The bacterial protein H-NS acts to silence horizontally acquired genes. H-NS physically interacts via its N-terminus with two paralogous proteins, Hha and YdgT. Deletion of hha and ydgT results in derepression of a subset of H-NS repressed genes. I compared expression of hha/ydgT-dependent genes in Salmonella strains lacking hns and hha/ydgT/hns. Deletion of all three genes does not result in greater gene expression than deletion of hns alone, indicating that Hha and YdgT cannot act to repress genes in the absence of H-NS. Further, I used site-directed mutagenesis to generate H-NS proteins incapable of binding Hha. Complementing an hns deletion with an Hha-blind H-NS molecule, H-NS I11A, recapitulated the pattern of gene expression in the hha/ydgT strain. Indicating that elimination of the Hha-H-NS interaction is sufficient to result in derepression of hha/ydgT repressed genes. Hha and YdgT repress gene expression by acting through H-NS and cannot act independently of H-NS.

The bacterial protein H-NS acts to silence horizontally acquired genes. H-NS physically interacts via its N-terminus with two paralogous proteins, Hha and YdgT. Deletion of hha and ydgT results in derepression of a subset of H-NS repressed genes. I compared expression of hha/ydgT-dependent genes in Salmonella strains lacking hns and hha/ydgT/hns. Deletion of all three genes does not result in greater gene expression than deletion of hns alone, indicating that Hha and YdgT cannot act to repress genes in the absence of H-NS. Further, I used site-directed mutagenesis to generate H-NS proteins incapable of binding Hha. Complementing an hns deletion with an Hha-blind H-NS molecule, H-NS I11A, recapitulated the pattern of gene expression in the hha/ydgT strain. Indicating that elimination of the Hha-H-NS interaction is sufficient to result in derepression of hha/ydgT repressed genes. Hha and YdgT repress gene expression by acting through H-NS and cannot act independently of H-NS.

Made available in DSpace on 2014-06-12T15:53:32Z (GMT). No. of bitstreams: 2 arquivo5149_1.pdf: 3970263 bytes, checksum: 9d5eb7ba6122760de6e5e455fb706f21 (MD5) license.txt: 1748 bytes, checksum: 8a4605be74aa9ea9d79846c1fba20a33 (MD5) Previous issue date: 2005 / Bactérias do gênero Yersinia possuem um sistema de secreção tipo III, responsável pela translocação de fatores protéicos conhecidos como Yops, para o interior de células eucarióticas do hospedeiro. A proteína YopH é uma tirosina fosfatase que atua desfosforilando moléculas sinalizadoras e impedindo a fagocitose em macrófagos. Para uma secreção eficiente, ela necessita da presença da chaperona SycH que permite o seu reconhecimento pela maquinaria de secreção. Com a finalidade de analisar a expressão da proteína YopH em E. coli, foi construído um promotor híbrido formado pelo promotor lac de Escherichia coli seguido do promotor yopH de Yersinia enterocolitica. Este promotor foi capaz de direcionar uma forte expressão da YopH, em E. coli, e uma síntese ótima de YopH foi observada com o aumento da temperatura (37oC) e em culturas em fase de crescimento. A expressão da YopH foi investigada em linhagens defectivas de E. coli para as proteínas homólogas às histonas, Hha e H-NS. A expressão foi significantemente maior a 24oC que a 37oC, na ausência de H-NS, mas não na ausência de Hha. Estes resultados são compatíveis com o papel da H-NS na regulação da atividade do promotor yoph, possivelmente através da presença de curvas em sua estrutura. Para determinar se a presença da chaperona SycH influenciaria na expressão da YopH, em E. coli, a sequência codificadora para esta proteína foi amplificada e clonada no plasmídio pBAD33. Foi observada a expressão da SycH em culturas de E. coli, apenas na presença de arabinose. A co-expressão das proteínas YopH e SycH, em EPEC, revelou uma redução na expressão da YopH, na presença de arabinose. O mesmo foi observado em culturas de EPEC contendo apenas o plasmídio pTZ/YopH, onde concentrações variadas de arabinose e glicose estariam influenciando a expressão da YopH. Para verificar o potencial da proteína YopH no diagnóstico da peste, diversos soros de pacientes suspeitos de peste e coelhos imunizados com Y. pestis foram testados por Western-blot. Não houve reconhecimento da YopH nos soros testados

Le génome des bactéries vivantes n’est pas une entité statique mais au contraire c’est quelque chose très dynamique évoluant avec le temps. Les bactéries évoluent en acquérant par transfert horizontal des gènes du matériel génétique. C’est le cas des EPEC qui ont acquis l’îlot LEE via ce mécanisme. La protéine H-NS joue un rôle important dans la reconnaissance de cet ADN étranger, dans la liaison à cet ADN et dans la répression de son expression quand ce n’est pas en profit du « fitness » de la bactérie. Comme résultat H-NS régule la majorité des gènes associés à la virulence chez les entérobactéries Salmonella, Yersinia et les EPEC. Les EPEC possèdent une protéine paralogue à H-NS et codée dans le premier opéron de leur îlot LEE, il s’agit de la protéine Ler. Une fois exprimée Ler induit l’expression des 4 opérons restant de la région parmi lesquels LEE5. Ler partage une grande homologie avec H-NS surtout au niveau de leurs domaines de reconnaissance de l’ADN. Malgré cette homologie H-NS réprime LEE5 tandis que Ler l’active. De plus si H-NS est un régulateur global agissant sur plus de 500 gènes chez E. coli Ler est une protéine spécifique qui ne va agir que sur un petit nombre de promoteurs tous impliqués dans la virulence L’étude qualitative et quantitative de l’interaction de H-NS et de Ler avec la région promotrice de LEE5 montre qu’elles partagent globalement les mêmes sites de fixation sur des régions étendues en amont et en aval du +1 de la transcription. Ces sites de fixation sont bien définis d’une dizaine de paires de bases. L’affinité de ces sites pour H-NS est variable. Trois sites de haute affinité pour H-NS ont été identifiés. La séquence de ces sites est similaire à celle du site consensus élaboré en étudiant le promoteur proU(Bouffartigues et al - 2007). Des différences dans l’interaction de ces deux protéines avec le promoteur LEE5 résident surtout autour du +1 et des boîtes -10 et -35. Il s’agit de la première étude comparant la fixation de H-NS et de Ler sur des régions étendues de ce promoteur dans le but d’expliquer la régulation différentielle de ces deux protéines paralogues. L’étude de l’expression de LEE5 in vivo nous a permis de proposer que le mécanisme essentiel d’action de Ler est dirigé contre la répression induite par H-NS et que le taux maximum d’expression du promoteur LEE5 wtobservé dans la souche mutante pour hnsen présence de Ler (en comparaison avec la souche double mutante où Ler est absente) n’est pas dû à une activation directe par Ler mais plutôt à une répression par StpA, sensible à la mutation des sites de haute affinité de H-NS. / The genes of the LEE5 operon of enteropathogenic E.coliencode for proteinsthat are essential for their virulence. Their expression istightlyregulated, with H-NS silencing the transcriptional expression of LEE5 while Ler, product of the first operon of thispathogenicityislandcancounteract the silencing of H-NS. We show that H-NS and Ler use the samebinding sites on the LEE5 promoterin vitro. However, around the transcription start site differences in DNA constraints are detectabledepending on the presence of H-NS or Ler. Modification of the central AT bases, characteristic of H-NS consensus binding sites, affect the binding of bothproteinsin vitro and the expression in vivo of the LEE5 promoter. Additionallywe show that an additionalrepressor, the H-NS homologue StpA, isimplicated in the LEE5 regulationleading to a new model of how Ler canrelieve the H-NS imposedrepression on the LEE5 promoter

No description available.

L’interaction avec les cellules hôtes est une étape primordiale du cycle infectieux des Salmonella. Elle implique entre autres des fimbriae permettant l’attachement des Salmonella aux cellules et des invasines permettant leur internalisation. Généralement, l’expression de ces facteurs est réprimée et ils ne sont exprimés qu’in vivo en des sites bien spécifiques. Notre objectif a été d’étudier les mécanismes de répression de l’expression des fimbriae Pef et de l’invasine Rck. Nos résultats montrent que les nucléoprotéines H-NS, Hha et YdgT régulent négativement l’expression de ces deux facteurs de virulence. Le mécanisme de répression de la transcription de l’opéron pef a été caractérisé et montre un rôle prépondérant d’H-NS. De plus, la régulation de cet opéron par Hha et YdgT semble être dépendante ou indépendante de H-NS en fonction des conditions de culture de la bactérie. La répression de l’opéron pefI-srgC, portant l’ORF rck, semble, quant à elle, plus complexe. A l’heure actuelle, seule la région cible de la répression par Hha et YdgT a pu être identifiée. Ces résultats renforcent l’hypothèse de l’existence de régulations par Hha-YdgT indépendantes de H-NS. / The interaction with host cells is an essential step of Salmonella infection cycle. Among other virulence factors, fimbriae allow attachment of Salmonella to eukaryotic cells and invasins enable cell internalisation. Generally, the expression of these factors is suppressed and they are only expressed in vivo at very specific locations. Our objective was to study the mechanisms of Pef fimbriae and Rck invasin repression. Our results show that the nucleoproteins H-NS, Hha and YdgT negatively regulate the expression of these two virulence factors. The mechanism of pef operon transcription repression was characterized and shows a predominant role of H-NS. Moreover, the regulation of this operon by Hha and YdgT appears to bedependent or independent of H-NS depending on bacterial culture conditions. Repression of the pefI-srgC operon, carrying rck ORF, shows a higher degree of complexity. Currently, only the Hha and YdgT targeted region for the repression has been identified. These results reinforce the hypothesis that Hha-YdgT can act independently of H-NS.

Le génome des bactéries vivantes n'est pas une entité statique mais au contraire c'est quelque chose très dynamique évoluant avec le temps. Les bactéries évoluent en acquérant par transfert horizontal des gènes du matériel génétique. C'est le cas des EPEC qui ont acquis l'îlot LEE via ce mécanisme. La protéine H-NS joue un rôle important dans la reconnaissance de cet ADN étranger, dans la liaison à cet ADN et dans la répression de son expression quand ce n'est pas en profit du " fitness " de la bactérie. Comme résultat H-NS régule la majorité des gènes associés à la virulence chez les entérobactéries Salmonella, Yersinia et les EPEC. Les EPEC possèdent une protéine paralogue à H-NS et codée dans le premier opéron de leur îlot LEE, il s'agit de la protéine Ler. Une fois exprimée Ler induit l'expression des 4 opérons restant de la région parmi lesquels LEE5. Ler partage une grande homologie avec H-NS surtout au niveau de leurs domaines de reconnaissance de l'ADN. Malgré cette homologie H-NS réprime LEE5 tandis que Ler l'active. De plus si H-NS est un régulateur global agissant sur plus de 500 gènes chez E. coli Ler est une protéine spécifique qui ne va agir que sur un petit nombre de promoteurs tous impliqués dans la virulence L'étude qualitative et quantitative de l'interaction de H-NS et de Ler avec la région promotrice de LEE5 montre qu'elles partagent globalement les mêmes sites de fixation sur des régions étendues en amont et en aval du +1 de la transcription. Ces sites de fixation sont bien définis d'une dizaine de paires de bases. L'affinité de ces sites pour H-NS est variable. Trois sites de haute affinité pour H-NS ont été identifiés. La séquence de ces sites est similaire à celle du site consensus élaboré en étudiant le promoteur proU(Bouffartigues et al - 2007). Des différences dans l'interaction de ces deux protéines avec le promoteur LEE5 résident surtout autour du +1 et des boîtes -10 et -35. Il s'agit de la première étude comparant la fixation de H-NS et de Ler sur des régions étendues de ce promoteur dans le but d'expliquer la régulation différentielle de ces deux protéines paralogues. L'étude de l'expression de LEE5 in vivo nous a permis de proposer que le mécanisme essentiel d'action de Ler est dirigé contre la répression induite par H-NS et que le taux maximum d'expression du promoteur LEE5 wtobservé dans la souche mutante pour hnsen présence de Ler (en comparaison avec la souche double mutante où Ler est absente) n'est pas dû à une activation directe par Ler mais plutôt à une répression par StpA, sensible à la mutation des sites de haute affinité de H-NS.

En la adaptación de las bacterias ante cambios ambientales juegan un importante papel las proteínas asociadas al nucleoide. Estas proteínas presentan una doble función: la estructuración del nucleoide bacteriano y otros procesos relacionados con el ADN como es la regulación de la expresión génica. Una de las proteínas asociadas al nucleoide mejor caracterizada es la proteína H-NS, que se encuentra ampliamente distribuída en bacterias G(-). Una de las características de H-NS es su capacidad de formar dímeros con miembros de la familia de proteínas Hha/YmoA, formando de esta manera complejos represores que intervienen en la regulación de determinados operones, como es el caso del operón hly de E. coli. En este trabajo, y en colaboración con el grupo de RMN de biomoléculas dirigido por el doctor Miquel Pons, se han realizado una serie de trabajos con la intención de conocer mejor las características estructurales de la proteína Hha y su interacción con H-NS, en los que se ha puesto de manifiesto que, aún sin ser unos de los residuos aminoacídicos más afectados en la interacción de Hha con H-NS, la cisteína en posición 18 juega un importante papel en el equilibrio conformacional de Hha cuando interacciona con H-NS. La sustitución de esta cisteína por una isoleucina da lugar a una proteína Hha mutante incapaz de complementar la mutación hha y que provoca una reducción en la tasa de crecimiento de E. coli en condiciones de baja osmolaridad. Este efecto podría venir explicado por la mayor resistencia a la fuerza iónica del medio de la interacción de esta proteína Hha mutante con la proteína H-NS, lo que podría provocar la desregulación de algún gen/es esenciales en condiciones de baja osmolaridad. Una segunda parte de esta Tesis Doctoral está dedicada al gen hns de Y. enterocolitica. Estudios previos realizados en nuestro grupo de investigación pusieron de manifiesto la esencialidad del gen hns en esta bacteria, ya que únicamente es posible obtener mutantes hns en Y. enterocolitica en presencia de algún miembro funcional de la familia de proteínas H-NS. En esta Tesis, nos centramos en el sistema que permite obtener un mutante hns en presencia de la proteína StpA, paráloga a H-NS en E. coli. Los resultados obtenidos permitieron comprobar que la presencia de StpA en Y. enterocolitica provoca drásticas alteraciones en su patrón de expresión proteico, efecto no observado en otras bacterias entéricas, y pusieron de manifiesto la importancia de las proteínas H-NS e YmoA en esta bacteria. La proteína YmoA, que interviene en la termorregulación de la expresión de factores de virulencia en Y. enterocolitica, es homologa a la proteína Hha de E. coli, y también es capaz de interaccionar con H-NS. El análisis de estos resultados ha puesto de manifiesto, por un lado, que la presencia de StpA en Y. enterocolitica simula un incremento no fisiológico en los niveles de proteína H-NS, y por otro lado, la importancia no solo de la presencia de las proteínas H-NS e YmoA en Y. enterocolitica, sino también la importancia de sus niveles relativos, ya que un incremento en los niveles de H-NS o una disminución en los de YmoA provocan una drástica alteración en el patrón de expresión proteico de Y. enterocolitica. / "Hha and YmoA family of proteins: structural studies and regulatory role in Y. enterocolitica"TEXT:H-NS protein is a nucleoid-associated protein, widely dstribute in Gram - bacteria. It has a dual function: nucleoid structure protein and others processes related to DNA like gene expression regulation. This protein is able to both oligomerize and heterodimerize with other proteins. One of the partners of these heterodimers are members of Hha/YmoA family of proteins.In the current work, we carry out the production of both Hha and H-NS proteins in order to perform structural studies by RMN. These studies show that cysteine at position 18 in Hha protein is not one of the most affected aminoacids for Hha/H-NS interaction. However, its location between two α-helix domains suggested that it might be an important residue for Hha conformation during its interaction with H-NS. Our results demonstrated that cys 18 substitution by ile, which hypothetically gives rise to a more open structure, genetates a non-functional protein. In addition, we could observe a toxic effect under low osmolarity condition in E. coli. Finally, a higher stability in H-NS/Hha interaction could be observed.The second part of this work deals with Y. enterocolitica hns gene. hns mutants can only be obtained in this bacteria in presence of some functional members of this protein family. This fact is an evidence of the essenciality of hns in Y. enterocolitica. For instance, an hns mutant can be isolated in presence of stpa gene, which is an hns paralogous gene in E.coli, but not present in Y. enterocolitica. Our results demonstrate that drastic effects in the protein expression pattern of Y. enterocolitica are produced in presence of StpA. The analysis of the previous results gave evidence of the importance of YmoA and H-NS proteins in Y. enterocolitica. Not only the presence of the proteins but also their relative levels turned out to be important, since both an increase in H-NS levels and a decrease in YmoA levels gave rise to a dramatic change in Y. enterocolitica protein expression pattern.

Una de las características de las células bacterianas es la capacidad de adaptarse rápidamente a los frecuentes cambios en las condiciones ambientales del entorno donde se encuentran. En los procariotas la regulación de la expresión génica constituye una herramienta fundamental para dicha adaptación a las condiciones ambientales, posibilitando que tales cambios se vean reflejados en los patrones de expresión génica. La capacidad de modificar el patrón de expresión génica en función de parámetros ambientales es un aspecto crucial en la supervivencia tanto de bacterias que se encuentran en el medio ambiente externo como de bacterias patógenas localizadas en el interior de un organismo hospedador. En este trabajo el primer objetivo fue establecer un modelo de regulación del gen hilA de Salmonella por las proteínas asociadas a cromatina H-NS y Hha, para intentar posteriormente extrapolar este modelo a los reguladores de tipo HilA de la cepa de E. coli 042. Posteriormente, nos planteamos caracterizar el fenotipo resultante de la mutación hha en la cepa de E. coli 042. Los resultados obtenidos revelaron que el gen hilA se induce en fase estacionaria en cultivos crecidos en medio LB a 37ºC. Las proteínas asociadas a cromatina H-NS y Hha reprimen la expresión de hilA bajo un conjunto de condiciones ambientales. En condiciones de baja temperatura, es decir a 25ºC, H-NS posee los papeles mayoritarios en la represión de hilA. Bajo condiciones las cuales simularían la presencia de un hospedador, es decir 37ºC, H-NS deja de actuar y si tiene lugar la inducción de hilA en fase estacionaria. Además de los factores temperatura y osmolaridad que interfieren con la represión de hilA por H-NS se caracterizó la acción antagonista de la proteína IHF sobre la represión mediada por H-NS en el gen hilA utilizando ensayos de transcripción in vitro. En atención a las proteínas tipo HilA encontradas en la cepa de E. coli 042, se pudo caracterizar que ambas proteínas EilA e YgeH son capaces de complementar en trans la mutación hilA en la cepa de Salmonella SV5015. La activación de proteínas efectoras por parte de las proteínas EilA e YgeH en Salmonella parece tener lugar de la misma manera que HilA, a través de la activación del gen invF. Los resultados de regulación transcripcional de los genes eilA e ygeH revelaron una represión por parte de la proteína H-NS, y los ensayos de EMSA apoyan estos resultados. Existe una regulación cruzada entre las islas de patogenicidad ETT2 y eip de la cepa 042. La proteína EilA parece poder activar la expresión de EivF en ausencia de la proteína YgeH. El fenotipo encontrado en el mutante hha de la cepa de E. coli 042 se resume en un aumento de la agregación celular y una deficiencia en la formación de biofilms a 37ºC. El fenotipo es dependiente de temperatura, solamente se observa a 37ºC. Dados de proteómica obtenidos con la construcción AggR::3XFLAG revelaron una sobreexpresión del regulador transcripcional AggR en el mutante hha de la cepa de E. coli 042. Finalmente, la secuenciación masiva de ARN del mutante hha de la cepa de E. coli 042 apoyan estos resultados y revelaron que la transcripción del gen hha envuelve dos patrones diferentes en función de la temperatura. Mientras que a 37ºC la transcripción tiene lugar en la cadena codificante a 25ºC se produce también una importante transcripción en la cadena antisentido, lo que podría interpretarse como que, a baja temperatura se expresa menos el gen hha. / In this work our first goal was to understand and clarify the regulatory role of the nucleoid-associated proteins H-NS and Hha in the regulation of the master regulator of Salmonella pathogenicity island 1 (SPI1), the hilA gene. Due to the presence of HilA orthologous proteins of E. coli 042 strain (EilA and YgeH), we extrapolated the regulation patterns of hilA gene to eilA and ygeH genes. Subsequently, we characterized the phenotype of the hha mutant in the E. coli 042 strain. The results obtained on hilA regulation showed a high induction in the stationary phase of growth when cells were grown in LB medium at 37ºC. The H-NS and Hha proteins repressed the hilA expression under determinate environmental conditions. At low temperature (25ºC) H-NS repressed the hilA gene and Hha enhanced the repression. At high temperature (37ºC) H-NS no longer repressed hilA and the induction of hilA gene took place. Besides temperature and osmolarity factors that interfere with the repression of H-NS in the hilA gene, we characterized an antagonist effect of IHF protein in the H-NS-mediated repression of hilA gene using in vitro transcription assays. In relation to the HilA type proteins found in the strain of E. coli 042, YgeH and EilA, both proteins were able to complement in trans the hilA mutation in Salmonella strain SV5015. The activation of effector proteins by EilA and YgeH proteins in Salmonella seemed to work in the same way than HilA, through invF gene activation. The EMSA assays and the results of transcriptional regulation of genes and ygeH and eilA suggested a repression by H-NS. We also observed a cross-regulation pathway between pathogenicity islands eip and ETT2 in the E. coli 042 strain. EilA protein activated EivF expression in the absence of YgeH proteins. The phenotype found in the hha mutant in the strain of E. coli 042 was both an increase in cell aggregation and a deficiency in biofilm formation. The phenotype was temperature dependent, and it was only observed at 37°C. Proteomics results of the AggR::3xFLAG construction obtained, revealed an overexpression of the transcriptional regulator AggR in the mutant strain hha. Finally, the whole transcriptome shotgun sequencing of the hha mutant of the E. coli 042 supported these findings and revealed that hha gene transcription involved two different patterns depending on the temperature. The transcriptional data suggested that at 37°C the transcription occurred in the coding strand, while at 25°C the transcription occurred in the antisense strand.

Bacteria lack nucleus and any other membrane-bound organelles. Hence all the cellular components, including proteins, DNA, RNA and other components are located within the cytoplasm. The region of the cell which encompasses the bacterial genomic DNA is termed ‘Nucleoid’. The nucleoid is composed largely of DNA and small amounts of proteins and RNA. The genomic DNA is organized in ways that are compatible with all the major DNA-related processes like replication, transcription and chromosome segregation. Proteins that play important role(s) in the structuring of DNA and having the potential to influence gene expression have been explored in all kingdoms of life. The organization of bacterial chromosome is influenced by several important factors. These factors include molecular crowding, negative supercoiling of DNA and NAPs (nucleoid-associated proteins) and transcription. Nucleoid-associated proteins are abundant and relatively low-molecular mass proteins which can bind DNA and function as architectural constituents in the nucleoid. Additionally, NAPs are involved in all the major cellular processes like replication, repair and gene transcription. At least a dozen distinct NAPs are known to be present in E. coli. HU, IHF (integration host factor), H-NS (histone-like nucleoid-structuring), Fis (Factor for inversion stimulation), Dps (DNA protection from starvation) are some of the abundant NAPs in E. coli. Most of these proteins bind DNA and show either DNA bending, bridging or wrapping which are directly relevant to their physiological role(s). As most of these proteins are involved in the regulation of transcription of many genes, they act as factors unifying gene regulation with nucleoid architecture and environment. Pathogenic bacteria have the ability to grow and colonize different environments and thus need to adapt to constantly changing conditions within the host. H-NS and IHF, being able to link environmental cues to the regulation of gene expression, play an important role in the bacterial pathogenesis. H-NS is one of the well studied NAPs in enterobacteria, and is known as a global gene silencer. It is also an important DNA structuring protein, involved in chromosome packaging. H-NS protein is a small (~15 kDa) protein, which is present at approximately 20000 copies/ cell. The most striking feature of H-NS is that although it binds DNA in a relatively sequence-independent fashion but is known to preferentially recognize and bind intrinsically curved DNA. It also constrains DNA supercoils in vitro, thereby affects DNA topology. H-NS also influences replication, recombination and genomic stability. In addition, it functions as a global regulator by regulating the expression of various genes which are linked to environmental adaptation. Various studies have shown the association of H-NS to AT-rich regions of the genome. About 5% of E. coli genes are regulated by H-NS, bulk of which are (~80%) negatively regulated. H-NS is involved in the silencing of horizontally-acquired genes, many of which are involved in pathogenesis, in a process known as xenogeneic silencing. H-NS is known to regulate the expression of various virulence factors like cytotoxins, fimbriae and siderophores in several pathogenic bacteria. Several studies have revealed that hns mutants show increased frequency of illegitimate recombination and reduction in intra-chromosomal recombination, indicating the involvement of H-NS in DNA repair/recombination. H-NS is known to act in several transposition systems, which it does so due to its ability to interact with other proteins involved and due to its DNA structure-specific binding activity. The prototypical IHF (Integration Host Factor) was originally discovered in E. coli as an essential co-factor for the site-specific recombination of phage λ. E. coli IHF belongs to DNABII structural family, along with HU and other proteins and consists of two subunits, IHFα and IHFβ. Thesubunits are ~10 kDa each and are essential for full IHF activity. Apart from its role in bacteriophage integration/excision, IHF also has roles in various processes such as DNA replication, transcription and also in several site-specific recombination systems. In most of these processes, IHF acts as an architectural component by facilitating the formation of nucleoprotein complexes by bending DNA at specific sites. IHF acts as a transcriptional regulator, influencing the global gene expression in E. coli and S. Typhimurium. Gene regulation by IHF requires its DNA architectural role, facilitating interactions between RNA polymerase and regulatory protein. The high intracellular concentration of IHF indicates that it might associate with DNA in a non-specific manner and contribute to chromatin organization. The binding of E. coli IHF causes the DNA to adopt U-turn and brings the non-adjacent sequences into close juxtaposition. IHF is also involved in gene regulation in several pathogenic organisms and is shown to regulate expression of many virulence factors. Despite extensive literature on NAPs, very little is known about NAPs and nucleoid architecture in M. tuberculosis. In the light of significant physiological roles played by NAPs in adaptation to environmental changes and in growth and virulence of bacteria, elucidation of their roles in M. tuberculosis is of paramount importance for a better understanding of its pathogen city. M. tuberculosis Rv3852 (hns) gene is predicted to encode a 134 amino acid protein with a molecular mass of 13.8 kDa. The amino acid sequence alignment revealed that M. tuberculosis H-NS and E. coli H-NS showed very low degree of sequence identity (6%). To explore the biochemical properties of M. tuberculosis H-NS, the sequence corresponding to Rv3852 was amplified via PCR, cloned and plasmid expressing M. tuberculosis hns was constructed. M. tuberculosis H-NS was over expressed and purified to homogeneity. E. coli H-NS was also over expressed and purified. Comparison of experimentally determined secondary structure showed considerable differences between M. tuberculosis and E. coli H-NS proteins. Chemical cross linking suggested that M. tuberculosis H-NS protein exists in both monomeric and dimeric forms in solution, consistent with the diametric nature of E. coli H-NS protein. Our studies have revealed that M. tuberculosis H-NS binds in a more structure-specific manner to DNA replication and repair intermediates, but displays lower affinity for double stranded DNA with relatively higher GC content. It bound to the Holliday junction (HJ), the central recombination intermediate, with high affinity. Furthermore, similar to M. tuberculosis H-NS, E. coli H-NS was able to bind to replication and recombination intermediates, but at a lower affinity than M. tuberculosis H-NS. To gain insights into homologous recombination in the context of nucleoid, we investigated the ability of M. tuberculosis RecA to catalyze DNA strand exchange between single-strand DNA and linear duplex DNA in the presence of increasing amounts of H-NS. We found that M. tuberculosis H-NS inhibited strand exchange mediated by its cognate RecA in a concentration dependent manner. Similar effect was seen in the case of E. coli H-NS, where it was able to suppress DNA strand exchange promoted by E. coli RecA, but at relatively higher concentrations, suggesting that H-NS proteins act as ‘roadblocks’ to strand exchange promoted by their cognate RecA proteins. H-NS and members of H-NS-family of NAPs are known to form rigid nucleoprotein filament structures on binding to DNA, which results in gene-silencing and is also implicated in chromosomal organization. Studies have also shown that H-NS mutants defective in gene silencing also lack the ability to form rigid nucleoprotein filament structure and that nucleoprotein filament structure is responsive to environmental factors. Our studies employing ligase-mediated DNA circularization assays reveal that both E. coli and M. tuberculosis H-NS proteins abrogate the circularization of linear DNA substrate by rigidifying the DNA backbone. These results suggest that M. tuberculosis H-NS could form nucleoprotein filament-like structures upon binding to DNA and these structures might be involved in transcriptional repression, chromosomal organization and protection of genomic DNA. In summary, these findings provide insights into the role of M. tuberculosis H-NS in homologous and/or homeologous recombination as well as transcriptional regulation and nucleoid organization. The second part of the thesis concerns the characterization of M. tuberculosis integration host factor (mIHF). The annotation of whole-genome sequence of M. tuberculosis H37Rv showed the presence of Mtihf gene (Rv1388) which codes for a putative 20-kDa integration host factor (mIHF). Amino acid sequence alignment revealed very low degree of sequence identity between mIHF and E. coli IHFαβ subunits. Unlike E. coli IHF, mIHF is essential for the viability of M. tuberculosis. The three-dimensional molecular modeling of mIHF based upon co crystal structure of Streptomycin coelicolor IHF (sIHF) duplex DNA, showed the presence of conserved Arg170, Arg171, Arg173, which were predicted to be involved in DNA binding and a conserved Pro150, in the tight turn. The coding sequence corresponding to the M. tuberculosis H37Rv ihf gene (Rv1388) was amplified, cloned and plasmid over expressing M. tuberculosis ihf (pMtihf) was constructed. Using pMtihf as a template and using specific primers, mutant ihf encoding plasmids were constructed in which, the arginine at position 170, 171, or 173 was replaced with alanine or aspartate and proline at position 150 was substituted with alanine. To explore the role of mIHF in cell viability, we investigated the ability of M. tuberculosis ihf to complement E. coli ΔihfA or ΔihfB strains against genotoxic stress. Despite low sequence identity between Mtihf and E. coli ihfA and ihfB, wild type Mtihf was able to rescue the UV and MMS sensitive phenotypes of E. coli ΔihfAand ΔihfBstrains, whereas Mtihf alleles bearing mutations in the DNA-binding residues failed to confer resistance against DNA-damaging agents. To further characterize the functions of mIHF, wild type and mutant versions of mIHF proteins were over expressed and purified to near homogeneity. Circular dichroism spectroscopy of wild type mIHF and mIHF mutant proteins revealed that they have similar secondary structures. By employing size-exclusion chromatography and blue-native PAGE, we determined that mIHF exists as a dimmer in solution. To understand the mechanistic basis of mIHF functions, we carried out electrophoretic mobility shift assays. In these assays, we found that wild-type mIHF showed high affinity and stable binding to DNA containing attB and attP sites and also to curved DNA, but not those mIHF mutants bearing mutations in DNA-binding residues. Because wild type mIHF was able to rescue the UV and MMS sensitive phenotypes of E. coli ΔihfA and ΔihfB strains, we ascertained the effect of overexpression of mIHF proteins on the bacterial nucleoid. Our results revealed that wild type mIHF was also able to cause significant nucleoid compaction upon its overexpression, but mutant mIHF proteins were unable to cause compaction of E. coli nucleoid structure. M. smegmatis IHF is known to stimulate L5 phage integrase mediated site-specific recombination, we investigated the ability of mIHF to promote site-specific recombination. In vitro recombination assays showed that M. tuberculosis IHF effectively stimulated the L5 integrase mediated site-specific recombination. Since DNA-bending activity of E. coli IHF is necessary for its functions in various processes like initiation of replication, site-specific recombination, transcriptional regulation and chromosomal organization, we asked whether mIHF possesses DNA bending activity. We employed ligase mediated DNA circularization assays, which revealed that like E. coli IHF, mIHF was able to bend DNA resulting in the covalent closure of DNA to yield circular DNA molecules. Interestingly mIHF also resulted in the formation of slower migrating linear DNA multimers, albeit to a lesser extent, which suggest that both E. coli IHF and mIHF show DNA-bending, but the mechanism is distinct. Further studies using atomic force microscopy showed that depending upon the placement of preferred binding site (curved-DNA sequence) mIHF promotes DNA compaction into nucleoid-like or higher order filamentous structures. Together, these findings provide insights into functions of mIHF in the organization of bacterial nucleoid and formation of higher-order nucleoprotein structures. Importantly, our studies revealed that the DNA-binding residues, the DNA bending mechanism and mechanism of action of mIHF during site-specific recombination were different from E. coli IHF protein. Together with extensive biochemical and in vitro data of bacterial growth, the findings presented in this thesis provide novel insights into the biological roles of H-NS and mIHF in M. tuberculosis.