Conformation and DNA binding properties of a single-stranded DNA binding region of sigma 70 subunit from Escherichia coli RNA polymerase are modulated by an interaction with the core enzyme

We have explored how IL-15 influences Th1 or Th2 type immune response in vivo. Intraperitoneal application of an IL-15-IgG2b fusion protein (FP) to mice did neither significantly affect the footpad swelling nor the production of hemagglutinizing antibodies in a delayed type hypersensitivity reaction to sheep red blood cells. In contrast, in an established murine Th2 model of sensitization to ovalbumin (OVA), IL-15-IgG2b FP plus OVA sensitization resulted in massively accelerated and enhanced allergen-specific IgE and IgG1 antibody production. In vitro, stimulation of spleen cells from OVA-sensitized mice with OVA+IL-15 or OVA+IL-15-IgG2b resulted in a significantly enhanced IgE production. IL-4 secretion was significantly induced by IL-15 but not by IL-15-IgG2b. An IL-2-IgG2b FP with the same Fc tail as the IL-15-IgG2b FP was used as control in both models. In striking contrast to the IL-15-IgG2b FP, IL-2-IgG2b significantly inhibited the Th2 type antibody production in vivo. The current study suggests that IL-15-IgG2b may be employed as a potent accelerator and enhancer of Th2 type immune responses in vivo, while IL-2-IgG2b can suppress the latter.     

Epitope mapping using histidine-tagged protein fragments: application to Escherichia coli RNA polymerase sigma 70

The pathogenic Neisseria have exploited the processes of horizontal DNA transfer and genetic recombination as mechanisms for the generation of extensive protein variation and modulation of gene expression. Localized recombinations have been well documented in members of multigene families as have alterations in short repetitive sequences. Here we report an analysis of the chromosomal structure of a defined lineage of Neisseria gonorrhoeae strain MSl1 pilin variants. This study reveals the occurrence of large rearrangements, including the amplification of a 26 kb region and an inversion involving more than a third of the chromosome. Additionally, a restriction site polymorphism that correlates with pilin expression has been observed. These findings highlight the flexibility of the gonococcal genome.     

Architecture of a complex between the sigma70 subunit of Escherichia coli RNA polymerase and the nontemplate strand oligonucleotide. Luminescence resonance energy transfer study

We used luminescence energy transfer measurements to determine the localization of 5'- and 3'-ends of a 12-nucleotide nontemplate strand oligonucleotide bound to sigma70 holoenzyme. Five single reactive cysteine mutants of sigma70 (cysteine residues at positions 1, 59, 366, 442, and 596) were labeled with a europium chelate fluorochrome (donor). The oligonucleotide was modified at the 5'- or at the 3'-end with Cy5 fluorochrome (acceptor). The energy transfer was observed upon complex formation between the donor-labeled sigma70 holoenzyme and the acceptor-labeled nontemplate strand oligonucleotide, whereas no interaction was observed with the template strand oligonucleotide. The oligonucleotide was bound in one preferred orientation. This observation together with the sequence specificity of single-stranded oligonucleotide interaction suggests that two mechanisms of discrimination between the template and nontemplate strand are used by sigma70: sequence specificity and strand polarity specificity. The bound oligonucleotide was found to be close to residue 442, confirming that the single-stranded DNA binding site of sigma70 is located in an alpha-helix containing residue 442. The 5'-end of the oligonucleotide was oriented toward the COOH terminus of the helix.     

Conformational changes of the H+-ATPase from Escherichia coli upon nucleotide binding detected by single molecule fluorescence

BACKGROUND: An antiendomysium antibody test using human umbilical cord as antigen has recently been introduced. METHODS: We determined IgA- and IgG-class antihuman umbilical cord (HUC-ab), antireticulin (ARA), and antigliadin antibodies (AGA) in 92 untreated adult coeliac patients, in 95 non-coeliac subjects, and in 4 coeliac patients with selective IgA deficiency. Tissue antibodies were measured with an indirect immunofluorescence method and AGA with an enzyme-linked immunosorbent assay. RESULTS: Of adult coeliac patients 85% were positive for IgA-class HUC-ab, 78% were positive for ARA, and 80% for AGA; the specificity for HUC-ab and ARA was 100%, and for AGA 86%. Combination of HUC-ab, ARA, and high-titre AGA increased the sensitivity to 96% without loss of specificity. IgG-class HUC-ab was positive in 12% of coeliac patients, in all four coeliac patients with IgA deficiency, and in none of the controls. CONCLUSIONS: The HUC-ab test is highly specific but not 100% sensitive for detecting adult coeliac disease. A combination of the IgA-class HUC-ab, ARA, and high-titre AGA tests is recommended. In selective IgA deficiency the IgG-class HUC-ab test seems to work well.     

The kinetics of sigma subunit directed promoter recognition by E. coli RNA polymerase

Time-resolved laser UV irradiation and controlled proteolysis have been used to study the sequential recognition of the lac UV5 promoter by Escherichia coli RNA polymerase. Local rearrangements in the DNA, the appearance of intimate protein-DNA contacts, and structural changes within the sigma subunit together provide specific signatures that define major species populated during this process. At 22 degreesC, a first closed complex is characterised by a transient conformational change in the sigma subunit and by a distortion in the -35 region. Subsequently, direct contacts at -34 and at positions -8, -5 and -3 on the non-template strand appear prior to DNA strand separation. The contact in the -35 consensus region involves only the sigma subunit. This intermediate possesses different structural parameters from that formed by quenching open complexes from 37 degreesC to 14 degreesC. Sigma thus appears as the principal partner acting during promoter recognition, a strongly coupled process involving two major intermediates only.     

Nucleic acids-protein interactions. Conformational changes induced by the binding of aromatic amines to polyadenylic acid

The binding of Tryptamine, Serotonine, Phenylethylamine and Histamine to poly(A) in its single stranded form at pH 7 leads to a decrease of its circular dichroism (C.D) amplitude without any appreciable alteration of the shape of the C.D. spectrum. The magnitude of the effect depends on the size of the aromatic ring and decreases in the order : tryptamine greater than tyramine greater than phenylethylamine greather than histamine. A method is described which allows the calculation of association constants from C.D. data. The C.D. amplitude decreases linearly with concentration of bound molecules. Binding of aromatic amines to poly(A) leads to a change in the proton chemical shifts of both the amine and the poly(A) protons. Quantitative analysis of P.M.R. data demonstrates that the shifts of poly(A) protons are linearly related to the concentration of bound molecules.     

Scanning force microscopy of Escherichia coli RNA polymerase.sigma54 holoenzyme complexes with DNA in buffer and in air

Scanning force microscopy (SFM) was used to visualize complexes of Escherichia coli RNA polymerase.sigma54 (RNAP.sigma54) and a 1036 base-pair linear DNA fragment containing the glnA promoter. In order to preserve the native hydration state of the protein-DNA complexes, the samples were injected directly into the SFM fluid cell and imaged in buffer. With this protocol, an apparent bending angle of 26(+/-34) degrees was determined for the specific complexes at the promoter. The bending angle of the unspecifically bound RNAP.sigma54 showed a somewhat broader distribution of 49(+/-48) degrees, indicating the existence of conformational differences as compared to the closed complex. In about two-thirds of the closed complexes, the RNA polymerase holoenzyme was located in a lateral position with respect to the DNA and the bend of the DNA was pointing away from the protein. This conformation was consistent with the finding that for the complexes at the promoter, the apparent contour length was reduced by only about 6 nm in buffer as compared to the free DNA. From these results we conclude that in the closed complex of RNAP. sigma54, the DNA was not wrapped around the polymerase, and we present a model for the trajectory of the DNA with respect to the RNA polymerase. The images acquired in buffer were compared to samples that were washed with water and then dried before imaging. Two artefacts of the washing and drying process were detected. First, extensive washing of the sample reduced the number of the specific complexes bound at the promoter (closed complex of RNAP.sigma54) from about 70% to 30%. This is likely to be a result of sliding of the RNAP.sigma54 holoenzyme along the DNA induced by the washing process. Second, the apparent DNA shortening of the contour length of RNAP.sigma54-DNA complexes at the promoter as compared to the contour length of the free DNA was 22 nm for the dried samples as opposed to only 6 nm for the undried samples imaged in buffer. This suggests an artefact of the drying process.