Mycobacterium tuberculosis has one ribosomal RNA operon. The survival of this bacillus thus depends on a transcription mechanism that can effectively couple gene expression to changes in the environment. σ factors are transcription proteins that bind to the RNA polymerase (RNAP) and dictate gene expression. Extra Cytoplasmic Function σ factors (ECF) are a subset of σ factors that coordinate environment-induced changes in transcription. The environment specific binding of ECF σ factors to the RNAP presents an effective mechanism for the bacillus to modulate gene expression. ECF σ factors, in turn, are regulated by their interaction with an anti-σ factor. The active σ factor is released from this complex upon specific cellular or environmental stimuli. The aim of this study was to understand the structural and mechanistic aspects of σ factor activation. Towards this goal, two ECF σ factors, σC and σL, were examined. Structural and biophysical studies on M. tuberculosis σC provided a novel insight into ECF σ factor regulation. Inter-domain interactions in σC were sufficient to occlude the DNA recognition regions even in the absence of an interacting protein. The structure of M. tuberculosis σL in complex with the anti-σ factor RslA provides a structural basis to rationalize the release of active σL under oxidative stress. The other chapters of this thesis include a description of the structure and biochemical features of a hypothetical protein Rv2704 that is co-transcribed with the primary σ factor σA. In an effort to understand the collaboration-competition-redundancy model of prokaryotic σ factors, we performed a computational analysis of this system compiling experimental data from the E. coli and B. subtilis model systems. These results are also presented in this thesis. Put together, the structural and biochemical characteristics of the σ factors presented in this thesis suggest substantial variations in the regulatory mechanisms of the M. tuberculosis σ factors when compared to the canonical E. coli or B. subtilis model systems. This thesis is organized as follows: Chapter 1: The introductory chapter of this thesis is organized to frame the pertinent mechanistic issues involved in the σ factor-regulatory protein interactions in the context of the underlying biology of M. tuberculosis. The first part of this chapter provides an overview of σ factors and a summary of the classification of these proteins and their roles in different prokaryotes. The latter part of this chapter is a summary of the pathogen M. tuberculosis in terms of its genetic composition, gene expression as well as aspects of virulence and pathogenecity. Chapter 2: This chapter describes the characterization of the ECF σ factor, σC. Here we report the structure of an ECF σ factor σC from M. tuberculosis. σC is essential for the lethality of M. tuberculosis in a mouse model of infection. Our studies suggest that M. tuberculosis σC differs from the canonical ECF σ factors as it has an N-terminal domain comprising of 126 amino acids that precedes the σC2 and σC4 domains. In an effort to understand the regulatory mechanism of this protein, the crystal structures of the σC2 and C4 domains of σC were determined. These promoter recognition domains are structurally similar to the corresponding domains of E. coli σA despite the low sequence similarity. Fluorescence experiments using the intrinsic tryptophan residues of σC2 as well as surface plasmon resonance measurements reveal that the σC2 and σC4 domains interact with each other. Mutational analysis suggests that the Pribnow box-binding region of σC2 is involved in this inter-domain interaction. Interactions between the promoter recognition domains in M. tuberculosis σC are thus likely to regulate the activity of this protein even in the absence of an anti-σ factor. Chapter 3 provides an account of the regulatory features of the ECF σ factor, σL. ECF σ factors are often regulated by their interactions with an anti-σ factor that can sense diverse environmental stimuli. Transcriptional responses to changes in the oxidation state are particularly important for M. tuberculosis as it adapts to the environment of the host alveoli and macrophages. Here we demonstrate that the protein RslA binds Zinc and can sequester σL in a reducing environment. Our data suggests that the cytosolic domain at the N-terminus of RslA alone is involved in binding σL. Under oxidizing conditions, the σL/RslA complex undergoes substantial conformational rearrangements that coincide with the release of the Zinc cofactor. In the absence of Zinc, the affinity of RslA for σL reduces by ca 8 fold compared to the holo form. The CXXC motif of RslA acts as a redox sensor. In response to oxidative stimuli, the proximal cysteines in this motif can form a disulfide bond with the release of the bound Zn2+ ion. This observation could be rationalized based on the crystal structure of the σL4/RslA complex. Put together, RslA is a distinct variant of the Zinc binding anti-σ factor (ZAS) family. The structural and biophysical parameters that control σL/RslA interactions demonstrate how variations in the rate of Zinc release and associated conformational changes in RslA could regulate the release of free σL in a measured response to oxidative stress. Chapter 4 is based on the biochemical and structural characterization of a hypothetical protein Rv2704. The gene for M. tuberculosis Rv2704 is located in the same operon as the principal σ factor σA. The biochemical and structural features of Rv2704 were thus examined to identify its role, if any, in the regulation of σA. This protein is a trimer in solution and adopts a chorismate mutase-like fold. The crystal structure reveals that Rv2704 is a member of the functionally diverse YjgF family of proteins. The important structural differences between Rv2704 and other YjgF proteins lie in the arrangement of secondary structural elements and the putative functional clefts between the subunit interface. Although Rv2704 does not interact with σA in vitro, the structural similarities to the YjgF family suggests that this protein could interact with a variety of metabolites, potentially influencing its function. Chapter 5 of this thesis is based on a computational analysis of σ factors. Four conformational segments of σ factors, referred to as σ1, σ2, σ3 and σ4 interact with specific regions of promoter DNA. ECF σ factors are a subset of σ factors that coordinate environment-induced transcription. ECF σ factors are minimalist σ factors with two DNA binding domains viz., σ2 and σ4 that recognize the –10 and –35 promoter elements and are unable to interact with either upstream-activating regions or the extended –10 element of the promoter. There are several ECF σ factors in a typical bacterium often characterized by substantial overlap in function. Here we present an analysis of B. subtilis ECF σ factors and their cognate promoters to understand functional overlap and redundancy in this class of proteins. As expected, conserved bases in the –10 element appear more critical for promoter selectivity than the –35 element. However, we note distinct conformational features in the –35 promoter interaction with the helix-turn-helix (HTH) motif when compared to a data-set of known HTH-DNA complexes. Furthermore, we note differences in –35 element interaction between σ factors that act alone and those that overlap in function. The σ factor promoter interactions were then examined vis-à-vis the estimated cellular concentration of these proteins and their affinity to bind the core RNAP. Put together, this analysis suggests that while the cellular protein concentration dictates the choice of an ECF σ factor to form a complex with the RNAP, conformational features of the –35 element serve to select potential collaborative members, a subset of which eventually initiate transcription. Collaborative arrangements and functional redundancy in ECF σ factors are thus possible within the limits placed by these two parameters. Chapter 6 is a summary of the work reported in this thesis and the conclusions that can be drawn based on these studies. The appendix section of this thesis comprises of technical details that were not included in the main text of this thesis. Appendix I describes the initial characterization of the M. tuberculosis σD/anti-σD complex. Appendix II provides the experimental protocols as well as some of the supplementary data to the work reported in Chapters 2-5 of this thesis.

The TRIB1 locus (8q24.13) is a novel locus associated with plasma TGs and CAD risk. Trib1 is a regulator of MAPK activity, and has been shown to regulate hepatic lipogenesis and VLDL production in mice. However, the functional relationship between common SNPs at the TRIB1 locus and plasma lipid traits is unknown; TRIB1 has not been identified as an eQTL. This cluster of SNPs falls within an intergenic region 25kb to 50kb downstream of the TRIB1 coding region. By phylogenetic footprinting analysis and DNA genotyping, we identified an evolutionarily conserved region (CNS1) within the risk locus that harbours two common SNPs in tight LD with GWAS risk SNPs and significantly associated with CAD. We investigated the regulatory function of CNS1 by luciferase reporter assays in HepG2 cells and demonstrate that this region has promoter activity. In addition, the rs2001844 risk allele significantly reduces luciferase activity, suggesting that altered expression of the EST-based gene may be associated with plasma TGs. We identified an EST within the risk locus directly downstream of CNS1. We performed 5'/3' RACE using HepG2 RNA, identified multiple variants of this EST-based gene, and confirmed its transcription start site within CNS1. We hypothesize that this EST is a long noncoding RNA due to low abundance, poor conservation, and absence of significant ORF. Over-expression of a short variant implicates its function in the regulation of target gene transcription, although the mechanism of action remains unknown. We conclude that the risk locus at 8q24.13 harbours a novel EST-based gene that may explain the relationship between GWAS SNPs at this locus and plasma lipid traits.

The TRIB1 locus (8q24.13) is a novel locus associated with plasma TGs and CAD risk. Trib1 is a regulator of MAPK activity, and has been shown to regulate hepatic lipogenesis and VLDL production in mice. However, the functional relationship between common SNPs at the TRIB1 locus and plasma lipid traits is unknown; TRIB1 has not been identified as an eQTL. This cluster of SNPs falls within an intergenic region 25kb to 50kb downstream of the TRIB1 coding region. By phylogenetic footprinting analysis and DNA genotyping, we identified an evolutionarily conserved region (CNS1) within the risk locus that harbours two common SNPs in tight LD with GWAS risk SNPs and significantly associated with CAD. We investigated the regulatory function of CNS1 by luciferase reporter assays in HepG2 cells and demonstrate that this region has promoter activity. In addition, the rs2001844 risk allele significantly reduces luciferase activity, suggesting that altered expression of the EST-based gene may be associated with plasma TGs. We identified an EST within the risk locus directly downstream of CNS1. We performed 5'/3' RACE using HepG2 RNA, identified multiple variants of this EST-based gene, and confirmed its transcription start site within CNS1. We hypothesize that this EST is a long noncoding RNA due to low abundance, poor conservation, and absence of significant ORF. Over-expression of a short variant implicates its function in the regulation of target gene transcription, although the mechanism of action remains unknown. We conclude that the risk locus at 8q24.13 harbours a novel EST-based gene that may explain the relationship between GWAS SNPs at this locus and plasma lipid traits.

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The TRIB1 locus (8q24.13) is a novel locus associated with plasma TGs and CAD risk. Trib1 is a regulator of MAPK activity, and has been shown to regulate hepatic lipogenesis and VLDL production in mice. However, the functional relationship between common SNPs at the TRIB1 locus and plasma lipid traits is unknown; TRIB1 has not been identified as an eQTL. This cluster of SNPs falls within an intergenic region 25kb to 50kb downstream of the TRIB1 coding region. By phylogenetic footprinting analysis and DNA genotyping, we identified an evolutionarily conserved region (CNS1) within the risk locus that harbours two common SNPs in tight LD with GWAS risk SNPs and significantly associated with CAD. We investigated the regulatory function of CNS1 by luciferase reporter assays in HepG2 cells and demonstrate that this region has promoter activity. In addition, the rs2001844 risk allele significantly reduces luciferase activity, suggesting that altered expression of the EST-based gene may be associated with plasma TGs. We identified an EST within the risk locus directly downstream of CNS1. We performed 5'/3' RACE using HepG2 RNA, identified multiple variants of this EST-based gene, and confirmed its transcription start site within CNS1. We hypothesize that this EST is a long noncoding RNA due to low abundance, poor conservation, and absence of significant ORF. Over-expression of a short variant implicates its function in the regulation of target gene transcription, although the mechanism of action remains unknown. We conclude that the risk locus at 8q24.13 harbours a novel EST-based gene that may explain the relationship between GWAS SNPs at this locus and plasma lipid traits.

Submitted by EDISON ANTONIO DE SOUZA null (esmidia@gmail.com) on 2016-01-06T16:51:45Z No. of bitstreams: 1 TESE_DOUTORADO_Edison_Souza.pdf: 947001 bytes, checksum: a8a8d690c84bc72a0b5e27d8ebeee92f (MD5) / Approved for entry into archive by Juliano Benedito Ferreira (julianoferreira@reitoria.unesp.br) on 2016-01-06T19:50:21Z (GMT) No. of bitstreams: 1 souza_ea_dr_bot_par.pdf: 573913 bytes, checksum: 30e1665c27c8c583a0b5ab8dc8bd89e0 (MD5) / Made available in DSpace on 2016-01-06T19:50:21Z (GMT). No. of bitstreams: 1 souza_ea_dr_bot_par.pdf: 573913 bytes, checksum: 30e1665c27c8c583a0b5ab8dc8bd89e0 (MD5) Previous issue date: 2015-12-16 / INFLUÊNCIA DO CONSUMO DA PRÓPOLIS NA EXPRESSÃO DE GENES RELACIONADOS AO SISTEMA IMUNOLOGICO DE ABELHAS Apis mellifera L. SUMETIDAS AO DESAFIO BACTERIANO. As abelhas Apis mellifera podem estar sujeitas a uma série de ameaças como parasitas e patógenos que acometem seu sistema imunológico. Tal fato torna necessária a busca por produtos naturais que possam contribuir com a melhora do sistema imune destes insetos, como a própolis. Diante do exposto, o objetivo foi analisar a influência do fornecimento da própolis em expressões de genes relacionados à imunidade de abelhas Apis mellifera L. submetidas ao desafio bacteriano. Ao longo de 30 dias, quatro colmeias receberam semanalmente os tratamentos com diferentes porcentagens de extrato alcoólico de própolis 30% (0%, 5%, 10%, 15%). O experimento foi casualizado em esquema fatorial 4 x 2 x 2x 3 (tratamentos x com ou sem bactéria x tempos x períodos), totalizando 48 amostras. Foram observadas as expressões dos genes abaecin, hymenoptaecin, apidaecin e defensin1. Como controle interno foi utilizado o gene actina. Os resultados foram comparados por ANOVA seguidos do teste de Tukey (P<0,05). Foram observadas alterações na expressão gênica das abelhas estudadas para todos os períodos e tratamentos, antes e após desafio bacteriano, para todos os genes propostos, sendo ainda verificada induções da expressão relativa nos três períodos. Conclui-se que nas condições do presente trabalho, a própolis pode induzir a expressão relativa dos genes abaecin, hymenoptaecin, apidaecin e defensin1, quando submetidas a desafio bacteriano. Entretanto, não se pôde caracterizar um tratamento com própolis que apresente uma maior expressão relativa para todos os genes simultaneamente. EFEITO DO CONSUMO DE PRÓPOLIS NAS ALTERAÇÕES COMPORTAMENTAIS E MORTALIDADE DE ABELHAS Apis mellifera L. SUBMETIDAS AO INSETICIDA FIPRONIL. Os inseticidas representam o maior risco direto para os polinizadores, como as abelhas Apis mellifera, sendo responsável pela redução das populações de abelhas e da produção apícola, tornando necessária a busca por substâncias que possam contribuir na melhora da saúde dessas abelhas, como a própolis. Este estudo verificou o efeito do consumo do extrato alcoólico de própolis no comportamento, quando submetidas a DL50 (0,2 µg/abelha) e subletal (1/500 DL50), e mortalidade das abelhas Apis mellifera L. quando submetidas a diferentes doses do inseticida fipronil (0,05; 0,1; 0,2; 0,3 e 0,4 µg/abelha). Ao todo foram utilizadas quatro colmeias, uma para cada tratamento (0, 5, 10 e 15% de inclusão de própolis), e em três períodos (0,15 e 30 dias) para verificar o efeito dos tratamentos ao longo do experimento. Para a realização dos testes de mortalidade e de alterações comportamentais foram selecionadas as abelhas campeiras das colmeias tratadas. Para o teste de mortalidade, os dados foram analisados em modelo linear misto generalizado, adicionado do Teste de Tukey (P<0,05) e a análise da avaliação das atividades comportamentais foi feita por (ANOVA) seguida do Teste de Tukey (P<0,05). As colmeias que consumiram própolis apresentaram menor taxa de mortalidade quando comparados com a colmeia controle (0%), com exceção no dia 0 em que a colmeia controle não diferiu do tratamento 10%. Verificou-se ainda que as abelhas que receberam o tratamento 10% apresentaram as menores taxas de mortalidade nos dias 15 e 30 de coleta. Além disso, foi observada mortalidade de 23% nas abelhas quando submetidas a DL50 do fipronil. Nos testes de alterações comportamentais e locomotoras não foram observadas influências dos tratamentos com própolis. Conclui-se que, para o presente estudo, a própolis influenciou na taxa de mortalidade e pode ter promovido um efeito protetor nas abelhas Apis mellifera L. quando submetidas a diferentes concentrações do inseticida fipronil, sendo ainda verificado que o tratamento 10% foi o mais eficaz, devido a ter apresentado as menores taxas de mortalidade nos dias 15 e 30. / INFLUENCE OF PROPOLIS CONSUMPTION IN GENES EXPRESSION RELATED TO IMMUNE SYSTEM OF Apis mellifera L. BEES SUBJECTED TO CHALLENGE BACTERIA. The Apis mellifera bees may be subject to a number of threats as parasites and pathogens that affect your immune system. This fact makes it necessary to look for natural products that can contribute to improving the immune system of these insects such as propolis. Given the above, the objective was to analyze the influence of the supply of propolis in gene expressions related to immunity of Apis mellifera L. bees subjected to bacterial challenge Over 30 days, four hives receive weekly treatments with different percentages of alcoholic extract of propolis 30% (0%, 5%, 10%, 15%). The experiment was randomized in a factorial 4 x 2 x 2x 3 (treatments x with or without bacteria x times x periods), totaling 48 samples. It was observed the expressions of abaecin, hymenoptaecin, apidaecin and defensing1 genes. As internal control was used actin gene. The results were compared by ANOVA followed by Tukey test (P <0.05). Alterations were observed in gene expression of bees studied for all periods and treatments before and after bacterial challenge for all proposed genes, were yet verified inductions of relative expression in the three periods. It is concluded that under the conditions of this study, propolis can induce the relative expression of genes abaecin, hymenoptaecin, apidaecin and defensin1, when subjected to bacterial challenge. However, it is not able to characterize a treatment with propolis presenting greater relative expression for all genes simultaneously. EFFECT OF PROPOLIS CONSUMPTION IN THE BEHAVIORAL CHANGES AND MORTALITY OF Apis mellifera L. BEES SUBMITTED TO PESTICIDE FIPRONIL. Pesticides pose the greatest direct risk for pollinators such as Apis mellifera bees, responsible for reducing bee populations and beekeeping, making it necessary to search for substances that can contribute to improving the health of these bees, such as propolis. Given this, the study found the effect of propolis alcoholic extract consumption behavior when subjected to DL50(0.2 µg/bee) and sublethal (1/500 DL50), and mortality of Apis mellifera L. bees submitted to different doses of the insecticide fipronil (0,05; 0.1, 0.2, 0.3 and 0.4 µg/bee). Four colonies were used, one for each treatment (0, 5, 10 and 15% inclusion of propolis), and in three periods (0,15 and 30 days) to determine the effect of the treatments throughout the experiment. To the achievement of mortality and behavioral changes tests the foraging bees from treated hives were selected. For the mortality test, the data were analyzed in generalized linear mixed model, added the Tukey test (P <0.05) and the analysis of the assessment of behavioral activities was made by (ANOVA) followed by Tukey test (P <0.05). Beehives who consumed propolis have a lower mortality rate compared to the hive control (0%), except on day 0 that the hive control did not differ from treatment 10%. It was also found that the hive that received treatment 10% was among the lowest mortality rates in the fifteenth and thirtieth collection day. Furthermore, the observed mortality was 23% in bees when subjected to LD50. In tests of locomotor and behavioral changes were observed influences of treatments with propolis. It concludes that, for this study, propolis influenced the mortality rate and may have promoted a protective effect on bees Apis mellifera L. when subjected to different concentrations of the insecticide fipronil, and also, that the treatment 10% was effective due to having presented the lowest mortality rates in the 15 and 30. However, treatments with propolis did not influence the behavioral and motor changes.

Orientador: Ricardo De Oliveira Orsi / Abstract: INFLUENCE OF PROPOLIS CONSUMPTION IN GENES EXPRESSION RELATED TO IMMUNE SYSTEM OF Apis mellifera L. BEES SUBJECTED TO CHALLENGE BACTERIA. The Apis mellifera bees may be subject to a number of threats as parasites and pathogens that affect your immune system. This fact makes it necessary to look for natural products that can contribute to improving the immune system of these insects such as propolis. Given the above, the objective was to analyze the influence of the supply of propolis in gene expressions related to immunity of Apis mellifera L. bees subjected to bacterial challenge Over 30 days, four hives receive weekly treatments with different percentages of alcoholic extract of propolis 30% (0%, 5%, 10%, 15%). The experiment was randomized in a factorial 4 x 2 x 2x 3 (treatments x with or without bacteria x times x periods), totaling 48 samples. It was observed the expressions of abaecin, hymenoptaecin, apidaecin and defensing1 genes. As internal control was used actin gene. The results were compared by ANOVA followed by Tukey test (P <0.05). Alterations were observed in gene expression of bees studied for all periods and treatments before and after bacterial challenge for all proposed genes, were yet verified inductions of relative expression in the three periods. It is concluded that under the conditions of this study, propolis can induce the relative expression of genes abaecin, hymenoptaecin, apidaecin and defensin1, when subjected to bacterial challenge. However, it i... (Complete abstract click electronic access below) / Resumo: INFLUÊNCIA DO CONSUMO DA PRÓPOLIS NA EXPRESSÃO DE GENES RELACIONADOS AO SISTEMA IMUNOLOGICO DE ABELHAS Apis mellifera L. SUMETIDAS AO DESAFIO BACTERIANO. As abelhas Apis mellifera podem estar sujeitas a uma série de ameaças como parasitas e patógenos que acometem seu sistema imunológico. Tal fato torna necessária a busca por produtos naturais que possam contribuir com a melhora do sistema imune destes insetos, como a própolis. Diante do exposto, o objetivo foi analisar a influência do fornecimento da própolis em expressões de genes relacionados à imunidade de abelhas Apis mellifera L. submetidas ao desafio bacteriano. Ao longo de 30 dias, quatro colmeias receberam semanalmente os tratamentos com diferentes porcentagens de extrato alcoólico de própolis 30% (0%, 5%, 10%, 15%). O experimento foi casualizado em esquema fatorial 4 x 2 x 2x 3 (tratamentos x com ou sem bactéria x tempos x períodos), totalizando 48 amostras. Foram observadas as expressões dos genes abaecin, hymenoptaecin, apidaecin e defensin1. Como controle interno foi utilizado o gene actina. Os resultados foram comparados por ANOVA seguidos do teste de Tukey (P<0,05). Foram observadas alterações na expressão gênica das abelhas estudadas para todos os períodos e tratamentos, antes e após desafio bacteriano, para todos os genes propostos, sendo ainda verificada induções da expressão relativa nos três períodos. Conclui-se que nas condições do presente trabalho, a própolis pode induzir a expressão relativa dos genes a... (Resumo completo, clicar acesso eletrônico abaixo) / Doutor

The TRIB1 locus (8q24.13) is a novel locus associated with plasma TGs and CAD risk. Trib1 is a regulator of MAPK activity, and has been shown to regulate hepatic lipogenesis and VLDL production in mice. However, the functional relationship between common SNPs at the TRIB1 locus and plasma lipid traits is unknown; TRIB1 has not been identified as an eQTL. This cluster of SNPs falls within an intergenic region 25kb to 50kb downstream of the TRIB1 coding region. By phylogenetic footprinting analysis and DNA genotyping, we identified an evolutionarily conserved region (CNS1) within the risk locus that harbours two common SNPs in tight LD with GWAS risk SNPs and significantly associated with CAD. We investigated the regulatory function of CNS1 by luciferase reporter assays in HepG2 cells and demonstrate that this region has promoter activity. In addition, the rs2001844 risk allele significantly reduces luciferase activity, suggesting that altered expression of the EST-based gene may be associated with plasma TGs. We identified an EST within the risk locus directly downstream of CNS1. We performed 5'/3' RACE using HepG2 RNA, identified multiple variants of this EST-based gene, and confirmed its transcription start site within CNS1. We hypothesize that this EST is a long noncoding RNA due to low abundance, poor conservation, and absence of significant ORF. Over-expression of a short variant implicates its function in the regulation of target gene transcription, although the mechanism of action remains unknown. We conclude that the risk locus at 8q24.13 harbours a novel EST-based gene that may explain the relationship between GWAS SNPs at this locus and plasma lipid traits.

En el llevat Saccharomyces cerevisiae els canvis en les condicions osmòtiques del medi extracel.lular són sensades per la MAP cinasa Hog1, la qual permet dur a terme l'adaptació cel.lular mitjançant la modulació de l'expressió gènica, de la traducció i de la progressió del cicle cel.lular. A l'inici d'aquest projecte de tesi, els mecanismes pels quals Hog1 controla l'expressió gènica no eren del tot coneguts. El nostre objectiu va ser caracteritzar el mecanisme molecular pel qual Hog1 modula la transcripció en resposta a estrès osmòtic. Hem aconseguit demostrar que el reclutament de Hog1 als promotors sensibles a estrès osmòtic per part del factor de transcripció és essencial per al reclutament i activació de la RNA polimerasa II, mecanisme que podria estar conservat en les cèl.lules eucariotes. També hem identificat noves activitats remodeladores de cromatina implicades en la resposta gènica a osmoestrès mediada per Hog1. Vàrem realitzar un cribatge genètic per identificar mutacions que provoquessin osmosensibilitat i una reducció en l'expressió de gens de resposta a estrès osmòtic. Aquest cribatge ens va permetre identificar nous reguladors de la transcripció mediada per osmoestrès: la histona deacetilasa Rpd3 i els complexes SAGA i mediador. Els nostres resultats permeten, doncs, definir un important paper per a Rpd3, SAGA i mediador en la inducció gènica mediada per Hog1, i han estat importants per assolir una millor visió de com les cinases activades per estrès regulen la iniciació de la transcripció. / In Saccharomyces cerevisiae, changes in the extracellular osmotic conditions are sensed by the HOG MAPK pathway, which elicits the program for cell adaptation, including modulation of gene expression, translation and cell-cycle progression. At the beginning of this PhD Project, the mechanisms by which Hog1 was controlling gene transcription were not completely understood. Our main objective was to characterize the molecular mechanisms by which the Hog1 MAPK modulates transcription upon osmostress. We have shown that anchoring of Hog1 to osmoresponsive promoters by the transcription factor is essential for recruitment and activation of RNA polymerase II, a mechanism that might be conserved among eukaryotic cells. In addition, we identified novel chromatin modifying and remodelling activities involved in the Hog1-mediated osmostress gene expression. We performed a genome-wide genetic screening searching for mutations that render cells osmosensitive and displayed reduced expression of osmoresponsive genes. Rpd3 histone deacetylase, SAGA and Mediator complexes were identified as novel regulators of osmostress-mediated transcription. Thus, our results define a major role for Rpd3, SAGA and Mediator in the Hog1-mediated osmostress gene induction, and have been important to achieve a better view of how a SAPK regulates transcription initiation.

Le suppresseur de tumeurs BAP1 est la déubiquitinase la plus fréquemment mutée dans le cancer humain. Ce dernier est impliqué dans la régulation des gènes cibles des facteurs de transcription E2Fs, qui sont des régulateurs centraux de la prolifération cellulaire en contrôlant, les points de contrôle du cycle cellulaire, la mitose, la réparation de l'ADN et l'apoptose. Dans le complexe BAP1, nous notons plusieurs protéines liant la chromatine, telles que les facteurs de transcription FOXKs (FOXK1 et FOXK2), qui sont connues pour recruter BAP1 sur ses gènes cibles. En effet, le complexe BAP1 est recruté à la chromatine pour assurer sa fonction de déubiquitination de la marque d’histone répressive H2AK119ub, et ainsi, réguler l'expression des gènes. Dans cette étude, nous avons cherché à étudier l'axe BAP1-FOXKs dans la régulation des fonctions cellulaires associées à ce complexe. Fait intéressant, FOXK1, mais pas FOXK2, est connue pour avoir des propriétés oncogéniques, car des niveaux d'expression plus élevés de FOXK1 ont été observés dans une variété de cancers et sont corrélés avec la progression tumorale, l'invasion et les métastases. Ce fait soulève de nombreuses questions sur la nature de la régulation entre ces protéines dont la question suivante : s’agit-il d’une relation de coopération ou antagonisme, entre le suppresseur de tumeurs BAP1 et l’oncogène FOXK1 ? De façon intéressante, nous avons découvert que les protéines FOXK1 et FOXK2 forment deux complexes mutuellement exclusifs avec le complexe BAP1, ce qui suggère qu'elles ont des fonctions moléculaires et cellulaires distinctes à travers ce complexe. Nos études phénotypiques en utilisant des fibroblastes primaires humains montrent que FOXK1 et FOXK2 régulent différemment la prolifération cellulaire, la sénescence cellulaire et la transformation oncogénique. En effet, FOXK1, mais pas FOXK2, favorise la prolifération cellulaire via l’activation de l'expression d'E2F1 et de ses gènes cibles. En conséquence, FOXK1 retarde la sénescence cellulaire et favorise une réplication prolongée des fibroblastes primaires. De plus, la surexpression de FOXK1 favorise la transformation oncogénique des fibroblastes primaires transduits par les oncoprotéines E1A et RAS V12G en augmentant la pénétrance et en diminuant le temps de latence de formation des tumeurs. Ces résultats confirment que ces facteurs disposent de fonctions de signalisation cellulaire distinctes et suggèrent qu'ils sont régulés de manière différentielle au niveau moléculaire. Afin d’investiguer davantage le mécanisme moléculaire qui pourrait distinguer entre les fonctions cellulaires de FOXK1 et FOXK2, nous avons cherché à étudier les modifications post-traductionnelles de ces facteurs. Fait intéressant, nos données de spectrométrie de masse ont révélé que seul FOXK1, mais pas FOXK2, est modifié par O-GlcNAcylation, une modification post-traductionnelle catalysée par l'enzyme OGT. Nos essaies in-vitro montrent que cette modification régule la fonction de FOXK1 dans la prolifération cellulaire car le mutant de la O-GlcNAcylation réduit l'impact prolifératif de FOXK1 sur des cellules. Nos essaies in-vivo, en utilisant un modèle de xénogreffe de cellules cancéreuses humaines chez la souris, confirment que la O-GlcNAcylation de FOXK1 favorise la croissance tumorale. Plus intéressant, le mutant de la O-GlcNAcylation de FOXK1 affecte la transformation oncogénique des fibroblastes primaires transduits par E1A et RAS V12G, en augmentant le temps de latence tumorale et diminuant la taille finale de la tumeur. Au niveau de la chromatine, la O-GlcNAcylation de FOXK1 favorise le recrutement de BAP1 sur les gènes cibles des facteurs E2Fs afin deubiquitiner H2AK119Ub et permettre leur expression. En conclusion, la O-GlcNAcylation est un mécanisme clé qui régule la fonction de FOXK1 dans la prolifération cellulaire, et qui contribue à son activité oncogénique. Dans une autre perspective de cette étude, et afin d'investiguer l'importance de l'axe de signalisation BAP1-FOXKs dans la fonction de suppression tumorale de BAP1, nous avons étudié le rôle fonctionnel de l’interaction BAP1-FOXKs dans un modèle murin. Nous avons généré un modèle de souris en utilisant le système d'édition de gènes CRISPR/Cas9 pour muter la thréonine 492 du gène bap1, en alanine et ainsi perturber l'interaction entre les FOXKs et BAP1 chez la souris. Des descendants hétérozygotes de Bap1T492A/+ ont été croisés pour générer des individus homozygotes et étudier leur phénotype. Fait intéressant, nos résultats montrent que les souris homozygotes Bap1T492A/T492A meurent au stade embryonnaire. De plus, les quelques souris homozygotes Bap1T492A/T492A viables échappant à la barrière de létalité (qui représentent seulement 4.7 % au lieu de 25%) sont remarquablement plus petites et certaines d'entre elles ont présenté des anomalies de développement. De plus, lors de l'analyse du système immunitaire des souris adultes homozygotes Bap1T492A/T492A, nous avons constaté une réduction importante dans les proportions des cellules NKT qui sont des combattants du système immunitaire pouvant éliminer les cellules cancéreuses. Ensemble, ces données montrent que l'axe BAP1-FOXKs est important pour le développement et fournissent de nouvelles informations sur la manière dont les événements de signalisation entre le suppresseur de tumeurs BAP1 et les facteurs FOXKs doivent être étroitement contrôlés pour maintenir une homéostasie cellulaire normale et prévenir le cancer. / The tumor suppressor BAP1 is one of the most frequently mutated deubiquitinase in human cancer. This latter is involved in the regulation of the E2F target genes, which are central regulators of cellular proliferation by controlling, cell cycle checkpoints, mitosis, DNA repair, and apoptosis. Importantly, in the BAP1 complex, we note several chromatin-binding proteins, such as FOXKs transcription factors, which are known to recruit BAP1 to its target genes. Indeed, the BAP1 complex is recruited to chromatin to ensure its deubiquitinating function of the repressive histone mark H2AK119ub and thus regulating gene expression. In this study, we sought to investigate the BAP1-FOXKs axis in regulating associated cellular functions. Interestingly, FOXK1 but not FOXK2, is known to have oncogenic properties as higher expression levels of FOXK1 has been observed in a variety of cancers and is correlated with tumor progression, invasion, and metastasis. These results raise many questions about the nature of the regulation between these proteins, including whether there is a cooperative or antagonistic relationship between the tumor suppressor BAP1 and the oncogene FOXK1? Interestingly, we found that FOXK1 and FOXK2 proteins are mutually exclusive for their interactions with the BAP1 complex, which suggests that they have distinct molecular and cellular functions within this complex. Our functional studies using human primary fibroblasts show that FOXK1 and FOXK2 regulate differentially cell proliferation, cellular senescence, and oncogenic transformation. Indeed, FOXK1, but not FOXK2, promotes cellular proliferation through the activation of the expression of E2F1 and its target genes. As a consequence, FOXK1 delays cellular senescence and promotes prolonged primary cell replication. In addition, overexpression of FOXK1 promotes oncogenic transformation of primary fibroblasts transduced by E1A and RAS V12G oncogenes, by increasing tumor penetrance and decreasing latency of tumor formation. These results confirm that these factors have distinct cellular signalling functions and suggest that they are regulated differentially on the molecular level. To further investigate the molecular mechanism, which could distinguish FOXK1 and FOXK2 cellular functions, we sought to study posttranslational modifications of these factors. Interestingly, our mass spectrometry data revealed that only FOXK1, but not FOXK2, is modified by O-GlcNAcylation, a protein posttranslational modification catalyzed by the enzyme OGT. Our in vitro data shows that this modification regulates FOXK1 function in cellular proliferation as the expression of the O-GlcNAc mutant reduces the proliferative potential of FOXK1. Our in-vivo data, using human cancer cell xenografts on mice, confirms that FOXK1 O-GlcNAcylation promotes tumor growth. More interestingly, FOXK1 O-GlcNAcylation mutants affect the oncogenic transformation of primary fibroblasts expressing E1A and RAS V12G by increasing tumor latency and decreasing tumor size. At the chromatin level, O-GlcNAcylation of FOXK1 promotes the recruitment of BAP1 to target genes of E2Fs factors in order to deubiquitinate H2AK119Ub and allow their expression. In conclusion, O-GlcNAcylation is a key mechanism that regulates the function of FOXK1 in cell proliferation, which contributes to its oncogenic activity. In another perspective of this study, and in order to investigate the importance of BAP1- FOXKs signaling axis in the tumor suppression function of BAP1, we sought to study the functional role of BAP1-FOXKs interaction in a murine model. We generated a mouse model using the CRISPR/Cas9 gene-editing system by mutating BAP1-threonine 492 into alanine and thus disrupting the interaction between FOXKs and BAP1. Heterozygous offspring of Bap1T492A/+ were crossed to generate homozygous litters to study their phenotypes. Interestingly, our results show that homozygous Bap1T492A/T492A mice are embryonic lethal. Moreover, a few homozygous Bap1T492A/T492A mice can escape the embryonic lethality (representing only 4.7% instead of 25%), are remarkably smaller, and some of them showed developmental abnormalities. Moreover, when analyzing the immune system of adult homozygous Bap1T492A/T492A mice, we found a significant reduction of NKT cells proportions, which could be central fighters against cancer cell development. Altogether, these data show that BAP1-FOXKs axis is important for development and provide novel insights into how signaling events between the tumor suppressor BAP1 and FOXKs should be tightly controlled to maintain normal cellular homeostasis and prevent cancer.