Regulatory and structural properties differentiating the chromosomal and the bacteriophage-associated Escherichia coli O157:H7 Cu, Zn Superoxide Dismutases

<p>Abstract</p> <p>Background</p> <p>Highly virulent enterohemorrhagic <it>Escherichia coli </it>O157:H7 strains possess three <it>sodC </it>genes encoding for periplasmic Cu, Zn superoxide dismutases: <it>sodC</it>, which is identical to the gene present in non-pathogenic <it>E. coli </it>strains, and <it>sodC</it>-F1 and <it>sodC</it>-F2, two nearly identical genes located within lambdoid prophage sequences. The significance of this apparent <it>sodC </it>redundancy in <it>E. coli </it>O157:H7 has not yet been investigated.</p> <p>Results</p> <p>We report that strains deleted of one or more <it>sodC </it>genes are less resistant than the wild type strain to a challenge with hydrogen peroxide, thus confirming their involvement in the bacterial antioxidant apparatus. To understand if the different <it>sodC </it>genes have truly overlapping functions, we have carried out a comparison of the functional, structural and regulatory properties of the various <it>E. coli </it>O157:H7 SodC enzymes. We have found that the chromosomal and prophagic <it>sodC </it>genes are differentially regulated <it>in vitro</it>. <it>sodC </it>is exclusively expressed in aerobic cultures grown to the stationary phase. In contrast, <it>sodC</it>-F1 and <it>sodC</it>-F2 are expressed also in the logarithmic phase and in anaerobic cultures. Moreover, the abundance of SodC-F1/SodC-F2 increases with respect to that of SodC in bacteria recovered from infected Caco-2 cells, suggesting higher expression/stability of SodC-F1/SodC-F2 in intracellular environments. This observation correlates with the properties of the proteins. In fact, monomeric SodC and dimeric SodC-F1/SodC-F2 are characterized by sharp differences in catalytic activity, metal affinity, protease resistance and stability.</p> <p>Conclusion</p> <p>Our data show that the chromosomal and bacteriophage-associated <it>E. coli </it>O157:H7 <it>sodC </it>genes have different regulatory properties and encode for proteins with distinct structural/functional features, suggesting that they likely play distinctive roles in bacterial protection from reactive oxygen species. In particular, dimeric SodC-F1 and SodC-F2 possess physico-chemical properties which make these enzymes more suitable than SodC to resist the harsh environmental conditions which are encountered by bacteria within the infected host.</p

A biosynthetic aspartate N-hydroxylase performs successive oxidations by holding intermediates at a site away from the catalytic center

Nitrosuccinate is a biosynthetic building block in many microbial pathways. The metabolite is produced by dedicated L-aspartate hydroxylases that use NADPH and molecular oxygen as co-substrates. Here, we investigate the mechanism underlying the unusual ability of these enzymes to perform successive rounds of oxidative modifications. The crystal structure of Streptomyces sp. V2 L-aspartate N-hydroxylase outlines a characteristic helical domain wedged between two dinucleotide-binding domains. Together with NADPH and FAD, a cluster of conserved arginine residues forms the catalytic core at the domain interface. Aspartate is found to bind in an entry chamber that is close to but not in direct contact with the flavin. It is recognized by an extensive H-bond network that explains the enzyme's strict substrate-selectivity. A mutant designed to create steric and electrostatic hindrance to substrate binding disables hydroxylation without perturbing the NADPH oxidase side-activity. Critically, the distance between the FAD and the substrate is far too long to afford N-hydroxylation by the C4a-hydroperoxyflavin intermediate, whose formation is confirmed by our work. We conclude that the enzyme functions through a catch-and-release mechanism. L-aspartate slides into the catalytic center only when the hydroxylating apparatus is formed. It is then re-captured by the entry chamber where it waits for the next round of hydroxylation. By iterating these steps, the enzyme minimizes the leakage of incompletely oxygenated products and ensures that the reaction carries on until nitrosuccinate is formed. This unstable product can then be engaged by a successive biosynthetic enzyme or undergoes spontaneous decarboxylation to produce 3-nitropropionate, a mycotoxin.</p

Cupricyclins, Novel Redox-Active Metallopeptides Based on Conotoxins Scaffold

Highly stable natural scaffolds which tolerate multiple amino acid substitutions represent the ideal starting point for the application of rational redesign strategies to develop new catalysts of potential biomedical and biotechnological interest. The knottins family of disulphide-constrained peptides display the desired characteristics, being highly stable and characterized by hypervariability of the inter-cysteine loops. The potential of knottins as scaffolds for the design of novel copper-based biocatalysts has been tested by engineering a metal binding site on two different variants of an ω-conotoxin, a neurotoxic peptide belonging to the knottins family. The binding site has been designed by computational modelling and the redesigned peptides have been synthesized and characterized by optical, fluorescence, electron spin resonance and nuclear magnetic resonance spectroscopy. The novel peptides, named Cupricyclin-1 and -2, bind one Cu2+ ion per molecule with nanomolar affinity. Cupricyclins display redox activity and catalyze the dismutation of superoxide anions with an activity comparable to that of non-peptidic superoxide dismutase mimics. We thus propose knottins as a novel scaffold for the design of catalytically-active mini metalloproteins

Towards structural and functional characterization of putative polyurethane degrading enzymes

Plastic pollution is a major environmental problem caused by the accumulation of plastic waste in the natural environment. The global production of plastic has increased rapidly over the past few decades, with 380 million tonnes per annum [1]. Around 70% of global production is concentrated in six major polymer types, the so-called commodity plastics [2]. These materials are inexpensive, versatile, and easy to work with, making them the preferred choice for the mass production of everyday objects. Our research is particularly focused on polyurethane (PUR) that is considered an adaptable material and can be found a wide range of applications, including insulation, adhesives, coatings, and foams [3]. The poor degradability of this material brought the scientific community in finding new solutions to harness the problem and, as in many other cases, enzymes revealed to be the leading players in this challenge. Framed in this context, in our research we are focused on finding enzyme candidates capable of degrading polyurethane fragments specifically attacking the urethane bond intrinsic of the polymer chemical structure. Among the copious amount of enzyme classes, Amidases [4], [5] caught our attention since their reaction with polyurethane would produce two fragments being a carbonyl and an amine moiety that could be recycled as valuable building blocks

Solid-state 13C CP MAS NMR spectroscopy of mushrooms gives directly the ratio between proteins and polysaccharides

The solid-state 13C CP MAS NMR technique has the potential of monitoring the chemical composition in the solid state of an intact food sample. This property has been utilized to study mushrooms of different species (Pleurotus ostreatus, Pleurotus eryngii, Pleurotus pulmunarius, and Lentinula edodes), already characterized by chemical analyses for protein and dietary fiber components. Solidstate 13C CP MAS NMR spectroscopy reveals a large difference in the ratio between the glucidic and the proteic resonances probably depending on the mushroom species. An accurate inspection by model compounds and suitable mixtures of proteins and saccharides gives a methodology to interpret these experimental data. A good correlation (R2 = 0.93; R2 = 0.81) has been obtained by comparing the NMR data with the results of the chemical analyses. The results suggest the possibility to perform a taxonomic study and/or a nutritional study on the basis of the ratio between protein and polysaccharide levels determined by NMR or chemical methodologies