The X-ray crystal structure of the Escherichia coli (Ec) direct oxygen sensor heme domain (Ec DosH) has been solved to 1.8 A using Fe multiple-wavelength anomalous dispersion (MAD), and the positions of Met95 have been confirmed by selenomethionine ((Se)Met) MAD. Ec DosH is the sensing part of a larger two-domain sensing/signaling protein, in which the signaling domain has phosphodiesterase activity. The asymmetric unit of the crystal lattice contains a dimer comprised of two differently ligated heme domain monomers. Except for the heme ligands, the monomer heme domains are identical. In one monomer, the heme is ligated by molecular oxygen (O(2)), while in the other monomer, an endogenous Met95 with S --> Fe ligation replaces the exogenous O(2) ligand. In both heme domains, the proximal ligand is His77. Analysis of these structures reveals sizable ligand-dependent conformational changes in the protein chain localized in the FG turn, the G(beta)-strand, and the HI turn. These changes provide insight to the mechanism of signal propagation within the heme domain following initiation due to O(2) dissociation.

Escherichia coli were transformed by electroporation to introduce a plasmid harboring a GFP gene-containing vector. The fluorescence of the purified GFP isolated from the transformant was quenched by myeloperoxidase (MPO)-generated HOCl, by peroxynitrous acid (ONOOH) and by enzymatically or radiolytically generated NO(2)(.) but not by other putative neutrophil-generated oxidants. Fluorescence from the bacterium was effectively quenched by HOCl but not peroxynitrite, oxidizing radicals derived from its O-O bond homolysis, or the other oxidants under study. Exposure of serum-opsonized bacteria to human neutrophils resulted in extensive loss of GFP fluorescence; fluorescence microscopy revealed that phagocytosed bacteria were completely quenched but that bacteria remaining in the external media were unquenched. Addition of sodium azide to the medium to inhibit MPO prevented neutrophil-mediated fluorescence quenching. Because the amount of HOCl required to inhibit bacterial fluorescence was an order of magnitude greater than required to inhibit colonial growth, these results imply that sufficient HOCl was formed within the neutrophil phagosome to kill the microbe.

Two transformed murine macrophage cell lines (RAW 264.7 ATCC TIB-71 and CRL-2278) were examined for oxidant production at various times following activation by using a set of fluorescence and ESR-active probes. Stimulation with a soluble agonist or activation with bacterial lipopolysaccharide plus γ-interferon caused only very small initial increases in O 2 consumption above basal rates; however, at 2-4 h post-activation, respiration increased to 2-3 fold and remained at these elevated levels over the subsequent lifetime of the cell (20-30 h). Oxidation reactions were confined primarily within the cell, as was demonstrated by using phagocytosable dichlorodihydrofluorescein-conjugated latex beads and cyclic hydroxylamines with differing membrane permeabilities. From the intrinsic reactivities of these probes and the time course of their oxidations, one infers induction of apparent peroxidase activity beginning at ∼2 h post-activation, coinciding with the increase in overall respiratory rate; this acquired capability was accompanied by accumulation of a stable horseradish peroxidase-reactive oxidant, presumably H 2 O 2 , in the extracellular medium,. Nitrite ion rapidly accumulated in the extracellular medium over a period of 5-8 h post-activation in both cell lines, indicating the presence of active nitric oxide synthase (iNOS) during that period. Prostaglandin endoperoxide H synthase (COX-2) activity was detected at 15-20 h post-activation by use of sensitive peroxide assay in conjunction with a COX-2 specific inhibitor (DuP-697). Superoxide formation was detected by reaction with hydroethidine within the first hour following activation, but not thereafter. Consistent with the absence of significant respiratory stimulation, the amount of O 2 ·-formed was very small; comparative reactions of cyclic hydroxylamine probes indicated that virtually none of the O 2 ·-was discharged into the external medium. Myeloperoxidase (MPO) activity was probed at various times post-activation by using fluorescein-conjugated polyacrylamide beads, which efficiently trap MPO-generated HOCl in neutrophils to give stable chlorofluorescein products. However, chlorination of the dye was not detected under any conditions in RAW cells, virtually precluding MPO involvement in their intracellular reactions. This same probe was used to determine changes in intraphagosomal pH, which increased slowly from ∼6.5 to ∼8.2 over a 20 h post-phagocytosis period. The cumulative data suggest activation is followed by sequential induction of an endogenous peroxidase, iNOS, and COX-2, with NADPH oxidase-derived O 2 ·-playing a minimal role in direct generation of intracellular oxidants. To account for reported observations of intracellular tyrosine nitration late in the life cycles of macrophages, we propose a novel mechanism wherein iNOS-generated NO 2 -is used by COX-2 to produce NO 2 · as a terminal microbicidal oxidant and nitrating agent.The existence of motile phagocytic cells involved with host defense in higher organisms has been known sin...

Using radioimmunoassays, we examined rates of removal of UV-induced pyrimidine-pyrimidone (6-4) photoproducts ((6-4)PDs) and cyclobutane pyrimidine dimers (CPDs) from 146-base pair nucleosome core DNA (and 166-base pair chromatosome DNA) of confluent human diploid fibroblasts. Dose-response experiments indicate that the yield of (6-4)PDs in core DNA is about 30% that of CPDs in the UV dose range of 0-200 J/m2. Repair experiments indicate that, at 40 J/m2, (6-4)PDs are removed much faster (approximately 75% in 2 h) from nucleosome core (and chromatosome) DNA than CPDs (10-15% in 2 h). A slow rate of removal of CPDs is also observed when the UV dose is reduced to 10 J/m2 (i.e. even when the level of CPDs is less than that of (6-4)PDs at 40 J/m2). These results indicate that (a) the accessibility of repair proteins to (6-4)PDs in nucleosomes is markedly different than their accessibility to CPDs and/or (b) repair enzymes are much more efficient at incising and removing (6-4)PDs than CPDs in human chromatin.

The Xenopus borealis somatic 5S ribosomal RNA gene was used as a model system to determine the mutual effects of nucleosome folding and formation of ultraviolet (UV) photoproducts (primarily cis-syn cyclobutane pyrimidine dimers, or CPDs) in chromatin. We analyzed the preferred rotational and translational settings of 5S rDNA on the histone octamer surface after induction of up to 0.8 CPD/nucleosome core (2.5 kJ/m(2) UV dose). DNase I and hydroxyl radical footprints indicate that UV damage at these levels does not affect the average rotational setting of the 5S rDNA molecules. Moreover, a combination of nuclease trimming and restriction enzyme digestion indicates the preferred translational positions of the histone octamer are not affected by this level of UV damage. We also did not observe differences in the UV damage patterns of irradiated 5S rDNA before or after nucleosome formation, indicating there is little difference in the inhibition of nucleosome folding by specific CPD sites in the 5S rRNA gene. Conversely, nucleosome folding significantly restricts CPD formation at all sites in the three helical turns of the nontranscribed strand located in the dyad axis region of the nucleosome, where DNA is bound exclusively by the histone H3-H4 tetramer. Finally, modulation of the CPD distribution in a 14 nt long pyrimidine tract correlates with its rotational setting on the histone surface, when the strong sequence bias for CPD formation in this tract is minimized by normalization. These results help establish the mutual roles of histone binding and UV photoproducts on their formation in chromatin.

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Using transient absorption spectroscopy and photoacoustic calorimetry (PAC), we have characterized carbon monoxide photodissociation and rebinding to two forms of the heme domain of Bradyrhizobium japonicum FixL. Transient absorption results for the complete heme domain (FixL residues 140-270) and a truncated heme domain (missing 11 residues on the N-teminal end and 14 amino acid residues on the C-terminal end of the full length heme domain) show similar rates for ligand rebinding to the five-coordinate heme domain and the absence of any transient intermediate on a microsecond time scale. Results from PAC studies show that both the truncated and complete heme domains undergo a contraction upon ligand photolysis. In addition, CO photolysis from the complete heme domain gives rise to an intermediate with a lifetime of approximately 150 ns which is absent in the truncated heme domain. We attribute the 150 ns phase to ligand release to the solvent which may be accelerated in the case of the truncated domain. The initial contraction is attributed to changes in the charge distribution due to reorganization of the surface salt bridge formed between Glu182 and Arg227 or possibly to reorientation of Arg206. Changes in the charge distribution may play an important role in communication between the sensor domain and the regulatory domain and thus may be part of the signal transduction pathway.

Nucleosome core particles undergo a conformational change at ionic strengths below 0.2 mM; the fluorescence anisotropy decay of bound ethidium indicates that under these conditions the particle adopts a highly extended structure. We have measured the distribution of UV-induced DNA damage (primarily cyclobutane-pyrimidine dimers) through a process termed photofootprinting. As the core particle is exposed to ionic strengths below 0.2 mM, the photofootprint pattern changes from that observed for native cores, with a characteristic 10.3 base repeat pattern presumably derived largely from the bending of DNA around the histone octamer, to a more evenly distributed pattern resembling that of free DNA. These results provide clear evidence that the DNA in the core particle at these very low ionic strengths, although still tightly bound to histones, is no longer bent to a significant degree.