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Signal-induced transcriptional activation by Dif requires the dTRAP80 mediator module.

The Mediator complex is the major multiprotein transcriptional coactivator complex in Drosophila melanogaster. Mediator components interact with diverse sets of transcriptional activator proteins to elicit the sophisticated regulation of gene expression. The distinct phenotypes associated with certain mutations in some of the Mediator genes and the specific in vitro interactions of Mediator gene products with transcriptional activator proteins suggest the presence of activator-specific binding subunits within the Mediator complex. However, the physiological relevance of these selective in vitro interactions has not been addressed. Therefore, we analyzed dTRAP80, one of the putative activator-binding subunits of the Mediator, for specificity of binding to a number of natural transcriptional activators from Drosophila. Among the group of activator proteins that requires the Mediator complex for transcriptional activation, only a subset of these proteins interacted with dTRAP80 in vitro and only these dTRAP80-interacting activators were defective for activation under dTRAP80-deficient in vivo conditions. In particular, activation of Drosophila antimicrobial peptide drosomycin gene expression by the NF-kappa B-like transcription factor Dif during induction of the Toll signaling pathway was dependent on the dTRAP80 module. These results, and the indirect support from the dTRAP80 artificial recruitment assay, indicate that dTRAP80 serves as a genuine activator-binding target responsible for a distinct group of activators.

Animals↗

Human mediator enhances activator-facilitated recruitment of RNA polymerase II and promoter recognition by TATA-binding protein (TBP) independently of TBP-associated factors.

Mediator is a general cofactor implicated in the functions of many transcriptional activators. Although Mediator with different protein compositions has been isolated, it remains unclear how Mediator facilitates activator-dependent transcription, independent of its general stimulation of basal transcription. To define the mechanisms of Mediator function, we isolated two forms of human Mediator complexes (Mediator-P.5 and Mediator-P.85) and demonstrated that Mediator-P.5 clearly functions by enhancing activator-mediated recruitment of RNA polymerase II (pol II), whereas Mediator-P.85 works mainly by stimulating overall basal transcription. The coactivator function of Mediator-P.5 was not impaired when TATA-binding protein (TBP) was used in place of TFIID, but it was abolished when another general cofactor, PC4, was omitted from the reaction or when Mediator-P.5 was added after pol II entry into the preinitiation complex. Moreover, Mediator- P.5 is able to enhance TBP binding to the TATA box in an activator-dependent manner. Our data provides biochemical evidence that Mediator functions by facilitating activator-mediated recruitment of pol II and also promoter recognition by TBP, both of which can occur in the absence of TBP-associated factors in TFIID.

Cells, Cultured↗

Analysis of a structural determinant in thrombin-protease nexin 1 complexes that mediates clearance by the low density lipoprotein receptor-related protein.

We recently identified a synthetic peptide, Pro47-Ile58, derived from the mature protease nexin 1 (PN1) sequence, that inhibited the low density lipoprotein receptor-related protein (LRP)-mediated internalization of thrombin-PN1 (Th-PN1) complexes. Presently, we have analyzed this sequence in Th-PN1 complex catabolism using two independent approaches: 1) An antibody was generated against Pro47-Ile58, which inhibited complex degradation by 70% but had no effect on the binding of the complexes to cell surface heparins. This places the structural determinant in PN1 mediating complex internalization by the LRP outside of the heparin-binding site. 2) Site-directed genetic variants of PN1 with a single Ala substitution at His48, or two Ala substitutions, one at His48 and another at Asp49, were expressed in Sf9 insect cells. The catabolic rate of complexes formed between Th and the singly substituted and doubly substituted variants was lowered to 50 and 15%, respectively, when compared with the catabolic rate of native Th-PN1 complexes. This is the first analysis of a structural determinant in a serine protease inhibitor (SERPIN) required for LRP-mediated internalization and in part may explain the cryptic nature of this site in the unreacted serine protease inhibitor.

Amino Acid Sequence↗

New insights into the formation of active nonsense-mediated decay complexes.

In the nonsense-mediated mRNA decay (NMD) pathway, an exon-junction protein complex (EJC) and hUpf proteins mediate rapid downregulation of aberrant mRNAs that terminate translation upstream of the last splice junction. Two EJC subunits, Y14 and RNPS1, have been proposed to act as a link between splicing and NMD by recruiting hUpf3 and the other hUpf proteins. New studies now present evidence that Y14 is directly involved in NMD, and that Y14 is required for hUpf3 activity. These findings suggest unforeseen intricacies in the formation of active NMD complexes.

Animals↗

Decreased activity of complement-mediated immune complex clearance in hemodialysis patients.

Complement-mediated immune complex (IC) clearance was examined in the sera from regular hemodialysis patients, who accumulated excess factor D in the circulation. Both complement activities for the inhibition of insoluble IC formation and the solubilization of insoluble IC were lower in the sera from these patients than in the sera from normal individuals. A similar decrease in complement activities was observed in normal serum fortified with excess factor D. In addition, complement-processed IC was found to be bound less effectively to human erythrocytes via complement receptor type 1 in the sera from these patients and from normal serum fortified with excess factor D than in normal serum. Gel-filtration HPLC analysis revealed a decrease in covalent binding of C3 fragments to IC solubilized in the sera from hemodialysis patients or in normal serum fortified with excess factor D. This supports the notion that lower complement-mediated IC clearance is due to the paucity of complement fragments bound to IC. It is suggested that some detrimental alterations in the complement system, probably due to excess factor D, cause decreased IC clearance activity in hemodialysis patients with chronic renal failure.

Antigen-Antibody Complex↗

Studies of a disposable biosensor based on the beta-cyclodextrin inclusion complex as mediator.

This paper reports the use of a disposable voltammetric biosensor based on a screen-printed basal electrode and highly efficient mediators, the beta-cyclodextrin inclusion complexes tetramethylbenzidine and ferrocene. The polyphenol oxidase, contained in the crude extract of mushroom, was immobilized in the membrane of the cross-linked beta-cyclodextrin polymer. The resulting biosensor gave excellent analytical performance due to the supramolecular complexation for mediators. It responded to the concentration of dopamine with high selectively in the range from 1.0 x 10(-9) to 1.0 x 10(-6) M with a detection limit as low as 5 x 10(-10) M. The response time for reaching 90% of its steady-state value was less than 60 s, and the activity was retained for at least 15 days.

Agaricales↗

Stacking interactions between aromatic amino acids and adenine ring of ATP in zinc mediated ternary complexes.

Spectrophotometric studies have provided evidence for zinc-mediated ternary complexes between ATP and aromatic amino acids. The hypochromicity observed in the 260 nm band of ATP increased in the order phenylalanine less than tyrosine less than tryptophan. Adding alanine did not produce any change of the ATP spectrum. The association constant was four fold higher for the ATP-Zinc-Tryptophan complex than for that of the ATP-Zinc-Alanine. The increased stability of the former complex was ascribed to the stacking interaction between indole and adenine rings. The maximum concentration of the ATP-Zinc-Tryptophan complex occurred at about pH 8.0. For these ternary complexes several possible stacked structures involving or not involving N(7) of adenine are discussed.

Adenine↗

Atom transfer radical cyclisation reactions mediated by copper complexes.

This article describes recent advances in the use of copper complexes in mediating atom transfer radical cyclisation reactions (ATRC). Recent developments have included the design of activated complexes which mediate the cyclisation of tri-, di-, and mono-halo derived substrates at ambient temperatures. Using this methodology, cyclisation to give a variety of ring sizes (4-18 membered rings) has been demonstrated. In addition tandem and radical-polar crossover reactions have also been developed. The design of solid supported and perfluorous complexes that mediate cyclisations may make this approach to the synthesis of rings more attractive towards industrial applications.

Journal Article↗

Modulation of the stability of a Lac repressor mediated looped complex by temperature and ions: allosteric regulation by chloride.

The lactose repressor of Escherichia coli (LacI) associates to a bidentate tetramer in solution and can simultaneously bind two operators to form a protein-mediated "looped complex". Studies have been conducted of the binding of LacI to two operators separated by approximately 11 helical turns of DNA. Quantitative DNase I footprint titration analysis of the stability of the LacI-mediated looped complex reveals that the Gibbs free energy of cyclization (delta Gzeroj) of the looped complex of 11.7 +/- 0.4 kcal/mol is invariant with temperature. van't Hoff analysis reveals a large and positive enthalpy of cyclization (delta H degrees = 12.3 +/- 2.4 kcal/mol) and an entropy that is small and positive (delta S degrees = 2.2 cal/deg). Quantitative DNase I footprint titration and kinetic dissociation studies were also conducted as a function of counter-ion type and concentration. Increasing concentrations of KCl or potassium glutamate destabilize the looped complex, a result completely accounted for by increases in the intrinsic DNA-binding free energies. While the value of delta Gzeroj is invariant with ion concentration, chloride is a positive regulator. The value of delta Gzeroj decreases by 1.5 kcal/mol upon substitution of chloride for glutamate. Measurements of delta Gzeroj conducted as a function of chloride concentration at constant ionic strength reveal that approximately one chloride ion per tetramer is bound upon looped complex formation. These results demonstrate specific allosteric regulation of the formation of the LacI-mediated looped complex by a mechanism distinct from the regulation of the constituent protein--DNA interactions.

Allosteric Regulation↗

Stability of a Lac repressor mediated "looped complex".

The quantitation of the stability of a protein-mediated "looped complex" of the Lac repressor and DNA containing two protein-binding sites whose centers of symmetry are separated by 11 helical turns (114 bp) was accomplished by footprint and gel mobility-shift titration techniques. Lac repressor binding to this DNA was only moderately cooperative; a cooperative free energy of -1.0 kcal/mol was calculated in a model-independent fashion from the individual-site loading energies obtained from the footprint titration studies. In order to partition the cooperative binding energy into components representing the dimer-tetramer association of Lac repressor and the cyclization probability of the intervening DNA, advantage was taken of the presence of experimental measures that were in proportion to the concentration of the looped complex present in solution. One measure was the DNase I hypersensitivity observed in footprint titrations in bands located between the two binding sites. The second measure resulted from the electrophoretic resolution in the gel mobility-shift titrations of the band representing the doubly liganded "tandem complex" from the band representing the singly liganded complexes, including the looped complex. Analysis of the footprint and mobility-shift titration data utilizing this additional information showed that approximately 65% of the molecules present in solution are looped complexes at pH 7.0, 100 mM KCl, and 20 degrees C when the binding sites on the DNA are saturated with protein. Reconciliation of the observed low binding cooperativity and the high proportion of looped complexes could only be obtained when the titration data were analyzed by a model in which Lac repressor tetramers dissociate into dimers in solution. The proportion of looped complexes present in solution is highly dependent on the dimer-tetramer association constant, delta Gtet. This result is consistent with the determination by high-pressure fluorescence techniques that Lac repressor tetramers dissociate with an association free energy comparable to their DNA-binding free energies [Royer, C. A., Chakerian, A. E., & Matthews, K. S. (1990) Biochemistry 29, 4959-4966]. However, when the value of delta Gtet of -10.6 kcal/mol (at 20 degrees C) reported by Royer et al. (1990) is assumed, the titration data demand that tetramers bind DNA with much greater affinity than dimers: a result inconsistent with the destabilization of tetramers by the operator observed in the dimer-tetramer dissociation studies.(ABSTRACT TRUNCATED AT 400 WORDS)

Base Sequence↗

Identification of sumoylated proteins by systematic immunoprecipitation of the budding yeast proteome.

The identification of post-translational modifications to proteins is critical for understanding many important aspects of biology. Utilizing a collection of epitope-tagged yeast strains, we developed a novel approach to determine which proteins are modified by the small ubiquitin-related modifier (SUMO). We crossed traits useful for the detection of SUMO conjugation into 4246 tandem affinity purification-tagged strains and successfully immunoprecipitated and screened 2893 of these proteins for association with SUMO ( approximately 70% of the expressed proteome detectable by immunoblot analysis). We found 82 proteins associated with SUMO, including many of low abundance. Because our screen was performed under non-denaturing conditions, we were able to identify multiple members of four complexes that were associated with SUMO: the RSC chromatin remodeling complex, the mediator complex, the TFIID complex, and the septin complex. In addition, we describe five new direct conjugates of SUMO, and we mutated SUMO conjugation sites in four proteins. This is the first attempt to immunoprecipitate a large fraction of the proteome of a eukaryote, and it demonstrates the utility of this method to identify post-translational modifications in the yeast proteome.

Cysteine Endopeptidases↗

A mammalian mediator subunit that shares properties with Saccharomyces cerevisiae mediator subunit Cse2.

The multiprotein Mediator complex is a coactivator required for activation of RNA polymerase II transcription by DNA bound transcription factors. We previously identified and partially purified a mammalian Mediator complex from rat liver nuclei (Brower, C.S., Sato, S., Tomomori-Sato, C., Kamura, T., Pause, A., Stearman, R., Klausner, R.D., Malik, S., Lane, W.S., Sorokina, I., Roeder, R.G., Conaway, J.W., and Conaway, R.C. (2002) Proc. Natl. Acad. Sci. U. S. A. 99, 10353-10358). Analysis by tandem mass spectrometry of proteins present in the most highly purified rat Mediator fractions led to the identification of a collection of new mammalian Mediator subunits, as well as several potential Mediator subunits including a previously uncharacterized protein encoded by the FLJ10193 open reading frame. In this study, we present direct biochemical evidence that the FLJ10193 protein, which we designate Med25, is a bona fide subunit of the mammalian Mediator complex. In addition, we present evidence that Med25 shares structural and functional properties with Saccharomyces cerevisiae Mediator subunit Cse2 and may be a mammalian Cse2 ortholog. Taken together, our findings identify a novel mammalian Mediator subunit and shed new light on the architecture of the mammalian Mediator complex.

Amino Acid Sequence↗

A standardized method for quantitating the complement-mediated immune complex solubilizing capacity of human serum.

A standardized radioassay for measuring the complement-mediated immune complex solubilizing capacity (CMSC) and the initial kinetics of the solubilization (IKS) reaction is described. The total complement (C)-mediated solubilizing capacity was determined after incubation of diluted serum and 125I-BSA-anti-BSA. Percentage C-mediated solubilization (CMS) was measured after centrifugation by determining the distribution of radioactivity. The dependency of CMSC upon factors such as serum dilution and buffer system used, amount of IC added to serum, serum storage conditions and centrifugation conditions was investigated in order to optimize the assay. The CVt of the standardized assay was 0.10-0.17 depending upon the CMSC level measured. Treatment which inactivates C factors (heating), interferes with C activation (EDTA) or activates and consumes C components (zymosan) markedly reduces the CMSC. Preliminary investigation of pathological sera showed that both IKS and CMSC were clearly reduced in SLE sera. By contrast, rheumatoid arthritis sera exhibited normal IKS and only marginal reduction in CMSC.

Adolescent↗

Mechanism and computer simulation of immune complex formation, opsonization, and clearance.

A computer simulation of immune complex formation, opsonization, and clearance has been developed (ICMODEL) that uses equations describing the kinetics of known immunologic processes and an additional pathologic process of immune complex-mediated tissue damage and antigen production. ICMODEL was used to (1) compare simulated with reported immune response kinetics, (2) evaluate the relative stability of the immune system described by the simulation, and (3) determine the conditions required to produce high immune complex levels as found in patients with immune complex-mediated disease. ICMODEL simulated primary and secondary immune responses as well as short- and long-term immunity. ICMODEL also depicted a relatively stable immune response system. Under certain conditions, however, the system could be perturbed, resulting in an unstable response. For example, when the rate constant regulating Fc gamma-mediated phagocytosis was decreased and the rate constant regulating immune complex-mediated tissue damage/antigen production was increased, immune complex concentrations oscillated with time and increased exponentially. These data suggest that ICMODEL can be used to define the specific parameters that, when perturbed, will give rise to increased immune complex concentrations. As such, this model has direct implications for studies of immune complex-mediated disease in human patients.

Animals↗

Reduced complement-mediated immune complex solubilizing capacity and the presence of incompletely solubilized immune complexes in SLE sera.

Reduced complement-mediated solubilization (CMS) of pre-formed immune complexes (IC) was demonstrated in sera from 11 out of 12 SLE patients. The presence of incompletely solubilized endogeneous IC in SLE sera was indicated by the following findings: (1) When IC positive SLE sera with reduced CMS capacity were mixed with normal donor sera they inhibited the CMS of the latter sera. (2) Resuspended PEG (2.75%) precipitates obtained from SLE sera inhibited the CMS of normal donor sera. (3) Non-solubilized or incompletely complement solubilized IC in SLE sera give a strong response in the PEG-CC assay for IC. The IC activity of SLE sera was clearly reduced in this assay when the endogeneous IC were solubilized prior to testing. In contrast, sera of 14 rheumatoid arthritis (RA) patients exhibited normal CMS. IC which could be further solubilized by complement were not demonstrable although all RA sera were IC positive.

Adult↗

Complement-mediated immune complex solubilization and precipitation inhibition in sera of patients with non-Hodgkin's lymphoma.

The complement functions of 42 patients with non-Hodgkin's lymphoma have been examined. The patients were divided into groups according to the severity of their disease: 1st--patients with high-grade lymphomas, 2nd--with low-grade lymphomas and 3rd--with chronic lymphocytic leukaemia. The adopted methods were the measurements of complement-mediated immune complex solubilizing capacity (CMSC) and the complement-mediated immune complex precipitation inhibition capacity (IPIC). The CMSC and IPIC values were examined parallel with CH50, C3 complement levels and with levels of circulating immune complexes (CIC) in the sera of patients. The results indicated that the acquired deficiency of complement functions could be established by CMSC and IPIC measurements in the sera of patients with high-grade lymphomas. These defects were found to be milder in the group with low-grade lymphomas, and were not detectable in CLL. The changes of CH50 levels were found to be similar to that of IPIC values and the decrease in C3 levels was detectable in high-grade and low-grade lymphomas too. Elevated CIC levels were found in those cases in which both CMSC and IPIC were decreased.

Antigen-Antibody Complex↗

[Fc-receptor mediated immune complex clearance function of the mononuclear phagocyte system in systemic lupus erythematosus].

Fc receptor mediated immune complex clearance function was measured in patients with systemic lupus erythematosus. Autologous erythrocytes were sensitized by human IgG anti-Rh(D) and used as immune complex model. An impaired Fc receptor function was demonstrable in 20 of 25 investigated patients. We have found a significant correlation between the seriousness of the defect and the step of the immunologic activity of the patients, but not between the impaired Fc receptor function and clinical activity and renal manifestation in our SLE patients. Further studies are necessary to determine the relevance of this phenomenon and to clear the possibility of therapeutical influence.

Adult↗

A transcriptional mediator protein that is required for activation of many RNA polymerase II promoters and is conserved from yeast to humans.

A temperature-sensitive mutation was obtained in Med6p, a component of the mediator complex from the yeast Saccharomyces cerevisiae. The mediator complex has been shown to enable transcriptional activation in vitro. This mutation in Med6p abolished activation of transcription from four of five inducible promoters tested in vivo. There was no effect, however, on uninduced transcription, transcription of constitutively expressed genes, or transcription by RNA polymerases I and III. Mediator-RNA polymerase II complex isolated from the mutant yeast strain was temperature sensitive for transcriptional activation in a reconstituted in vitro system due to a defect in initiation complex formation. A database search revealed the existence of MED6-related genes in humans and Caenorhabditis elegans, suggesting that the role of mediator in transcriptional activation is conserved throughout the evolution.

Amino Acid Sequence↗