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At least 883 records · Page 49Linked to original sources
PubMed1996

Monitoring of CD95 (APO-1/Fas) ligand expression in human T cells by quantitative RT-PCR.

CD95 (APO-1/Fas) receptor/ligand interaction is a key regulatory pathway for apoptosis in lymphoid cells. We developed a quantitative RT-PCR for the human CD95-L to determine expression levels in lymphoid cell lines and in lymphocytes derived from blood of healthy individuals. In untreated peripheral blood T lymphocytes and T cell lines constitutive expression of the CD95-L mRNA was found at low levels. Stimulation of T cells by treatment with PMA and ionomycine (P/I) lead up to a 100-fold maximal increase in CD95-L mRNA after 4 h. CD95-L mRNA is produced by activated CD8 and CD4T cells. In vivo increased CD95-L mRNA expression was found in freshly isolated T cells during the acute phase of EBV infection. In contrast to T cells, CD95-L mRNA could be induced in some B lineage cell lines only after five days of stimulation. Since defective or accelerated CD95/CD95-L interaction is considered to be involved in the pathogenesis of lymphoproliferation, autoimmunity and AIDS, the quantitative RT-PCR assay described in this paper may provide a powerful tool for monitoring CD95-L expression in these diseases.

Journal Article↗
PubMedDate not supplied

[The key enzymes of the alternative pathways of serine utilization in gluconeogenesis in chickens during individual development].

It has been shown that in embryonic liver and kidney of chicks, serine is involved into gluconeogenesis almost exclusively via serine-pyruvate aminotransferase. This relationship stands true also for the liver of adult hens. On the contrary, in the kidney of adult hens, there is a significant increase in the activity of serine dehydratase, as compared to the level of the activity of this enzyme in embryogenesis and in the liver of adult hens.

Animals↗
PubMed1990

Transfer RNA and the formation of the heme and chlorophyll precursor, 5-aminolevulinic acid.

5-Aminolevulinic acid is the first committed precursor for the synthesis of porphyrins such as hemes and chlorophylls. In many organisms aminolevulinate is synthesized from glutamate in a three-step pathway (C5 pathway). The key step in this conversion is a tRNA-mediated reduction of glutamate to glutamate-1-semialdehyde. tRNA is a specific cofactor for an NADPH-dependent enzyme, Glu-tRNA reductase, which is capable of sequence-specific recognition of Glu-tRNA(Glu). tRNA(Glu) is a dual-function molecule; it participates both in protein and in aminolevulinate biosynthesis. This reduction reaction represents a novel role for tRNA where it participates in a metabolic conversion of its amino acid into a low molecular weight metabolite which is subsequently not used in peptide bond synthesis.

Aldehyde Oxidoreductases↗
PubMed1988

[Activity and characteristics of the regulation of glycolytic proteins in Staphylococcus aureus].

Lactate has been determined to be the ground glyucolysis product in the staphylococci strains under study. Acetate and CO2 are produced in small quantities. Considerable differences in storing lactate under aerobic and unaerobic conditions have not been found. Pasteur effect reaches 20.5--23.3%. The controlling glycoysis unit study has shown that it may locate on the different sections of Embden-Meyergof-Parnas pathway. The key regulation enzyme activity of hexokinase, phosphofructokinase and pyruvatekinase has been determined.

Acetates↗
PubMed2026

[Effects and mechanisms of Jiawei Yigong San on the Th17/Treg balance in food allergy].

Objective To explore the effects and mechanisms of Jiawei Yigong San (JWYGS) on the T helper type 17 (Th17)/regulatory T (Treg) cell balance in food allergy (FA). Methods Active components, action targets of JWYGS, and FA-related targets, were screened via network pharmacology. Overlapping targets between JWYGS and FA were used to construct a protein-protein interaction (PPI) network. Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses were performed to predict key signaling pathways. Molecular docking was conducted to validate the binding affinity between the main active components and the predicted targets. Mice were randomly divided into control group, model group, JWYGS low-dose, medium-dose, and high-dose groups, and dexamethasone (DXM) group. An ovalbumin (OVA)-induced FA model was established. During the OVA challenge period, mice received daily intragastric administration, after which allergy and diarrhea scores were assessed. Small intestinal pathology was evaluated by HE staining. Serum ovalbumin-specific immunoglobulin E (OVA-sIgE), interleukin 6 (IL-6), IL-17, IL-2, and IL-10 were measured by ELISA. Small intestinal IL-6, IL-17, and IL-10 protein expression was detected by immunohistochemistry. Splenic Th17 and Treg cells were quantified by flow cytometry, and the Th17/Treg ratio was calculated. The mRNA expression of IL-6, retinoic acid receptor-related orphan receptor γt (RORγt), and forkhead box protein P3 (FOXP3) in the small intestine was detected by qPCR. Results Network pharmacology identified 235 active components of JWYGS and 136 common targets. GO and KEGG enrichment analyses highlighted cytokine response and Th17 differentiation. Molecular docking confirmed stable binding between core components and targets. Compared with the control group, the model group exhibited aggravated allergy and diarrhea scores, marked small intestinal inflammation and mucosal damage, elevated serum levels of OVA-sIgE, IL-6, IL-17 and IL-2, along with increased splenic Th17 cell frequency and Th17/Treg ratio. Intestinal IL-6 and IL-17 protein levels as well as IL-6 and RORγt mRNA expression were upregulated, whereas serum IL-10 levels were decreased, and intestinal expression of IL-10 protein and FOXP3 mRNA was downregulated. After JWYGS treatment, allergy and diarrhea scores were significantly reduced. Small intestinal inflammation and mucosal damage were alleviated. Serum levels of OVA-sIgE, IL-17, IL-6 and IL-2, Th17 cell frequency and the Th17/Treg ratio, intestinal IL-6 and IL-17 protein levels were decreased. IL-6 and RORγt mRNA expression was downregulated. Serum IL-10 levels were increased and intestinal expression of IL-10 protein and FOXP3 mRNA was upregulated. Moreover, the JWYGS high-dose group demonstrated comparable efficacy to the DXM group. Conclusion JWYGS can ameliorate symptoms and reverse the Th17/Treg imbalance in FA mice, potentially by inhibiting IL-6 transcription and regulating RORγt/FOXP3 expression.

Animals↗
PubMed1994

TCR-dependent and -independent signaling mechanisms differentially regulate lymphokine gene expression in the murine T helper clone D10.G4.1.

The signaling mechanisms that regulate lymphokine gene expression in the murine Th2 clone D10.G4.1 were investigated by comparing the steady state mRNA levels of six lymphokine genes in response to cellular treatment with various activators and inhibitors of several key signaling pathways. A surprising degree of differential regulation was found. All of the genes studied (IL-3, IL-4, IL-5, IL-6, IL-10, and granulocyte-macrophage (GM)-CSF) were induced by the lectin Con A and the TCR idiotype-specific mAb 3D3. However, the induction of the IL-3, IL-4, and GM-CSF genes, but not the IL-5, IL-6, and IL-10 genes, was strongly inhibited by cyclosporin A. Furthermore, IL-5, IL-6, and IL-10 genes were independently induced by IL-1 alpha, the phorbol ester PMA, and by forskolin, an activator of adenylate cyclase. Results of studies performed with use of the Ca2+ ionophore A23187 indicated that elevation of intracellular Ca2+ levels is sufficient to fully induce IL-3 and IL-4 gene expression. Protein kinase C activation was also required for full induction of the GM-CSF gene and seemed to be obligatory for maximal IL-5 gene expression. The patterns of mRNA induction by the different stimuli broadly correlated with increased rates of transcription. In addition to their induction by IL-1 alpha, the IL-5, IL-6, and IL-10 genes were also induced by mAbs to CD2 and to CD45. In contrast, adding CD45 mAb strongly inhibited the induction of IL-3, IL-4, and GM-CSF genes through TCR stimulation. These results indicate that distinct groups of lymphokine genes may be differentially regulated by signaling pathways that are activated by stimulation of the TCR and other cell surface molecules.

Animals↗
PubMed1993

Hepatic production of very low density lipoprotein, catabolism of low density lipoprotein, biliary lipid secretion, and bile salt synthesis in rats fed a bean (Phaseolus vulgaris) diet.

Rats fed a bean diet develop a significant hypocholesterolemia. The catabolism of low density lipoprotein (LDL; d 1.019-1.063 g/ml) was studied in vivo and in vitro in the isolated perfused liver of rats fed either a casein or a bean diet. The clearance of LDL was significantly increased by 100% from 0.38 +/- 0.04 to 0.63 +/- 0.04 ml/h x 100 g body wt in vivo in the bean-fed rat. Similarly, the clearance of homologous and heterologous (human) LDL was also increased by 100% in the isolated perfused liver of bean-fed animals. Spleen, kidney, and hepatic cholesterogenesis was increased by 150% in these animals. Bile salt synthesis was increased from 1.54 +/- 0.02 to 2.84 +/- 0.09 nmol/min x g liver wt (P < 0.02) and biliary cholesterol output by 200% from 0.81 +/- 0.03 to 2.18 +/- 0.04 nmol/min x g (P < 0.02) in the isolated perfused liver of rats fed a bean diet. These results explained the depletion of hepatic cholesterol and were consistent with the LDL turnover studies, suggesting that apoB/E receptor activity was increased in these animals. ApoB and triglyceride secretion in the d < 1.060 g/ml lipoprotein fraction of liver perfusates remained normal in the bean-fed rats. In contrast, total sinusoidal cholesterol output isolated in the d < 1.060 g/ml fraction significantly decreased by 100% after 90 min of perfusion. Cholesterol output in the d > 1.060 g/ml lipoprotein fraction was unmodified by the bean diet. These data demonstrate that key metabolic pathways of hepatic cholesterol are modified in the bean-fed rat.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1998

Studies using antigen-presenting cells lacking expression of both B7-1 (CD80) and B7-2 (CD86) show distinct requirements for B7 molecules during priming versus restimulation of Th2 but not Th1 cytokine production.

The differentiation of CD4+ T cells into a Th1 vs Th2 phenotype profoundly influences the outcome of autoimmune and infectious diseases. B7 costimulation has been shown to affect the production of both Th1 and Th2 cytokines, depending on the system studied. There is, consequently, great interest in manipulating the B7 costimulatory signal for therapeutic purposes. To optimally manipulate this key immunoregulatory pathway, the contribution of B7 costimulation to cytokine production requires further clarification. We have compared the B7 requirement for cytokine production by naive vs previously activated T cells using DO11.10 TCR transgenic CD4+ T cells and splenic APCs from mice lacking B7 expression. Our data indicate that induction of IL-4 production and Th2 differentiation by naive T cells is highly dependent on B7 molecules, whereas IL-4 production by previously activated T cells is B7 independent. The predominant contribution of B7-mediated signals to Th1 cytokine production by both naive and primed T cells is upon IL-2 production (and expansion) rather than IFN-gamma (effector cytokine) production. Thus, our studies demonstrate that the antigenic experience of a T cell at the time of B7 blockade may determine whether blockade predominantly affects T cell expansion, differentiation, or effector cytokine production. These differential effects of B7 costimulation on IL-2 vs IFN-gamma production and on IL-4 production by naive vs primed T cells have important implications for understanding how B7:CD28/CTLA4 blockade can be effectively used to manipulate cytokine production in vivo.

Amino Acid Sequence↗
PubMed2001

Protein kinase CK2: signaling and tumorigenesis in the mammary gland.

Breast cancer is a major cause of cancer death in women, and the genetic abnormalities leading to the common sporadic forms of the disease are still under active investigation. CK2 has been reported to be upregulated in human breast cancer, which these studies confirm; CK2 is also upregulated in rat carcinogen-induced breast tumors. Transgenic mice overexpressing CK2alpha in the mammary gland develop mammary hyperplasia, dysplasia, and eventually adenocarcinomas, demonstrating that dysregulated expression of CK2 can contribute to transformation of the mammary epithelium. These mammary tumors have evidence of activation of the Wnt and NFkappaB pathways and upregulation of c-Myc. CK2 is capable of phosphorylating the key signaling molecule in the Wnt pathway, the transcriptional cofactor beta-catenin, and regulating its turnover. CK2 is known to phosphorylate IkappaB and thereby regulate basal NFkappaB levels; in the mammary cell lines and tumors, CK2 activity correlates with NFkappaB levels and inhibition of CK2 downregulates NFkappaB. Thus, CK2 may promote breast cancer through dysregulation of key pathways of transcriptional control in the mammary epithelium, and inhibition of CK2 has a potential role in the treatment of breast and other cancers.

Adenocarcinoma↗
PubMed1990

Dynamic Monte Carlo simulations of globular protein folding/unfolding pathways. I. Six-member, Greek key beta-barrel proteins.

In the context of a simplified diamond lattice model of a six-member, Greek key beta-barrel protein that is closely related in topology to plastocyanin, the nature of the folding and unfolding pathways have been investigated using dynamic Monte Carlo techniques. The mechanism of Greek key assembly is best described as punctuated "on site construction". Folding typically starts at or near a beta-turn, and then the beta-strands sequentially form by using existing folded structure as a scaffold onto which subsequent tertiary structure assembles. On average, beta-strands tend to zip up from one tight bend to the next. After the four-member, beta-barrel assembles, there is a long pause as the random coil portion of the chain containing the long loop thrahes about trying to find the native state. Thus, there is an entropic barrier that must be surmounted. However, while a given piece of the protein may be folding, another section may be unfolding. A competition therefore exists to assemble a fairly stable intermediate before it dissolves. Folding may initiate at any of the tight turns, but the turn closer to the N terminus seems to be preferred due to well-known excluded volume effects. When the protein first starts to fold, there are a multiplicity of folding pathways, but the number of options is reduced as the system gets closer to the native state. In the early stages, the excluded volume effect exerted by the already assembled protein helps subsequent assembly. Then, near the native conformation, the folded parts reduce the accessible conformational space available to the remaining unfolded sections. Unfolding essentially occurs in reverse. Employing a simple statistical mechanical theory, the configurational free energy along the reaction co-ordinate for this model has been constructed. The free energy surface, in agreement with the simulations, provides the following predictions. The transition state is quite near the native state, and consists of five of the six beta-strands being fully assembled, with the remaining long loop plus sixth beta-strand in place, but only partially assembled. It is separated from the beta-barrel intermediate by a free energy barrier of mainly entropic origin and from the native state by a barrier that is primarily energetic in origin. The latter feature is in agreement with the "Cardboard Box" model described by Goldenberg and Creighton but, unlike their model, the transition state is not a high-energy distorted form of the native state.(ABSTRACT TRUNCATED AT 250 WORDS)

Algorithms↗
PubMed2001

VEGF increases permeability of the endothelial cell monolayer by activation of PKB/akt, endothelial nitric-oxide synthase, and MAP kinase pathways.

VEGF is a key regulator of vascular permeability. However, its signaling pathways are incompletely understood. We tested the hypothesis that VEGF regulates endothelial cell (EC) permeability by activating PKB/akt, NOS, and MAP kinase dependent pathways using human umbilical vein EC (HUVEC). Permeability was measured from FITC-dextran 70-kDa flux across the EC monolayer at baseline and after VEGF at 0.034, 0.068, 1, 10, and 100 nM. VEGF increased HUVEC permeability to FITC-dextran in a dose-dependent manner. VEGF (1 nM) increased permeability from 3.9 x 10(-6) +/- 0.7 x 10(-6) to 14.0 x 10(-6) +/- 1.7 x 10(-6) cm/s (mean +/- SEM; P < 0.001). Permeability changes were also assessed after treatment with 1, 10, and 100 nM wortmannin (PI 3-kinase inhibitor); 0.01, 0.1, and 1.0 nM LY294002 (PI 3-kinase inhibitor); 200 microM l-NMMA (NOS inhibitor); 2.7 microM AG126 (p42/44(MAPK) inhibitor); and 0.006, 0.06, and 0.6 microM SB203580 (p38(MAPK) inhibitor). All inhibitors blocked VEGF-induced permeability changes. Our data demonstrate that (1) VEGF increases permeability of EC monolayers in a dose-dependent fashion, and (2) VEGF-induced permeability is mediated through PI-3 kinase-PKB, NOS, and MAP-kinase signaling cascades. These observations suggest that microvascular hyperpermeability associated with inflammation and vascular disease is mediated by activation of these EC signaling pathways.

Capillary Permeability↗
PubMed1990

Maximum activities of key enzymes of glycolysis, glutaminolysis, pentose phosphate pathway and tricarboxylic acid cycle in normal, neoplastic and suppressed cells.

1. Maximal activities of some key enzymes of glycolysis, the pentose phosphate pathway, the tricarboxylic acid cycle and glutaminolysis were measured in homogenates from a variety of normal, neoplastic and suppressed cells. 2. The relative activities of hexokinase and 6-phosphofructokinase suggest that, particularly in neoplastic cells, in which the capacity for glucose transport is high, hexokinase could approach saturation in respect to intracellular glucose; consequently, hexokinase and phosphofructokinase could play an important role in the regulation of glycolytic flux in these cells. 3. The activity of pyruvate kinase is considerably higher in tumorigenic cells than in non-tumorigenic cells and higher in metastatic cells than in tumorigenic cells: for non-tumorigenic cells the activities range from 28.4 to 574, for tumorigenic cells from 899 to 1280, and for metastatic cells from 1590 to 1627 nmol/min per mg of protein. 4. The ratio of pyruvate kinase activity to 2 x phosphofructokinase activity is very high in neoplastic cells. The mean is 22.4 for neoplastic cells, whereas for muscle from 60 different animals it is only 3.8. 5. Both citrate synthase and isocitrate dehydrogenase activities are present in non-neoplastic and neoplastic cells, suggesting that the full complement of tricarboxylic-acid-cycle enzymes are present in these latter cells. 6. In neoplastic cells, the activity of glutaminase is similar to or greater than that of hexokinase, which suggests that glutamine may be as important as glucose for energy generation in these cells.

Cell Line↗
PubMed1998

Dual 1,25-dihydroxyvitamin D3 signal response pathways in osteoblasts: cross-talk between genomic and membrane-initiated pathways.

Osteoblasts are key regulatory cells in the control of systemic calcium ion (Ca2+) homeostasis. They, along with cells in the kidney and intestine, function as an integral part of the vitamin D endocrine system. The hormonally active form of vitamin D, 1,25-dihydroxyvitamin D3 (1,25[OH]2D3), interacts with osteoblasts at several levels to modulate their phenotype and function. The interactions involve distinct receptor systems that operate on unique time scales. Rapid nongenomic actions (milliseconds to minutes), mediated through membrane receptor systems, do not require protein synthesis and include activation of voltage-sensitive Ca2+ channels, induction of phospholipid and sphingolipid turnover, elevation of intracellular Ca2+ concentrations, priming of parathyroid hormone (PTH)-sensitive ion channels, and activation of second messenger systems. In the longer term (many hours to days), interactions mediated through binding of 1,25(OH)2D3 to nuclear receptors, present in mature osteoblasts, modulate transcription of target genes. Target genes for 1,25(OH)2D3 including those encoding for the bone matrix proteins osteopontin (OPN) and osteocalcin (OCN), possess vitamin D response elements (VDRE) upstream of the transcriptional start site. In addition, it is now clear that a number of intermediate effects (1 to 3 hours) also occur. These effects require longer times than the aforementioned rapid effects, but precede the long-term consequences of activation of nuclear receptors. These include alterations in the phosphorylation state of various proteins secreted by osteoblasts, including OPN, attributable to activation/inactivation of various intracellular protein kinases and phosphatases. Intermediate effects are likely to involve both membrane-initiated rapid actions and transcriptional effects on early genes that do not require the nuclear receptor for 1,25(OH)2D3. These intermediate effects, therefore, represent ideal targets for the study of the interaction or "cross-talk" between rapid membrane-initiated, nongenomic effects and nuclear receptor-mediated, genomic effects of 1,25(OH)2D3 on osteoblasts. Intermediate effects also invite the study of rapid, non-nuclear receptor-mediated genomic effects of 1,25(OH)2D3 on osteoblasts. Complete understanding of the mechanisms by which 1,25(OH)2D3 exerts its pleiotropic effects on osteoblasts and other target cells, contributing to control of Ca2+ homeostasis, requires integration of the concepts learned from studies of both rapid and long-term pathways.

Animals↗
PubMed2003

Studies on structure-function relationships of indolepyruvate decarboxylase from Enterobacter cloacae, a key enzyme of the indole acetic acid pathway.

Enterobacter cloacae, isolated from the rhizosphere of cucumbers, produces large amounts of indole-3-acetic acid. Indolepyruvate decarboxylase, the key enzyme in the biosynthetic pathway of indole-3-acetic acid, catalyses the formation of indole-3-acetaldehyde and carbon dioxide from indole-3-pyruvic acid. The enzyme requires the cofactors thiamine diphosphate and magnesium ions for catalytic activity. Recombinant indolepyruvate decarboxylase was purified from the host Escherichia coli strain JM109. Specificity of the enzyme for the substrates indole-3-pyruvic acid, pyruvic acid, benzoylformic acid, and seven benzoylformic acid analogues was investigated using a continuous optical assay. Stopped-flow kinetic data showed no indication for substrate activation in the decarboxylation reaction of indole-3-pyruvic acid, pyruvic acid or benzoylformic acid. Size exclusion chromatography and small angle X-ray solution scattering experiments suggested the tetramer as the catalytically active state and a pH-dependent subunit association equilibrium. Analysis of the kinetic constants of the benzoylformic acid analogues according to Hansch et al. [Hansch, C., Leo, A., Unger, S.H., Kim, K.H., Nikaitani, D & Lien, E.J. (1973) J. Med. Chem.16, 1207-1216] and comparison with indole-3-pyruvic acid conversion by pyruvate decarboxylases from Saccharomyces cerevisiae and Zymomonas mobilis provided some insight into the catalytic mechanism of indolepyruvate decarboxylase.

Binding Sites↗
PubMed2002

Interleukin-3, but not granulocyte-macrophage colony-stimulating factor and interleukin-5, inhibits apoptosis of human basophils through phosphatidylinositol 3-kinase: requirement of NF-kappaB-dependent and -independent pathways.

Basophils are key effector cells of allergic reactions. Although proinflammatory cytokines, such as interleukin (IL)-3, granulocyte-macrophage colony-stimulating factor (GM-CSF) and IL-5, inhibit eosinophil apoptosis in vitro, little is known about basophil apoptosis, and the signalling mechanisms required for basophil survival remain undefined. To address this issue, we used a novel negative-selection system to isolate human basophils to a purity of > 95%, and evaluated apoptosis by morphology using light and transmission electron microscopy, and by annexin-V binding and propidium iodide incorporation using flow cytometry. In this study, we demonstrated that the spontaneous rate of apoptotic basophils was higher than that of eosinophils as, at 24 hr, 57.6 +/- 4.7% of basophils underwent apoptosis compared with 39.5 +/- 3.8% of eosinophils. In addition, basophil cell death was significantly inhibited when cultured with IL-3 for 48 hr (84.6 +/- 4.9% vehicle-treated cells versus 40.9 +/- 3.9% IL-3-treated cells). IL-3 also up-regulated basophil CD69 surface expression. The effects of IL-3 on apoptosis and CD69 surface expression of human basophils were completely blocked by LY294002 (LY), a potent inhibitor of phosphatidylinositol 3-kinase (PI3-K), but only partially inhibited by lactacystin, a proteasome inhibitor that prevents degradation of IkappaB and NF-kappaB translocation. These observations reveal the novel finding that IL-3 prevents basophil apoptosis through the activation of PI3-K, which is only partially NF-kappaB dependent. As basophils are active participants in allergic reactions and IL-3 is one of the abundant proinflammatory cytokines in secretions from allergic tissue, we suggest that IL-3-mediated inhibition of basophil apoptosis may exacerbate the inflammation associated with allergic disorders.

Antigens, CD↗
PubMed2003

(De)regulation of key enzyme steps in the shikimate pathway and phenylalanine-specific pathway of the actinomycete Amycolatopsis methanolica.

Prephenate dehydratase (PDT), chorismate mutase (CM) and 3-deoxy-D-arabino-7-heptulosonate 7-phosphate (DAHP) synthase are key regulatory enzymes in aromatic amino acid biosynthesis in the actinomycete Amycolatopsis methanolica. Deregulated, feedback-control-resistant mutants were isolated by incubation of A. methanolica on glucose mineral agar containing the toxic analogue p-fluoro-DL-phenylalanine (pFPhe). Several of these mutants had completely lost PDT sensitivity to Phe inhibition and Tyr activation. Mutant characterization yielded new information about PDT amino acid residues involved in Phe and Tyr effector binding sites. A. methanolica wild-type cells grown on glucose mineral medium normally possess a bifunctional CM/DAHP synthase protein complex (with DS1, a plant-type DAHP synthase). The CM activity of this protein complex is feedback-inhibited by Tyr and Phe, while DS1 activity is mainly inhibited by Trp. Isolation of pFPhe-resistant mutants yielded two feedback-inhibition-resistant CM mutants. These were characterized as regulatory mutants, derepressed in (a) synthesis of CM, now occurring as an abundant, feedback-inhibition-resistant, separate protein, and (b) synthesis of an alternative DAHP synthase (DS2, an E. coli-type DAHP synthase), only inhibited by Tyr and Trp. DS1 and DS2 thus are well integrated in A. methanolica primary metabolism: DS1 and CM form a protein complex, which stimulates CM activity and renders it sensitive to feedback inhibition by Phe and Tyr. Synthesis of CM and DS2 proteins appears to be controlled co-ordinately, sensitive to Phe-mediated feedback repression.

3-Deoxy-7-Phosphoheptulonate Synthase↗
PubMed2006

Beyond microarrays: find key transcription factors controlling signal transduction pathways.

BACKGROUND: Massive gene expression changes in different cellular states measured by microarrays, in fact, reflect just an "echo" of real molecular processes in the cells. Transcription factors constitute a class of the regulatory molecules that typically require posttranscriptional modifications or ligand binding in order to exert their function. Therefore, such important functional changes of transcription factors are not directly visible in the microarray experiments. RESULTS: We developed a novel approach to find key transcription factors that may explain concerted expression changes of specific components of the signal transduction network. The approach aims at revealing evidence of positive feedback loops in the signal transduction circuits through activation of pathway-specific transcription factors. We demonstrate that promoters of genes encoding components of many known signal transduction pathways are enriched by binding sites of those transcription factors that are endpoints of the considered pathways. Application of the approach to the microarray gene expression data on TNF-alpha stimulated primary human endothelial cells helped to reveal novel key transcription factors potentially involved in the regulation of the signal transduction pathways of the cells. CONCLUSION: We developed a novel computational approach for revealing key transcription factors by knowledge-based analysis of gene expression data with the help of databases on gene regulatory networks (TRANSFAC and TRANSPATH. The corresponding software and databases are available at http://www.gene-regulation.com.

Binding Sites↗