-end visualization and analysis package. VisANT is a freely available, open-source tool for researchers, and offers an online interface for a large range of published data sets on biomolecular interactions, including those entered by users. This system is integrated with standard databases for organized annotation, including GenBank, KEGG and SwissProt. VisANT is a Java-based, platform-independent tool suitable for a wide range of biological applications, including studies of pathways, gene regulation and systems biology. CONCLUSION: VisANT has been developed to provide interactive visual mining of biological interaction data sets. The new software provides a general tool for mining and visualizing such data in the context of sequence, pathway, structure, and associated annotations. Interaction and predicted association data can be combined, overlaid, manipulated and analyzed using a variety of built-in functions. VisANT is available at http://visant.bu.edu.

Animals↗

1,25(OH)2-vitamin D3, a steroid hormone that produces biologic effects via both genomic and nongenomic pathways.

The hormonally active form of vitamin D is 1,25(OH)2-vitamin D3 [1,25(OH)2D3]. This seco-steroid is the key mediator of the vitamin D endocrine system which produces biological effects in over 28 target tissues. In these target tissues, the biological responses may be generated both by a signal transduction mechanism which involves a nuclear receptor for 1,25(OH)2D3 that modulates gene transcription or a signal transduction pathway which involves rapid opening of Ca2+ channels which are externally located on the plasma membrane. This paper reviews the evidence in support of the pleiotropic effects of this steroid hormone and presents evidence that the receptor of the genomic effects is likely to be separate from the receptor/membrane recognition element which initiates the rapid nongenomic biological effects.

Animals↗

Biological function of the dTDP-rhamnose synthesis pathway in Streptococcus mutans.

We have cloned a new gene locus that comprises three genes concerned with the biosynthesis of the serotype c-specific polysaccharide antigen in Streptococcus mutans. The genes encode proteins exhibiting significant homology to the rfbA, rfbB, and rfbD gene products that are involved in the anabolism of dTDP-L-rhamnose from D-glucose-1-phosphate. This anabolism pathway pertains to biosynthesis of the O antigen of lipopolysaccharide in gram-negative bacteria. The cell extract of Escherichia coli expressing each of the cloned genes of S. mutans exhibited enzymatic activity corresponding to the homologous counterpart of the rfb gene products. Rhamnose was not detected in the cell wall preparation purified from the mutant in which each of the three cloned genes was insertionally inactivated. Rabbit antiserum against S. mutans serotype c-specific antigen did not react with the autoclaved extracts from these mutants. These results indicate that the gene products identified in the present study are involved in the dTDP-L-rhamnose synthesis pathway and that the pathway relates to the biosynthesis of the serotype-specific polysaccharide antigen of S. mutans. Southern hybridization analysis revealed that genes homologous to the cloned genes involved in the dTDP-L-rhamnose synthesis pathway were widely distributed in a variety of streptococci. This is the first report of the biological function of the dTDP-rhamnose pathway in streptococci.

Blotting, Southern↗

Immunoelectron microscopic localization of the ubiquitin-activating enzyme E1 in HepG2 cells.

As the first enzyme in the ubiquitin system the ubiquitin-activating enzyme E1 plays a pivotal role in all pathways of protein ubiquitination. In an effort to learn more about the cell biology of this pathway, we have purified the 110-kDa enzyme to homogeneity and generated a panel of distinct monoclonal antibodies to it. Using quantitative electron microscopic immunolocalization with these anti-E1 monoclonal antibodies, we find that E1 is abundant both within the cytoplasm and nucleus. Within the cytoplasm, E1 was found throughout the cytoplasmic volume as well as enriched along the cytoplasmic face of the rough endoplasmic reticulum and associated with the dense material along the desmosomal junctions. E1 was also found associated with the cytoplasmic surface of endosomal/lysosomal vacuoles. Interestingly, E1 was also found within the mitochondria. The lumen of rough endoplasmic reticulum, Golgi complex, endosomes, and lysosomes were negative. The specific localization of E1 to distinct subcellular organelles suggests that E1 may play multiple physiological roles within the cell.

Antibodies, Monoclonal↗

Are there special considerations relevant to trials of biologic agents?

Although biologic agents have been developed to effect change in observed or hypothesized pathogenic pathways, discrepancies between biological and clinical effects are well recognized. In trials of these agents, biological and clinical effects need to be evaluated. While the biological effects require assessment to test the proposed primary effect and significant influences, clinical evaluation should use the same set of assessment procedures as pharmacological agents. The disease controlling antirheumatic therapy (DC-ART) classification with its requirement for longterm efficacy poses problems for the biological agents, which, in general, have demonstrated short term benefit. They may be best accommodated in a new "remission induction" category or, alternatively, as part of longterm combination therapy either with pharmaceuticals or with other biologicals to fulfill DC-ART requirements.

Antirheumatic Agents↗

How Escherichia coli and Saccharomyces cerevisiae build Fe/S proteins.

Owing to the versatile electronic properties of iron and sulfur, iron sulfur (Fe/S) clusters are perfectly suited for sensing changes in environmental conditions and regulating protein properties accordingly. Fe/S proteins have been recruited in a wide array of diverse biological processes, including electron transfer chains, metabolic pathways and gene regulatory circuits. Chemistry has revealed the great diversity of Fe/S clusters occurring in proteins. The question now is to understand how iron and sulfur come together to form Fe/S clusters and how these clusters are subsequently inserted into apoproteins. Iron, sulfide and reducing conditions were found to be sufficient for successful maturation of many apoproteins in vitro, opening the possibility that insertion might be a spontaneous event. However, as in many other biological pathways such as protein folding, genetic analyses revealed that Fe/S cluster biogenesis and insertion depend in vivo upon auxiliary proteins. This was brought to light by studies on Azotobacter vinelandii nitrogenase, which, in particular, led to the concept of scaffold proteins, the role of which would be to allow transient assembly of Fe/S cluster. These studies paved the way toward the identification of the ISC and SUF systems, subjects of the present review that allow Fe/S cluster assembly into apoproteins of most organisms. Despite the recent discovery of the SUF and ISC systems, remarkable progress has been made in our understanding of their molecular composition and biochemical mechanisms. Such a rapid increase in our knowledge arose from a convergent interest from researchers engaged in unrelated fields and whose complementary expertise covered most experimental approaches used in biology. Also, the high conservation of ISC and SUF systems throughout a wide array of organisms helped cross-feeding between studies. The ISC system is conserved in eubacteria and most eukaryotes, while the SUF system arises in eubacteria, archaea, plants and parasites. ISC and SUF systems share a common core function made of a cysteine desulfurase, which acts as a sulfur donor, and scaffold proteins, which act as sulfur and iron acceptors. The ISC and SUF systems also exhibit important differences. In particular, the ISC system includes an Hsp70/Hsp40-like pair of chaperones, while the SUF system involves an unorthodox ATP-binding cassette (ABC)-like component. The role of these two sets of ATP-hydrolyzing proteins in Fe/S cluster biogenesis remains unclear. Both systems are likely to target overlapping sets of apoproteins. However, regulation and phenotypic studies in E. coli, which synthesizes both types of systems, leads us to envisage ISC as the house-keeping one that functions under normal laboratory conditions, while the SUF system appears to be required in harsh environmental conditions such as oxidative stress and iron starvation. In Saccharomyces cerevisiae, the ISC system is located in the mitochondria and its function is necessary for maturation of both mitochondrial and cytosolic Fe/S proteins. Here, we attempt to provide the first comprehensive review of the ISC and SUF systems since their discovery in the mid and late 1990s. Most emphasis is put on E. coli and S. cerevisiae models with reference to other organisms when their analysis provided us with information of particular significance. We aim at covering information made available on each Isc and Suf component by the different experimental approaches, including physiology, gene regulation, genetics, enzymology, biophysics and structural biology. It is our hope that this parallel coverage will facilitate the identification of both similarities and specificities of ISC and SUF systems.

Escherichia coli↗

Theoretical and computational studies of the glucose signaling pathways in yeast using global gene expression data.

We have combined DNA microarray experiments with novel computational methods as a means of defining the topology of a biological signal transduction pathway. By DNA microarray techniques, we previously acquired data on expression over time of all genes in the yeast Saccharomyces following addition of glucose to wild-type cells and to cells mutated in one or more components of the Ras signaling network. In addition, we examined the time course of expression following activation of components of the Ras signaling network in the absence of glucose addition. In this current study, we have applied a novel theoretical and computational framework to these data to identify the network topology of the glucose signaling pathway in yeast and the role of Ras components in that network. The computational approach involves clustering genes by expression pattern, postulating a signaling network topology superstructure that includes all possible component interconnections and then evaluating the feasibility of the superstructure interconnections by optimization methods using Mixed Integer Linear Programming techniques. This approach is the first rigorous mathematical framework for addressing the biological network topology issue, and the novel formulation features the introduction of discrete variables for the connectivity and logical expressions that connect the experimental observations to the network structure. This analysis yields a topology for the glucose signaling pathway that is consistent with, and an extension of, known biological interactions in glucose signaling.

Computer Simulation↗

The clinical and biologic importance of neovascularization and angiogenic signaling pathways in chronic lymphocytic leukemia.

Angiogenesis has been found to be an important regulator in the growth and metastasis of solid tumors. More recent studies have also demonstrated the importance of this biologic process in normal hematopoietic cell development and the pathophysiology of several hematologic malignancies. This review provides an overview of the clinical and biologic importance of angiogenesis in chronic lymphocytic leukemia (CLL). Patients with CLL have detectable levels of both plasma and cellular pro- and anti-angiogenic cytokines, as well as abnormal neovascularization in the marrow and lymph nodes. Recent evidence suggests a vascular endothelial growth factor (VEGF)-based autocrine pathway promotes the survival of CLL B cells in part through upregulation of anti-apoptotic proteins. Additionally, interactions between CLL B cells and their microenvironment generate alterations in the secretion of angiogenic factors that result in enhanced leukemic B-cell resistance to apoptotic cell death. From a clinical standpoint, interpatient variation is observed in markers of angiogenesis and appears to have prognostic implications. Several clinical trials evaluating the efficacy of anti-angiogenic agents for treatment of patients with CLL are underway with promising preliminary results. Additional research is needed to identify the regulation of aberrant and critical angiogenic pathways in CLL B cells, to determine how angiogenic markers can be used to improve prognostication for CLL patients, and to explore how the angiogenic characteristics of CLL B cells can best be manipulated for therapeutic benefit.

Angiogenesis Inducing Agents↗

An arginine to cysteine(252) mutation in insulin receptors from a patient with severe insulin resistance inhibits receptor internalisation but preserves signalling events.

AIMS/HYPOTHESIS: We examined the properties of a mutant insulin receptor (IR) with an Arg(252) to Cys (IR(R252C)) substitution in the alpha-subunit originally identified in a patient with extreme insulin resistance and acanthosis nigricans. METHODS: We studied IR cell biology and signalling pathways in Chinese Hamster Ovary cells overexpressing this IR(R252C). RESULTS: Our investigation showed an impairment in insulin binding to IR(R252C) related mostly to a reduced affinity of the receptor for insulin and to a reduced rate of IR(R252C) maturation; an inhibition of IR(R252C)-mediated endocytosis resulting in a decreased insulin degradation and insulin-induced receptor down-regulation; a maintenance of IR(R252C) on microvilli even in the presence of insulin; a similar autophosphorylation of mutant IR(R252C) followed by IRS 1/IRS 2 phosphorylation, p85 association with IRS 1 and IRS 2 and Akt phosphorylation similar to those observed in cells expressing wild type IR (IRwt); and finally, a reduced insulin-induced Shc phosphorylation accompanied by decreased ERK1/2 phosphorylation and activity and of thymidine incorporation into DNA in cells expressing IR(R252C) as compared to cells expressing IRwt. CONCLUSION/INTERPRETATION: These observations suggest that: parameters other than tyrosine kinase activation participate in or control the first steps of IR internalisation or both; IR-mediated IRS 1/2 phosphorylation can be achieved from the cell surface and microvilli in particular; Shc phosphorylation and its subsequent signalling pathway might require IR internalisation; defective IR endocytosis correlates with an enhancement of some biological responses to insulin and attenuation of others.

Acanthosis Nigricans↗

Inhibitory effect of a presenilin 1 mutation on the Wnt signalling pathway by enhancement of beta-catenin phosphorylation.

Mutations in the presenilin 1 (PS1) gene are the most common genetic factor underlying the development of early onset familial Alzheimer's disease (FAD). Accumulating evidence has shown that FAD-linked mutations of PS1 enhance the generation of amyloid-beta (1-42) protein. Recently, beta-catenin has been shown to interact with PS1. beta-catenin is essential for the Wnt signalling pathway. However, the biological significance of the interaction between beta-catenin and PS1 in this signalling pathway remains to be clarified. In this study, we investigated the effect of FAD-linked PS1 (M146L) mutation in the Wnt signalling pathway using the conditioned medium containing Wnt-3A. The expression of mutated PS1 inhibited the Wnt-3A-induced accumulation of beta-catenin. Chase analysis of beta-catenin in Wnt-3A-stimulated cells following cycloheximide treatment revealed that PS1 mutation enhanced the generation of the higher molecular mass form of beta-catenin, most likely, ubiquitinated beta-catenin. In addition, the expression of mutated PS1 elevated the level of phosphorylated beta-catenin, which is targeted to the ubiquitin/proteasome pathway. Thus, it appears that PS1 (M146L) mutation down-regulates the Wnt-3A-induced accumulation of beta-catenin due to an increase in the level of phosphorylated beta-catenin.

Acetylcysteine↗

Transforming growth factor beta1, bone connection.

Transforming Growth Factor beta1 (TGF beta1) exerts its functions both during embryogenesis, and in adult organism. TGF beta1 regulates cell proliferation, differentiation, motility and apoptosis. TGF beta1 is the most abundant growth factor in human bone. It is implicated in the pathogenesis of several bone diseases such as otosclerosis. During embryonic development, TGF beta1 plays a role in the migration of cells to the site of future skeletogenesis, the epithelial-mesenchymal interaction, and the formation of cellular condensations which dictates the general shape of the future skeletal elements. It also influences normal skeleton development by playing a critical role in inducing mesenchymal cell differentiation to either chondrocytes or osteoblasts. During Adult life, TGF beta1 has an influence on the maintenance of normal skeleton by playing a critical role on bone-forming cell namely, the osteoblast. TGF beta1 affects osteoblast differentiation, matrix formation, and mineralization. In MC3T3-E1 osteoblast-like cell line TGF beta1 inhibited the expression of the Runx2 and osteocalcin osteoblast differentiation markers. It interacts with many will known pathways in osteoblasts biology, such as Prostaglandin E2, Parathyroid hormone related peptide and Wnt-beta-catenin pathways. TGF beta1 exerts effects on osteocytes too. Treatment of pre-osteocytes with TGF alpha1 decreased cell death. Studied performed on osteoclast revealed that it inhibits both their proliferation and activity. This review briefly discusses the relation between this cytokine and the skeleton development and maintenance.

Animals↗

Inhibition of interferon regulatory factor-1 expression results in predominance of cell growth stimulatory effects of interferon-gamma due to phosphorylation of Stat1 and Stat3.

Interferon-gamma (IFN-gamma) is a potent inhibitor of hematopoiesis in vitro and has been implicated in the pathophysiology of human bone marrow failure syndromes. IFN-gamma both inhibits cell cycling and induces expression of the Fas-receptor, resulting in subsequent apoptosis of hematopoietic progenitor cells. IFN regulatory factor-1 (IRF-1) mediates some of these suppressive effects by activation of downstream inducible genes, such as double-stranded RNA-activatable protein kinase and inducible nitric oxide synthase. However, under certain experimental conditions, IFN-gamma appears to stimulate proliferation of hematopoietic cells. Based on the hypothesis that IFN-gamma-receptor triggering may activate diverse signaling cascades, we designed experiments to determine which intracellular mechanisms (in addition to the IRF-1 transduction pathway) influence the biologic effects of IFN-gamma. Using antisense technique, we inhibited the IRF-1-mediated pathway in KG1a cells stimulated with IFN-gamma. In contrast to the suppressive effects of IFN-gamma observed in control cells, untreated and IFN-gamma-treated KG-1a cells that were transduced with retroviral vectors expressing IRF-1 antisense mRNA showed enhanced proliferation. The increased growth rate was associated with decreased levels of IRF-1 mRNA and protein but unchanged levels of IRF-2. We inferred that IFN-gamma could also activate a stimulatory transduction pathway that, under specific conditions, may control the cellular response to this cytokine. The family of Stat proteins is involved in signal transduction of hematopoietic growth factors. We showed that, in KG-1a cells, IFN-gamma also induced phosphorylation of Stat1 and Stat3, whereas p42 MAP kinase was phosphorylated regardless of the presence of IFN-gamma. Using electrophoresis mobility shift assays, IFN-gamma enhanced Stat1-Stat1 homodimer and Stat1-Stat3 heterodimer formation, suggesting that, in addition to inhibitory signals mediated by IRF-1, IFN-gamma may activate proliferative signals by phosphorylation of Stat1 and Stat3 proteins. The observations made in experiments with KG-1a cells were confirmed in primary hematopoietic cells. After inhibition of the IRF-1 pathway by transduction of an antisense IRF-1 retrovirus into human CD34+ cells, IFN-gamma produced an aberrant stimulatory effect on hematopoietic colony formation. Conversely, in control vector-transduced CD34+ cells, the typical inhibitory response to IFN-gamma was seen. Our results indicate that inhibitory cytokines such as IFN-gamma may exhibit diverse biologic effects depending on the intracellular balance of transcriptional regulators, in turn influenced by the activation and differentiation status of the target cells.

Calcium-Calmodulin-Dependent Protein Kinases↗

A cytokine-selective defect in interleukin-1 beta-mediated acute phase gene expression in a subclone of the human hepatoma cell line (HEPG2).

Several well-differentiated human hepatoma cell lines (HepG2, Hep3B) have been used to identify factors which regulate hepatic gene expression during the host response to inflammation/tissue injury (acute phase response). Studies in these cell lines, as well as in primary cultures of rat, rabbit, and mouse hepatocytes, have demonstrated that interleukin-1 beta (IL-1 beta), tumor necrosis factor (TNF-alpha), and interferon-beta 2 (IFN-beta 2) each mediate changes in expression of several hepatic acute phase genes. In this study we identify a subclone of the HepG2 cell line in which there is a selective defect in IL-1 beta-mediated acute phase gene expression. Recombinant human IL-1 beta mediates an increase in synthesis of the positive acute phase complement protein factor B and a decrease in synthesis of negative acute phase protein albumin in the parent uncloned HepG2 cell line (HG2Y), but not in the subclone HG2N. Recombinant human IFN-beta 2 and TNF-alpha, however, regulate acute phase protein synthesis in the subclone HG2N; i.e. IFN-beta 2 and TNF-alpha increase synthesis of factor B and decrease synthesis of albumin in both HG2Y and HG2N cells. Equilibrium binding analysis with 125I-rIL-1 beta at 4 degrees C showed that both HG2N and HG2Y cells bind IL-1 beta specifically and saturably. HG2N and HG2Y possess 3.8 and 4.0 x 10(3) plasma membrane receptors/cell with affinities of 0.96 and 1.07 x 10(-9) M, respectively. Thus, the defect in this subclone of the HepG2 cell line is likely to involve the signal transduction pathway for the biological activity of IL-1 beta and will be useful in elucidation of this signal transduction pathway.

Acute-Phase Proteins↗

Worming pathways to and from DAF-16/FOXO.

In Caenorhabditis elegans, the insulin/IGF-1 signaling pathway controls many biological processes such as life span, fat storage, dauer diapause, reproduction and stress response . This pathway is comprised of many genes including the insulin/IGF-1 receptor (DAF-2) that signals through a conserved PI 3-kinase/AKT pathway and ultimately down-regulates DAF-16, a forkhead transcription factor (FOXO). DAF-16 also receives input from several other pathways that regulate life span such as the germline and the JNK pathway [Hsin, H., Kenyon, C., 1999. Signals from the reproductive system regulate the lifespan of C. elegans. Nature 399, 362-366; Oh, S.W., Mukhopadhyay, A., Svrzikapa, N., Jiang, F., Davis, R.J., Tissenbaum, H.A., 2005. JNK regulates lifespan in Caenorhabditis elegans by modulating nuclear translocation of forkhead transcription factor/DAF-16. Proc. Natl. Acad. Sci. USA 102, 4494-4499]. Therefore, DAF-16 integrates signals from multiple pathways and regulates its downstream target genes to control diverse processes. Here, we discuss the signals to and from DAF-16, with a focus on life span regulation.

Aging↗

Efficient determination of low-frequency normal modes of large protein structures by cluster-NMA.

The structure-function relationship is critical to understanding the biologically relevant functions of protein structures. Various experimental techniques and numerical modeling methods, normal mode analysis (NMA) in particular, have been employed to gain insight into this relationship. Experimental methods are often unable to provide all the desired information and comprehensive modeling techniques are often too computationally expensive. The authors build upon and optimize their cluster normal mode analysis (cNMA) tool, which uses embedded rigid-bodies and harmonic potentials to capture the biologically significant, low-frequency, oscillations of protein structures. cNMA represents atomic details with a scalable number of degrees-of-freedom, which can be chosen independent of structure size. This representation overcomes the otherwise quadratic order memory requirements and cubic order computational complexity associated with traditional all-atom NMA. cNMA is two orders of magnitude faster than traditional all-atom NMA when clustering by residue (very high resolution) and in the more traditional application using a fixed number of clusters, cNMA computationally scales as O(n), which is two orders of complexity faster than all-atom NMA. cNMA is presented and very large example structures with up to 10(6) atoms are analyzed on a notebook PC in the time scale of minutes/hours. The resulting mode shapes help identify biologically significant, conformational pathways.

Cluster Analysis↗