Mon projet de recherche avait pour but de caractériser le rôle de deux protéines, ArgR et PepA, qui agissent en tant que facteurs accessoires de la recombinaison au niveau de deux sites cer du plasmide ColE1 présent dans la bactérie Escherichia coli. Ces deux protéines, couplées aux deux recombinases à tyrosine XerC et XerD, permettent la catalyse de la recombinaison site spécifique au niveau de la séquence cer, convertissant les multimères instables de ColE1 en monomères stables. Cette étude a principalement porté sur la région C-terminale de la protéine ArgR. Cette région de la protéine ArgR possède une séquence en acides-aminés et une structure similaire à celle de la protéine AhrC de Bacillus subtilis. De plus, AhrC, le répresseur de l’arginine de cette bactérie, est capable de complémenter des Escherichia coli mutantes déficientes en ArgR. Les régions C-terminales de ces protéines, montrent une forte similarité. De précédents travaux dans notre laboratoire ont démontré que des mutants d’ArgR comprenant des mutations dans cette région, en particulier les mutants ArgR149, une version tronquée d’ArgR de 149 acides-aminés, et ArgR5aa, une version comprenant une insertion de cinq acides-aminés dans la partie C-terminale, perdaient la capacité de permettre la recombinaison au niveau de deux sites cer présents dans le plasmide pCS210. Malgré cette incapacité à promouvoir la réaction de recombinaison en cer, ces deux mutants étaient toujours capables de se lier spécifiquement à l’ADN et de réprimer une fusion argA :: lacZ. Dans ce travail, les versions mutantes et sauvages d’ArgR furent surexprimées en tant que protéines de fusion 6-histidine. Des analyses crosslinking ont montré que la version sauvage et ArgR5aa pouvaient former des hexamères in-vitro de manière efficace, alors qu’ArgR149 formait des multimères de plus faible poids moléculaire. Des formes tronquées d’ArgR qui comportaient 150 acides-aminés ou plus, étaient encore capables de permettre la recombinaison en cer. Les mutants par substitution ArgRL149A et ArgRL151A ont tous montré que les substitutions d’un seul acide-aminé au sein de cette région avaient peu d’effets sur la recombinaison en cer. Les expériences de crosslinking protéine-à-protéine ont montré que le type sauvage et les formes mutantes d’ArgR étaient capables d’interagir avec la protéine accessoire PepA, également impliquée dans la recombinaison en cer. Les expériences de recombinaison in-vitro utilisant la forme sauvage et les formes mutantes d’ArgR combinées avec les protéines PepA, XerC et XerD purifiées, ont montré que le mutant ArgR149 ne soutenait pas la recombinaison, mais que le mutant ArgR5aa permettait la formation d’une jonction d’Holliday. Des expériences de topologie ont montré que PepA était capable de protéger l’ADN de la topoisomérase 1, et d’empêcher ArgRWt de se lier à l’ADN. Les deux mutants ArgR149 et ArgR5aa protègent aussi l’ADN avec plus de surenroulements. Quand on ajoute PepA, les profils de migration montrent un problème de liaison des deux mutants avec PepA. D’autres expériences impliquant le triplet LEL (leucine-acide glutamique-leucine) et les acides-aminés alentour devraient être réalisés dans le but de connaitre l’existence d’un site de liaison potentiel pour PepA. / My research project involved the role of two proteins, ArgR and PepA, which act as accessory factors in the ColE1 cer recombination system from the gram negative bacteria Escherichia coli. These two proteins, in addition to the tyrosine recombinases XerC and XerD, catalyze a site-specific recombination event at the cer sequence which converts unstable multimeric forms of ColE1 into more stable monomers. Our study mainly focused on the C-terminal end of the ArgR. This region of the ArgR protein possesses a structural and amino acid sequence similarity with the AhrC protein from Bacillus subtilis. Moreover, AhrC, the Arginine repressor of this bacterium, is able to complement Escherichia coli mutants deficient in ArgR. The C-terminal regions of these proteins, display a very high region of similarity. Previous work from our laboratory has shown that ArgR mutants with mutations in this region, especially the mutants ArgR149, a truncated 149 amino acids form of ArgR, and ArgR5aa, a form containing a five amino acid insertion in the C-terminal part, lost the ability to perform a recombination reaction at two cer sites in the plasmid pCS210. Despite this defect in promoting cer recombination, the mutants were still able to bind specifically to DNA, and to repress an argA :: lacZ genetic fusion. In this work, both wild type and mutant ArgR proteins were overexpressed as 6-histidine fusion proteins. Crosslinking analysis showed that both wild type and ArgR5aa efficiently formed hexamers in vitro, while ArgR149 formed lower molecular weight multimers. Truncated forms of ArgR that were 150 amino acids or longer, were able to support cer recombination. The substitution mutants between positions 149 to 151 all showed that single amino acid substitutions at this region had little effect on cer recombination. Protein-protein crosslinking experiments showed that wild type and mutant forms of ArgR, were able to interact with and the other accessory protein involved in cer recombination, PepA. In vitro recombination experiments using wild type and mutant forms of ArgR, combined with purified PepA, XerC and XerD showed that the ArgR149 mutant did not support recombination, but the ArgR5aa mutant did promote Holliday junction formation, raising the possibility that these two mutants interact differently with the Xer recombination machinery. Topology experiments showed that after adding topoisomerase 1, PepA is able to protect DNA from topoisomerase 1, and prevent ArgRWt binding to DNA. The two mutants ArgR149 and ArgR5aa are protecting DNA with more supercoiling. When PepA is added, migration profiles with the two mutants showed a binding problem with PepA. Other experiments involving the LEL triplet (leucine-glutamic acid-leucine) and amino-acids around it should be done in order to know the existence of a possible binding site for PepA.

O peptídeo sintético idêntico ao C-terminal da proteína S100A9 murina (pS100A9m) possui efeito antinociceptivo em diferentes modelos de dor inflamatória aguda. No presente estudo, o efeito do pS100A9m foi avaliado sobre a dor neuropática induzida pela constrição crônica (CCI) do nervo ciático em ratos. Ainda, foram investigados os possíveis mecanismos envolvidos neste efeito. A nocicepção foi avaliada pelos testes de hiperalgesia, alodinia e dor espontânea. Os animais foram tratados com diferentes doses do pS100A9m pelas vias intraplantar, oral ou intratecal 14 dias após a CCI e a nocicepção avaliada após 1 hora. As três vias de administração bloquearam a hiperalgesia, a alodinia e a dor espontânea decorrentes da dor neuropática. A duração do efeito do pS100A9m varia de acordo com a via utilizada e com o fenômeno nociceptivo testado. Ainda, a injeção intraplantar do peptídeo, na pata contralateral à CCI, inibiu a hiperalgesia e a alodinia observadas após a constrição do nervo. Quando o pS100A9m foi administrado pela via intraplantar no 7° dia após a CCI, ele também induziu inibição da hiperalgesia inflamatória que é observada nesse período. Os prováveis mecanismos envolvidos no efeito antinociceptivo do pS100A9m foram investigados pela administração de antagonistas de receptores de serotonina, noradrenalina, GABA (A e B) e opióides. Os resultados obtidos demonstraram que apenas o antagonista de receptor GABAB reverteu completamente o efeito antinociceptivo do pS100A9m sobre a dor neuropática, detectada no 14º dia pós-cirúrgico. Além disso, foram avaliadas as expressões das proteínas Egr-1, Fos e TNFα na medula dos ratos submetidos à CCI e tratados com o peptídeo 7 ou 14 dias do procedimento cirúrgico. O aumento na expressão das proteínas Egr-1 e Fos foi evidenciado tanto no 7º como no 14º dia após a CCI, em animais que não receberam nenhum tratamento ou aqueles que foram tratados com o veículo do peptídeo. Por outro lado, o pS100A9m inibiu a expressão destas duas proteínas no lado ipsolateral à CCI no corno dorsal da medula espinhal dos animais. Com relação ao TNFα, apenas no 7º dia após a CCI foi detectado o aumento na expressão desta proteína. Ainda, foi neste período que o pS100A9m acarretou inibição da expressão do TNFα no corno ventral de animais submetidos ao procedimento cirúrgico. Estes resultados demonstram que o C-terminal da S100A9 murina inibe a dor neuropática experimental por uma ação dependente de receptores GABAB, sugerindo que este peptídeo possivelmente promova uma ativação dos mecanismos inibitórios espinhais, acarretando em redução da ativação de neurônios na medula. Desta forma, o pS100A9m demonstra um potencial terapêutico para o tratamento de dores persistentes. / The synthetic peptide identical to the C-terminus of murine S100A9 protein (mS100A9p) has antinociceptive effect on different acute inflammatory pain models. In this study, the effect of mS100A9p was evaluated on neuropathic pain induced by chronic constriction injury (CCI) of the sciatic nerve in rats, and the possible mechanisms involved in this effect were investigated. Hyperalgesia, allodynia, and spontaneous pain were assessed to evaluate nociception. Rats were treated with different doses of mS100A9p by intraplantar, oral, or intrathecal routes on day 14 after CCI, and nociception was evaluated 1 hour later. These three routes of administration blocked hyperalgesia, allodynia and spontaneous pain. The duration of mS100A9p effect depends on the route used and the phenomenon analyzed. Moreover, intraplantar injection of mS100A9p in the contralateral paw inhibited the hyperalgesia and allodynia induced by CCI. When mS100A9p was administered by intraplantar route on day 7 after CCI, it reversed the inflammatory hyperalgesia observed in this period. The mechanisms likely involved in the antinociceptive effect of mS100A9p were investigated by administration of antagonists of serotonin, norepinephrine, GABA (A and B) and opioid receptors. Only the GABAB receptor antagonist completely reversed the antinociceptive effect of mS100A9p on neuropathic pain on day 14 after CCI. Besides, the expression of Egr-1, Fos and TNFα proteins was evaluated in the spinal cord of rats submitted to CCI and treated with mS100A9p on days 7 or 14 after CCI. The expression of Egr-1 and Fos was increased in animals not treated or treated with vehicle on days 7 and 14 after CCI. On the other hand, mS100A9p inhibited the expression of these two proteins in the dorsal horn of spinal cord ipsilateral to CCI. The increase in TNFα expression was observed exclusively on day 7 after CCI. In the same time period, mS100A9p nhibited the expression of TNFα in the ventral horn of spinal cord of animals submitted to CCI. The results obtained herein demonstrate that the C-terminus of murine S100A9 protein inhibits the experimental neuropathic pain by a GABAB-dependent action, suggesting that this peptide promotes the activation of spinal inhibitory mechanisms leading to the reduction of activation of spinal neurons. Therefore, mS100A9p demonstrates a potential therapeutic use in persistent pain syndromes.

O peptídeo sintético idêntico ao C-terminal da proteína S100A9 murina (pS100A9m) possui efeito antinociceptivo em diferentes modelos de dor inflamatória aguda. No presente estudo, o efeito do pS100A9m foi avaliado sobre a dor neuropática induzida pela constrição crônica (CCI) do nervo ciático em ratos. Ainda, foram investigados os possíveis mecanismos envolvidos neste efeito. A nocicepção foi avaliada pelos testes de hiperalgesia, alodinia e dor espontânea. Os animais foram tratados com diferentes doses do pS100A9m pelas vias intraplantar, oral ou intratecal 14 dias após a CCI e a nocicepção avaliada após 1 hora. As três vias de administração bloquearam a hiperalgesia, a alodinia e a dor espontânea decorrentes da dor neuropática. A duração do efeito do pS100A9m varia de acordo com a via utilizada e com o fenômeno nociceptivo testado. Ainda, a injeção intraplantar do peptídeo, na pata contralateral à CCI, inibiu a hiperalgesia e a alodinia observadas após a constrição do nervo. Quando o pS100A9m foi administrado pela via intraplantar no 7° dia após a CCI, ele também induziu inibição da hiperalgesia inflamatória que é observada nesse período. Os prováveis mecanismos envolvidos no efeito antinociceptivo do pS100A9m foram investigados pela administração de antagonistas de receptores de serotonina, noradrenalina, GABA (A e B) e opióides. Os resultados obtidos demonstraram que apenas o antagonista de receptor GABAB reverteu completamente o efeito antinociceptivo do pS100A9m sobre a dor neuropática, detectada no 14º dia pós-cirúrgico. Além disso, foram avaliadas as expressões das proteínas Egr-1, Fos e TNFα na medula dos ratos submetidos à CCI e tratados com o peptídeo 7 ou 14 dias do procedimento cirúrgico. O aumento na expressão das proteínas Egr-1 e Fos foi evidenciado tanto no 7º como no 14º dia após a CCI, em animais que não receberam nenhum tratamento ou aqueles que foram tratados com o veículo do peptídeo. Por outro lado, o pS100A9m inibiu a expressão destas duas proteínas no lado ipsolateral à CCI no corno dorsal da medula espinhal dos animais. Com relação ao TNFα, apenas no 7º dia após a CCI foi detectado o aumento na expressão desta proteína. Ainda, foi neste período que o pS100A9m acarretou inibição da expressão do TNFα no corno ventral de animais submetidos ao procedimento cirúrgico. Estes resultados demonstram que o C-terminal da S100A9 murina inibe a dor neuropática experimental por uma ação dependente de receptores GABAB, sugerindo que este peptídeo possivelmente promova uma ativação dos mecanismos inibitórios espinhais, acarretando em redução da ativação de neurônios na medula. Desta forma, o pS100A9m demonstra um potencial terapêutico para o tratamento de dores persistentes. / The synthetic peptide identical to the C-terminus of murine S100A9 protein (mS100A9p) has antinociceptive effect on different acute inflammatory pain models. In this study, the effect of mS100A9p was evaluated on neuropathic pain induced by chronic constriction injury (CCI) of the sciatic nerve in rats, and the possible mechanisms involved in this effect were investigated. Hyperalgesia, allodynia, and spontaneous pain were assessed to evaluate nociception. Rats were treated with different doses of mS100A9p by intraplantar, oral, or intrathecal routes on day 14 after CCI, and nociception was evaluated 1 hour later. These three routes of administration blocked hyperalgesia, allodynia and spontaneous pain. The duration of mS100A9p effect depends on the route used and the phenomenon analyzed. Moreover, intraplantar injection of mS100A9p in the contralateral paw inhibited the hyperalgesia and allodynia induced by CCI. When mS100A9p was administered by intraplantar route on day 7 after CCI, it reversed the inflammatory hyperalgesia observed in this period. The mechanisms likely involved in the antinociceptive effect of mS100A9p were investigated by administration of antagonists of serotonin, norepinephrine, GABA (A and B) and opioid receptors. Only the GABAB receptor antagonist completely reversed the antinociceptive effect of mS100A9p on neuropathic pain on day 14 after CCI. Besides, the expression of Egr-1, Fos and TNFα proteins was evaluated in the spinal cord of rats submitted to CCI and treated with mS100A9p on days 7 or 14 after CCI. The expression of Egr-1 and Fos was increased in animals not treated or treated with vehicle on days 7 and 14 after CCI. On the other hand, mS100A9p inhibited the expression of these two proteins in the dorsal horn of spinal cord ipsilateral to CCI. The increase in TNFα expression was observed exclusively on day 7 after CCI. In the same time period, mS100A9p nhibited the expression of TNFα in the ventral horn of spinal cord of animals submitted to CCI. The results obtained herein demonstrate that the C-terminus of murine S100A9 protein inhibits the experimental neuropathic pain by a GABAB-dependent action, suggesting that this peptide promotes the activation of spinal inhibitory mechanisms leading to the reduction of activation of spinal neurons. Therefore, mS100A9p demonstrates a potential therapeutic use in persistent pain syndromes.

Mon projet de recherche avait pour but de caractériser le rôle de deux protéines, ArgR et PepA, qui agissent en tant que facteurs accessoires de la recombinaison au niveau de deux sites cer du plasmide ColE1 présent dans la bactérie Escherichia coli. Ces deux protéines, couplées aux deux recombinases à tyrosine XerC et XerD, permettent la catalyse de la recombinaison site spécifique au niveau de la séquence cer, convertissant les multimères instables de ColE1 en monomères stables. Cette étude a principalement porté sur la région C-terminale de la protéine ArgR. Cette région de la protéine ArgR possède une séquence en acides-aminés et une structure similaire à celle de la protéine AhrC de Bacillus subtilis. De plus, AhrC, le répresseur de l’arginine de cette bactérie, est capable de complémenter des Escherichia coli mutantes déficientes en ArgR. Les régions C-terminales de ces protéines, montrent une forte similarité. De précédents travaux dans notre laboratoire ont démontré que des mutants d’ArgR comprenant des mutations dans cette région, en particulier les mutants ArgR149, une version tronquée d’ArgR de 149 acides-aminés, et ArgR5aa, une version comprenant une insertion de cinq acides-aminés dans la partie C-terminale, perdaient la capacité de permettre la recombinaison au niveau de deux sites cer présents dans le plasmide pCS210. Malgré cette incapacité à promouvoir la réaction de recombinaison en cer, ces deux mutants étaient toujours capables de se lier spécifiquement à l’ADN et de réprimer une fusion argA :: lacZ. Dans ce travail, les versions mutantes et sauvages d’ArgR furent surexprimées en tant que protéines de fusion 6-histidine. Des analyses crosslinking ont montré que la version sauvage et ArgR5aa pouvaient former des hexamères in-vitro de manière efficace, alors qu’ArgR149 formait des multimères de plus faible poids moléculaire. Des formes tronquées d’ArgR qui comportaient 150 acides-aminés ou plus, étaient encore capables de permettre la recombinaison en cer. Les mutants par substitution ArgRL149A et ArgRL151A ont tous montré que les substitutions d’un seul acide-aminé au sein de cette région avaient peu d’effets sur la recombinaison en cer. Les expériences de crosslinking protéine-à-protéine ont montré que le type sauvage et les formes mutantes d’ArgR étaient capables d’interagir avec la protéine accessoire PepA, également impliquée dans la recombinaison en cer. Les expériences de recombinaison in-vitro utilisant la forme sauvage et les formes mutantes d’ArgR combinées avec les protéines PepA, XerC et XerD purifiées, ont montré que le mutant ArgR149 ne soutenait pas la recombinaison, mais que le mutant ArgR5aa permettait la formation d’une jonction d’Holliday. Des expériences de topologie ont montré que PepA était capable de protéger l’ADN de la topoisomérase 1, et d’empêcher ArgRWt de se lier à l’ADN. Les deux mutants ArgR149 et ArgR5aa protègent aussi l’ADN avec plus de surenroulements. Quand on ajoute PepA, les profils de migration montrent un problème de liaison des deux mutants avec PepA. D’autres expériences impliquant le triplet LEL (leucine-acide glutamique-leucine) et les acides-aminés alentour devraient être réalisés dans le but de connaitre l’existence d’un site de liaison potentiel pour PepA. / My research project involved the role of two proteins, ArgR and PepA, which act as accessory factors in the ColE1 cer recombination system from the gram negative bacteria Escherichia coli. These two proteins, in addition to the tyrosine recombinases XerC and XerD, catalyze a site-specific recombination event at the cer sequence which converts unstable multimeric forms of ColE1 into more stable monomers. Our study mainly focused on the C-terminal end of the ArgR. This region of the ArgR protein possesses a structural and amino acid sequence similarity with the AhrC protein from Bacillus subtilis. Moreover, AhrC, the Arginine repressor of this bacterium, is able to complement Escherichia coli mutants deficient in ArgR. The C-terminal regions of these proteins, display a very high region of similarity. Previous work from our laboratory has shown that ArgR mutants with mutations in this region, especially the mutants ArgR149, a truncated 149 amino acids form of ArgR, and ArgR5aa, a form containing a five amino acid insertion in the C-terminal part, lost the ability to perform a recombination reaction at two cer sites in the plasmid pCS210. Despite this defect in promoting cer recombination, the mutants were still able to bind specifically to DNA, and to repress an argA :: lacZ genetic fusion. In this work, both wild type and mutant ArgR proteins were overexpressed as 6-histidine fusion proteins. Crosslinking analysis showed that both wild type and ArgR5aa efficiently formed hexamers in vitro, while ArgR149 formed lower molecular weight multimers. Truncated forms of ArgR that were 150 amino acids or longer, were able to support cer recombination. The substitution mutants between positions 149 to 151 all showed that single amino acid substitutions at this region had little effect on cer recombination. Protein-protein crosslinking experiments showed that wild type and mutant forms of ArgR, were able to interact with and the other accessory protein involved in cer recombination, PepA. In vitro recombination experiments using wild type and mutant forms of ArgR, combined with purified PepA, XerC and XerD showed that the ArgR149 mutant did not support recombination, but the ArgR5aa mutant did promote Holliday junction formation, raising the possibility that these two mutants interact differently with the Xer recombination machinery. Topology experiments showed that after adding topoisomerase 1, PepA is able to protect DNA from topoisomerase 1, and prevent ArgRWt binding to DNA. The two mutants ArgR149 and ArgR5aa are protecting DNA with more supercoiling. When PepA is added, migration profiles with the two mutants showed a binding problem with PepA. Other experiments involving the LEL triplet (leucine-glutamic acid-leucine) and amino-acids around it should be done in order to know the existence of a possible binding site for PepA.

No description available.

Systematic studies of basal nonsense suppression, orthogonality of tRNAPyl variants, and cross recognition between codons and tRNA anticodons are reported. E. coli displays detectable basal amber and opal suppression but shows a negligible ochre suppression. Although detectable, basal amber suppression is fully inhibited when a pyrrolysyl-tRNA synthetase (PylRS)-tRNAPyl_CUA pair is genetically encoded. trnaPyl_CUA is aminoacylated by an E. coli aminoacyl-tRNA synthetase at a low level, however, this misaminoacylation is fully inhibited when both PylRS and its substrate are present. Besides that it is fully orthogonal in E. coli and can be coupled with PylRS to genetically incorporate a NAA at an ochre codon, tRNAPyl_UUA is not able to recognize an UAG codon to induce amber suppression. This observation is in direct conflict with the wobble base pair hypothesis and enables using an evolved M. jannaschii tyrosyl-tRNA synthetase-tRNAPyl_UUA pair and the wild type or evolved PylRS-tRNAPyl_UUA pair to genetically incorporate two different NAAs at amber and ochre codons. tRNAPyl_UCA is charged by E. coli tryptophanyl-tRNA synthetase, thus not orthogonal in E. coli. Mutagenic studies of trnaPyl_UCA led to the discovery of its G73U form which shows a higher orthogonality. Mutating trnaPyl_CUA to trnaPyl_UCCU not only leads to the loss of the relative orthogonality of tRNAPyl in E. coli but also abolishes its aminoacylation by PylRS.

In my master thesis I deal with a design reconstruction of the current public transport terminus of Nemocnice - Bohunice. Terminus layout includes transfering the tramway line from Osová stop to the hub, the new tramway stop is a setting-back track. There is preserved the utilization of hub by existing city and regional lines of buses and troley buses and newly established regional bus lines (401,402,403,404) and also the entrance to the Bohunice hospital parking in the design. This design provides a safe flow of passengers and pedestrians and their safe road crossing.

Indiana University-Purdue University Indianapolis (IUPUI) / In mammalian cells DNA double strand breaks (DSBs) are highly variable with respect to sequence and structure all of which are recognized by the DNA- dependent protein kinase (DNA-PK), a critical component for the resolution of these breaks. Previously studies have shown that DNA-PK does not respond the same way to all DSBs but how DNA-PK senses differences in DNA substrate sequence and structure is unknown. Here we explore the enzymatic mechanism by which DNA-PK is activated by various DNA substrates. We provide evidence that recognition of DNA structural variations occur through distinct protein-protein interactions between the carboxy terminal (C-terminal) region of Ku80 and DNA-dependent protein kinase catalytic subunit (DNA-PKcs). Discrimination of terminal DNA sequences, on the other hand, occurs independently of Ku 80 C-terminal interactions and results exclusively from DNA-PKcs interactions with the DNA. We also show that sequence differences in DNA termini can drastically influence DNA repair through altered DNA-PK activation. Our results indicate that even subtle differences in DNA substrates influence DNA-PK activation and ultimately Non-homologous End Joining (NHEJ) efficiency.