Ph.D. / Biochemistry and Molecular Biology / The Bacillus subtilis spx gene encodes a global regulator that controls transcription initiation in response to oxidative stress by interaction with RNA polymerase (RNAP). It resides in the yjbC-spx operon and is transcribed from at least four promoters, three (P[subscript]1, P[subscript]2 and P[subscript]B) residing upstream of yjbC and one (P[subscript]M) located in the intergenic region between yjbC and spx. We uncovered a second intergenic promoter, P[subscript]3, from which transcription is elevated in cells treated with the thiol-specific oxidant diamide, by primer extension analysis. P[subscript]3 is recognized by the σ[superscript]A form of RNA polymerase (RNAP) in vitro without the involvement of a transcriptional activator. Deletion analysis together with point mutation analysis uncovered two negative cis-acting control elements within the P[subscript]3 promoter. Previously published studies and transcription factor/transformation array technology uncovered two transcriptional repressors, PerR and YodB that were potential candidates for the missing trans-acting factors affecting P[subscript]3 promoter utilization. PerR was previously characterized as the regulator of the inducible peroxide stress response in B. subtilis, while YodB is a novel DUF24/MarR type repressor that controls genes that are induced in response to phenolic compounds and oxidative stress. The derepression of spx was detected in both perR and yodB mutants by examining the level of spx expression using the spx-bgaB fusion construct. The additive effect was observed in the perR yodB double mutant. The regions of spx P[subscript]3 DNA required for transcriptional repression by YodB and PerR were confirmed by DNase I footprinting analysis. PerR protects an area from approximately position -3 to +35. YodB binds a region from approximately positions -3 to -32. The binding of YodB and PerR proteins to spx P[subscript]3 promoter DNA was impaired by addition of diamide and H[subscript]2O[subscript]2 in vitro as determined by DNase I footprinting analysis. Besides spx, YodB also controls the divergently transcribed yodC gene which encodes a putative nitroreductase that is induced by disulfide stress. Microarray and proteome analyses were performed to identify other genes controlled by YodB. yocJ (azoR1), encoding the putative FMN-dependent NADH-azoreductase, was the most strongly derepressed by yodB null mutation and was induced in response to diamide, catechol, MHQ and nitrofurantoin stress. bsrB encoding a small 6S RNA located downstream of azoR1, is co-transcribed with azoR1 and increased in concentration in response to thiol-reactive compounds. The yodB mutant confers a catechol and MHQ resistance phenotype due to AzoR1 overproduction. In addition, the yodBmhqR double mutant, bearing the deletion of the mhqR gene encoding a MarR-like repressor, that overproduces AzoR1 and MhqR-regulated paralog AzoR2, exhibits hyper-resistance to thiol-reactive compounds. Thus, the detoxification of thiol-reactive substances in YodB and MhqR regulons show overlapping functions. DNase I footprinting analysis, together with promoter sequence alignments, uncovered YodB boxes which contain a common 15 bp consensus sequence for YodB-DNA interaction. The YodB protein contains three cysteine residues Cys6, Cys101 and Cys108. The conserved Cys6 contributes to the repression of spx and azoR1 transcription by YodB. Moreover, mass spectrometry revealed YodB Cys modifications by catechol and MHQ.

Bacterial RNA polymerase (RNAP) is a multisubunit complex essential for transcription of DNA into RNA. As a key enzyme responsible for regulation of gene expression it interprets regulatory signals from the cell and based on these cues RNAP adjusts transcription level of particular genes. This process is affected both by the regular subunits of RNAP as well as other transcription factors (TFs) directly or indirectly interacting with RNAP. The general focus of this Thesis was to extend the knowledge about the complex transcriptional regulatory networks and about the connections between individual pathways. The main specific topic and the main publication of the thesis are focused on the HelD protein, a novel binding partner of RNAP in Bacillus subtilis. We showed that HelD binds between the secondary channel of RNAP and alpha subunits of the core form of the enzyme. We proved that HelD stimulates transcription in an ATP dependent manner by enhancing transcriptional cycling and elongation. We revealed a new connection in the transcription regulatory machinery when we demonstrated that the stimulatory effect of HelD can be amplified by delta, a small subunit of RNAP specific for gram positive (G+) bacteria. Two other publications of the thesis are dealing with the delta subunit. We solved the 3D...

Ce travail a pour objectif de réorienter un cristal liquide nématique par la photoisomérisation de deux composés azoïques greffés sur des lames de verre, le DR19 et le DR1. Dans une première étape, nous avons procédé à la silanisation de ces composés photosensibles afin de pouvoir les greffer chimiquement sur des substrats siliciques. Nous avons ensuite greffé ces chromophores sur de la silice mésoporeuse afin d’optimiser la méthode de greffage. Deux paramètres ont été pris en compte dans cette étude : la nature du solvant et le taux d’hydratation de la surface. Une analyse quantitative, structurale et spectroscopique des matériaux hybrides, nous a permis de conclure à la chimisorption des deux azosilanes sur la surface de la silice. Les greffages du DR19Si en milieu éthanolique aqueux d’une part, et du DR1Si dans le THF sur de la silice hydratée d’autre part, ont donné les meilleurs résultats du point de vue quantitatif. A partir de ces résultats, nous avons procédé au greffage des azosilanes sur les lames de verre en mettant en évidence l’importance du film d’eau physisorbé en surface. La caractérisation chimique par les spectroscopies UV/Visible et SPX a démontré la présence des chromophores sur la surface des lames. Une modélisation par SPX des lames de verre fonctionnalisées a été également effectuée puis confirmée par MFA. Enfin, l’action de ces lames fonctionnalisées par greffage sur la réorientation du 5CB a été appréciée au moyen d’un montage pompe-sonde. L’efficacité cinétique et quantitative des chromophores greffés sur une surface a été comparée à celle des chromophores libres dispersés dans la mésophase. / This work aims to reorientate a nematic liquid crystal by the photoisomerization of two azo compounds grafted on glass slides, the DR19 and the DR1. First, we have proceeded to the silanisation of these photosensitive compounds in order to be able to graft them chemically on silica substrates. Then we have grafted these chromophores on mesoporous silica in order to optimize the grafting method. Two parameters have been taken into account in this study: the nature of the solvent and the surface hydration rate. A quantitative, structural and spectroscopic analysis of hybrid materials enabled us to conclude to the chemisorption of both azosilanes on silica surface. Quantitatively, the DR19Si grafting in an ethanolic aqueous solution, and the DR1Si one, in a THF solution on hydrated silica gave the best results. From these results, we have proceeded to the azosilanes grafting on the glass slides while highlighting the importance of the physisorbed water film on the surface. Chemical characterization by UV/Visible and XPS spectroscopy has shown the presence of chromophores on the slides surface. A modelling by XPS, of the functionalized glass slides was also carried out and confirmed by AFM. Lastly, the action of these slides functionalized by grafting on the 5CB reorientation has been appreciated by means of an experimental pump-probe set-up. The kinetic and quantitative effectiveness of grafted chromophores on a surface have been compared with the one of free chromophores dispersed in the mesophase.