The aldehyde dehydrogenase AldA contributes to the hypochlorite defense and is redox-controlled by protein S-bacillithiolation in Staphylococcus aureus

Staphylococcus aureus produces bacillithiol (BSH) as major low molecular weight (LMW) thiol which functions in thiol-protection and redox-regulation by protein S-bacillithiolation under hypochlorite stress. The aldehyde dehydrogenase AldA was identified as S-bacillithiolated at its active site Cys279 under NaOCl stress in S. aureus. Here, we have studied the expression, function, redox regulation and structural changes of AldA of S. aureus. Transcription of aldA was previously shown to be regulated by the alternative sigma factor SigmaB. Northern blot analysis revealed SigmaB-independent induction of aldA transcription under formaldehyde, methylglyoxal, diamide and NaOCl stress. Deletion of aldA resulted in a NaOCl-sensitive phenotype in survival assays, suggesting an important role of AldA in the NaOCl stress defense. Purified AldA showed broad substrate specificity for oxidation of several aldehydes, including formaldehyde, methylglyoxal, acetaldehyde and glycol aldehyde. Thus, AldA could be involved in detoxification of aldehyde substrates that are elevated under NaOCl stress. Kinetic activity assays revealed that AldA is irreversibly inhibited under H2O2 treatment in vitro due to overoxidation of Cys279 in the absence of BSH. Pre-treatment of AldA with BSH prior to H2O2 exposure resulted in reversible AldA inactivation due to S-bacillithiolation as revealed by activity assays and BSH-specific Western blot analysis. Using molecular docking and molecular dynamic simulation, we further show that BSH occupies two different positions in the AldA active site depending on the AldA activation state. In conclusion, we show here that AldA is an important target for S-bacillithiolation in S. aureus that is up-regulated under NaOCl stress and functions in protection under hypochlorite stress

Modeling allosteric signal propagation using protein structure networks

Allosteric communication in proteins can be induced by the binding of effective ligands, mutations or covalent modifications that regulate a site distant from the perturbed region. To understand allosteric regulation, it is important to identify the remote sites that are affected by the perturbation-induced signals and how these allosteric perturbations are transmitted within the protein structure. In this study, by constructing a protein structure network and modeling signal transmission with a Markov random walk, we developed a method to estimate the signal propagation and the resulting effects. In our model, the global perturbation effects from a particular signal initiation site were estimated by calculating the expected visiting time (EVT), which describes the signal-induced effects caused by signal transmission through all possible routes. We hypothesized that the residues with high EVT values play important roles in allosteric signaling. We applied our model to two protein structures as examples, and verified the validity of our model using various types of experimental data. We also found that the hot spots in protein binding interfaces have significantly high EVT values, which suggests that they play roles in mediating signal communication between protein domains

Modulation of host cell processes by T3SS effectors

Two of the enteric Escherichia coli pathotypes-enteropathogenic E. coli (EPEC) and enterohaemorrhagic E. coli (EHEC)-have a conserved type 3 secretion system which is essential for virulence. The T3SS is used to translocate between 25 and 50 bacterial proteins directly into the host cytosol where they manipulate a variety of host cell processes to establish a successful infection. In this chapter, we discuss effectors from EPEC/EHEC in the context of the host proteins and processes that they target-the actin cytoskeleton, small guanosine triphosphatases and innate immune signalling pathways that regulate inflammation and cell death. Many of these translocated proteins have been extensively characterised, which has helped obtain insights into the mechanisms of pathogenesis of these bacteria and also understand the host pathways they target in more detail. With increasing knowledge of the positive and negative regulation of host signalling pathways by different effectors, a future challenge is to investigate how the specific effector repertoire of each strain cooperates over the course of an infection

Kristallstruktur und Intramolekularer Elelktronentransfer

Title page Table of contents Theoretical part Materials and Methods Results Discussion Conclusion ReferencesThe main aim of the present doctoral work was to show that Adx can be photoreduced without presence of AR, and hence, to probe the "shuttle" mechanism. In order to achieve the aim, the truncated form of Adx, Adx(1-108), was covalently modified with Ru(bpy)2(mbpy). Ru(bpy)2(mbpy)-Adx(1-108) was characterized by X-ray crystallography, biophysical and biochemical methods. Possible electron-transfer pathways within the covalent 1:1 Ru(bpy)2(mbpy)-Adx(1-108) complex were predicted. Photoreduction of the [2Fe- 2S] cluster of adrenodoxin was confirmed by EPR measurements. The electron- transfer rate is concentration dependent and indicates that intermolecular electron transfer takes place. The monomolecular intramolecular rate was derived at zero concentration of the Ru(bpy)2(mbpy)-Adx(1-108) complex. Comparative investigation of the covalent 1:1 Ru(bpy)2(mbpy)-Adx(1-108) complex with the wild-type Adx and unmodified Adx(1-108) showed that, in general, reduction of Adx, one-electron carrier, is accompanied by a transfer of two electrons. However, spin quantification of the reduced [2Fe-2S] cluster indicated that only one of two irons is in Fe2+ state. At present, there is no clear explanation for this unusual feature and it needs further investigation. In general, the combination of theory and present experimental data provides a basis for further investigations of the mechanism of the electron transfer in the P450-system.Das Hauptziel der vorliegenden Arbeit war, mittels einer Photoreduktion des Adrenodoxins zu zeigen, dass das Eisen-Schwefel-Protein ohne Adrenodoxinreduktase reduziert und damit das Shuttle-Modell für Adrenodoxin überprüft werden kann. Um dieses Hauptziel zu erreichen, wurde eine verkürzte Form des Adrenodoxins, Adx(1-108), mit dem Ru(bpy)2(mbpy)-Komplex kovalent modifiziert. Ru(bpy)2(mbpy)-modifiziertes Adx(1-108) wurde mittels Röntgenstrukturanalyse, biophysikalischer und biochemischer Methoden untersucht. Anhand der Struktur des 1:1 Ru(bpy)2(mbpy)-Adx(1-108)-Komplexes wurden mögliche Elektronentransferwege innerhalb des Komplexes vorgeschlagen. Photoreduktion des Eisen-Schwefel-Zentrums des Adrenodoxins wurde anhand von EPR-Messungen nachgewiesen. Die Elektronentransferrate ist konzentrationsabhängig und zeigt, dass intermolekulare Elektronenübertragung stattfindet. Die intramolekulare Rate wurde bei unendlicher Verdünnung des Ru(bpy)2(mbpy)-Adx(1-108)-Komplexes berechnet. Bei der vergleichenden Untersuchung des 1:1 Ru(bpy)2(mbpy)-Adx(1-108)-Komplexes mit dem Wildtyp- Adrenodoxin und freiem Adx(1-108) wurde festgestellt, dass Adrenodoxin als Ein-Elektrontransferprotein eine Tendenz zeigt, bei Übertragung von zwei Elektronen reduziert zu werden, obwohl die Spinquantifizierung deutlich zeigt, dass nur ein Eisenatom den Fe2+-Zustand einnimmt. Die Ursache für das ungewöhnliche Verhalten des Proteins ist unklar und muss weiter untersucht werden. Die Kombination der theoretischen Kenntnisse mit experimentellen Daten erlaubt einen Einblick in den Mechanismus des Elektronentransports im P450-System. Damit wurde die Grundlage für weiterführende Untersuchungen zum Elektronentransport im Cytochrom P450-System geschaffen

Проектирование пользовательского взаимодействия в иммерсивных системах нового поколения

This article explores the issues of designing intelligent systems using augmented reality (AR) and virtual reality (VR) technologies. These technologies are based on the use of three-dimensional representation of the surrounding real or pre-designed virtual scene, the capabilities of these systems for determining the orientation of user and objects in space, intelligent analysis algorithms and machine learning. The complexity of developing individual algorithms, the need to take into account the specifics of the subject area for each applied system, interactive display based on threedimensional and other types of representations necessitates the development of new approaches and design principles. The article focuses on the capabilities of OSTIS Technology for use in these tasks, and also provides examples of building a system for technical description of equipment and a guided quest in augmented reality

3D-представление объектов в интеллектуальных компьютерных системах нового поколения

This article is dedicated to the issues of constructing and using a three-dimensional representation in various tasks of applied intelligent systems, as well as corresponding systems of spatial positioning and orientation. The description of the representation itself, as well as the principles of its construction, is implemented within the knowledge base of the OSTIS system, which allows for deep integration of various tasks and methods, and also subsequently leads to an increased degree of convergence of various research domains

Автоматизация образовательной деятельности в рамках экосистемы OSTIS

An analysis of the need for a comprehensive restructuring of the education system, taking into account the requirements of the digital economy, is presented. The ways of solving some problems of the implementation of the educational process at the level of general school education are determined. A semantic approach to building a complex of intelligent learning subsystems including teaching, assisting learning and analytical to accompany the learning process ones within the framework of the OSTIS ecosystem is proposed

Serotonin is required for pharyngeal arch morphogenesis in zebrafish

Serotonin (5-HT) is not only a neurotransmitter but also a mediator of developmental processes in vertebrates. In this study, we analyzed the importance of 5-HT during zebrafish development. The expression patterns of three zebrafish tryptophan hydroxylase isoforms (Tph1A, Tph1B, Tph2), the rate-limiting enzymes in 5-HT synthesis, were analyzed and compared to the appearance and distribution of 5-HT. 5-HT was found in the raphe nuclei correlating with tph2 expression and in the pineal gland correlating with tph1a and tph2 expression. tph2 deficient fish generated with antisense morpholino oligonucleotides exhibited morphogenesis defects during pharyngeal arch development. The correct specification of neural crest cells was not affected in tph2 morphants as shown by the expression of early markers, but the survival and differentiation of pharyngeal arch progenitor cells were impaired. An organizing role of 5-HT in pharyngeal arch morphogenesis was suggested by a highly regular pattern of 5-HT positive cells in this tissue. Moreover, the 5-HT2B receptor was expressed in the pharyngeal arches and its pharmacological inhibition also induced defects in pharyngeal arch morphogenesis. These results support an important role of Tph2-derived serotonin as a morphogenetic factor in the development of neural crest derived tissues

Light-induced reduction of bovine adrenodoxin via the covalently bound ruthenium(II) bipyridyl complex: Intramolecular electron transfer and crystal structure

Bovine adrenodoxin (Adx) plays an important role in the electron-transfer process in the mitochondrial steroid hydroxylase system of the bovine adrenal cortex. Using electron paramagnetic resonance (EPR) spectroscopy, we showed that photoreduction of the [2Fe-2S] cluster of Adx via (4'-methyl-2,2'-bipyridine)bis(2,2'-bipyridine)ruthenium(II) [Ru(bpy)2(mbpy)] covalently attached to the protein surface can be used as a new approach to probe the "shuttle" hypothesis for the electron transfer by Adx. The 1.5 A resolution crystal structure of a 1:1 Ru(bpy)2(mbpy)-Adx(1-108) complex reveals the site of modification, Cys95, and allows to predict the possible intramolecular electron-transfer pathways within the complex. Photoreduction of uncoupled Adx, mutant Adx(1-108), and Ru(bpy)2(mbpy)-Adx(1-108) using safranin T as the mediating electron donor suggests that two electrons are transferred from the dye to Adx. The intramolecular photoreduction rate constant for the ruthenated Adx has been determined and is discussed according to the predicted pathways