Katharina F. Pirker

Crystal structure of the FimD usher bound to its cognate FimC―FimH substrate

Type 1 pili are the archetypal representative of a widespread class of adhesive multisubunit fibres in Gram-negative bacteria. During pilus assembly, subunits dock as chaperone-bound complexes to an usher, which catalyses their polymerization and mediates pilus translocation across the outer membrane. Here we report the crystal structure of the full-length FimD usher bound to the FimC–FimH chaperone–adhesin complex and that of the unbound form of the FimD translocation domain. The FimD–FimC–FimH structure shows FimH inserted inside the FimD 24-stranded β-barrel translocation channel. FimC–FimH is held in place through interactions with the two carboxy-terminal periplasmic domains of FimD, a binding mode confirmed in solution by electron paramagnetic resonance spectroscopy. To accommodate FimH, the usher plug domain is displaced from the barrel lumen to the periplasm, concomitant with a marked conformational change in the β-barrel. The amino-terminal domain of FimD is observed in an ideal position to catalyse incorporation of a newly recruited chaperone–subunit complex. The FimD–FimC–FimH structure provides unique insights into the pilus subunit incorporation cycle, and captures the first view of a protein transporter in the act of secreting its cognate substrate.

Independent evolution of four heme peroxidase superfamilies

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Transcriptome analysis of nitrate assimilation in Aspergillus nidulans reveals connections to nitric oxide metabolism

Nitrate is a dominant form of inorganic nitrogen (N) in soils and can be efficiently assimilated by bacteria, fungi and plants. We studied here the transcriptome of the short‐term nitrate response using assimilating and non‐assimilating strains of the model ascomycete Aspergillus nidulans. Among the 72 genes positively responding to nitrate, only 18 genes carry binding sites for the pathway‐specific activator NirA. Forty‐five genes were repressed by nitrate metabolism. Because nirA‐ strains are N‐starved at nitrate induction conditions, we also compared the nitrate transcriptome with N‐deprived conditions and found a partial overlap of differentially regulated genes between these conditions. Nitric oxide (NO)‐metabolizing flavohaemoglobins were found to be co‐regulated with nitrate assimilatory genes. Subsequent molecular characterization revealed that the strongly inducible FhbA is required for full activity of nitrate and nitrite reductase enzymes. The co‐regulation of NO‐detoxifying and nitrate/nitrite assimilating systems may represent a conserved mechanism, which serves to neutralize nitrosative stress imposed by an external NO source in saprophytic and pathogenic fungi. Our analysis using membrane‐permeable NO donors suggests that signalling for NirA activation only indirectly depends on the nitrate transporters NrtA (CrnA) and NrtB (CrnB).

Free radicals generated during oxidation of green tea polyphenols: Electron paramagnetic resonance spectroscopy combined with density functional theory calculations

Electron paramagnetic resonance spectroscopy and density functional theory calculations have been used to investigate the redox properties of the green tea polyphenols (GTPs) (-)-epigallocatechin gallate (EGCG), (-)-epigallocatechin (EGC), and (-)-epicatechin gallate (ECG). Aqueous extracts of green tea and these individual phenols were autoxidized at alkaline pH and oxidized by superoxide anion (O(2)(-)) radicals in dimethyl sulfoxide. Several new aspects of the free radical chemistry of GTPs were revealed. EGCG can be oxidized on both the B and the D ring. The B ring was the main oxidation site during autoxidation, but the D ring was the preferred site for O(2)(-) oxidation. Oxidation of the D ring was followed by structural degradation, leading to generation of a radical identical to that of oxidized gallic acid. Alkaline autoxidation of green tea extracts produced four radicals that were related to products of the oxidation of EGCG, EGC, ECG, and gallic acid, whereas the spectra from O(2)(-) oxidation could be explained solely by radicals generated from EGCG. Assignments of hyperfine coupling constants were made by DFT calculations, allowing the identities of the radicals observed to be confirmed.

Interactions of hydrogen sulfide with myeloperoxidase

The actions of hydrogen sulfide in human physiology have been extensively studied and, although it is an essential mediator of many biological functions, the underlying molecular mechanisms of its actions are ill‐defined. To elucidate the roles of sulfide in inflammation, we have investigated its interactions with human myeloperoxidase (MPO), a major contributor to inflammatory oxidative stress.

Transiently produced hypochlorite is responsible for the irreversible inhibition of chlorite dismutase.

Chlorite dismutases (Clds) are heme b-containing prokaryotic oxidoreductases that catalyze the reduction of chlorite to chloride with the concomitant release of molecular oxygen. Over time, they are irreversibly inactivated. To elucidate the mechanism of inactivation and investigate the role of the postulated intermediate hypochlorite, the pentameric chlorite dismutase of “Candidatus Nitrospira defluvii” (NdCld) and two variants (having the conserved distal arginine 173 exchanged with alanine and lysine) were recombinantly produced in Escherichia coli. Exchange of the distal arginine boosts the extent of irreversible inactivation. In the presence of the hypochlorite traps methionine, monochlorodimedone, and 2-[6-(4-aminophenoxy)-3-oxo-3H-xanthen-9-yl]benzoic acid, the extent of chlorite degradation and release of molecular oxygen is significantly increased, whereas heme bleaching and oxidative modifications of the protein are suppressed. Among other modifications, hypochlorite-mediated formation of chlorinated tyrosines is demonstrated by mass spectrometry. The data obtained were analyzed with respect to the proposed reaction mechanism for chlorite degradation and its dependence on pH. We discuss the role of distal Arg173 by keeping hypochlorite in the reaction sphere for O–O bond formation.

Free radicals in the fruit of three strawberry cultivars exposed to drought stress in the field

In strawberry fruits harvested after different periods of drought stress, no effects of drought or time of harvest were observed on the total free radical contents of frozen fruit of one cultivar (Fragaria ananassa cv. Symphony) or on the amounts of unstable free radicals reacting with the spin trap α-(4-pyridyl-1-oxide)-N-t-butylnitrone (4-POBN) in crushed fruits of a second cultivar (Fragaria vesca cv. Semperflorens). In contrast, with freeze-dried samples, distinct effects of drought stress were seen with two out of three varieties studied, and there were also differences between harvests. Over all samples, there was an inverse relationship between the free radical content of freeze-dried fruit and the water content of fresh fruit. The free radical levels were approximately ten times higher in the freeze-dried fruits, than in the equivalent frozen samples (expressed on a dry weight basis). Massive free radical generation, therefore, accompanies the freeze-drying process and the differences between stressed and control samples indicate an effect of drought stress on the levels of free radical scavenging compounds in the fruit.

Influence of pH on the speciation of copper(II) in reactions with the green tea polyphenols, epigallocatechin gallate and gallic acid

Changes in speciation of copper(II) in reactions with epigallocatechin gallate (EGCG) and gallic acid (GA) as a function of pH have been investigated by multifrequency (X- and S-band) EPR spectroscopy in the fluid and frozen states. The EPR spectra show the formation of three distinct mononuclear species with each of the polyphenols, and these are interpreted in terms of one mono- and two bis-complexes. However, di- or polymeric complexes dominate the Cu(II) speciation in the pH range 4–8, and it is only at alkaline pH values that these mononuclear complexes make appreciable contributions to the metal speciation. Each mononuclear complex displays linewidth anisotropy in fluid solution as a consequence of incomplete averaging of the spin Hamiltonian parameters through molecular motion. Rotational correlation times for the individual complexes have been estimated by analysing the lineshape anisotropy of the fluid solution spectra using parameters determined by simulation of the rigid limit spectra. These show that the molecular masses increase with increasing pH, indicating either coordination of increasing numbers of polyphenol molecules as ligands to the copper or the increasing involvement of polyphenol dimers as ligands in the copper coordination sphere.

Quantification of Reactive Oxygen Species Generation by Photoexcitation of PEGylated Quantum Dots

Photocatalytic generation of reactive oxygen species (ROS) from quantum dots (QDs) has been widely reported yet quantitative studies of ROS formation and their quantum yields are lacking. This study investigates the generation of ROS by water soluble PEGylated CdSe/ZnS QDs with red emission. PEGylation of QDs is commonly used to confer water solubility and minimise uptake by organs of the reticuloendothelial system; therefore studies of ROS formation are of biomedical relevance. Using non-photolytic visible wavelength excitation, the superoxide anion radical is shown to be the primary ROS species generated with a quantum efficiency of 0.35%. The yield can be significantly enhanced in the presence of the electron donor, nicotinamide adenine dinucleotide (NADH), as demonstrated by oxygen consumption measurements and electron paramagnetic resonance spectroscopy with in situ illumination. Direct production of singlet oxygen is not detectable from the QDs alone. A comparison is made with ROS generation by the same QDs complexed with a sulfonated phthalocyanine which can generate singlet oxygen via Förster resonance energy transfer between the QDs and the phthalocyanine.

Structure and heme-binding properties of HemQ (chlorite dismutase-like protein) from Listeria monocytogenes

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