A hipertensão arterial essencial é caracterizada pela elevação crônica da pressão arterial e representa o principal fator de risco para doenças cardiovasculares e renais. O rim participa do controle da pressão arterial e alterações intrínsecas no manuseio renal de sódio desempenham papel importante na patogênese da hipertensão essencial. Os túbulos proximais renais são responsáveis pela reabsorção da maior parte do sódio filtrado nos glomérulos e a maior parte da reabsorção de sódio neste segmento faz-se através da troca de Na+ por H+ em membrana apical, mediada pela isoforma 3 do trocador Na+/H+ (NHE3). Entretanto, os dados existentes referentes à modulação renal do NHE3 em modelos de hipertensão são ainda conflitantes. Este estudo teve como objetivo avaliar as possíveis alterações funcionais do trocador Na+/H+ NHE3 em túbulo proximal renal na linhagem SHR no estágio de préhipertensão (5 semanas) e de hipertensão (14 semanas) e investigar se estas alterações são acompanhadas de alterações na atividade e na expressão da proteína cinase A (PKA) e de proteínas fosfatase-1 (PP1). Por meio de microperfusão estacionária in vivo mediu-se a atividade do NHE3 em túbulo proximal e verificou-se que a reabsorção de bicarbonato foi reduzida em 62 ± 6 % (P < 0,001) na transição do J-SHR para o A-SHR enquanto foi aumentada em 113 ± 10 % (P < 0,001) na transição entre o J-WKY e o A-WKY. A atividade estimulada do NHE3 em J-SHR é decorrente da redistribuição do NHE3 do domínio intermicrovilar (IMV) para o domínio das microvilosidades (MMV) e do baixo nível de fosforilação da serina 552, sítio consenso para a PKA. Por outro lado, durante a fase de hipertensão, a atividade diminuída do NHE3 deve-se à sua redistribuição para o IMV e ao aumento da fosforilação na serina 552. Para testar a hipótese de que os níveis de fosforilação do NHE3 estariam aumentados em túbulo proximal de SHR adulto devido ao aumento da atividade da PKA e/ou à diminuição na atividade da PP1, foram avaliados tanto os níveis de fosforilação quanto a atividade do NHE3 em SHR jovens e adultos em resposta ao 6MB-cAMP (análogo ao cAMP que ativa especificamente a PKA). O JSHR apresentou um aumento tanto nos níveis de fosforilação da serina 552 (179 ± 14 %, P < 0,001) quanto nos de inibição da atividade (65 ± 10 %, P < 0,001) do NHE3 em relação ao J-SHR em resposta ao 6MB-cAMP. Já no A-SHR, a fosforilação da serina 552 aumentou moderadamente (36 ± 4 %, P < 0,01), assim como inibiu moderadamente (23 ± 9 %, P < 0,05) a atividade do NHE3 em resposta ao 6MBcAMP. Adicionalmente, verificou-se que não houve alteração da atividade da PKA entre os animais nem ao longo da idade e nem entre as linhagens. Por sua vez, o JSHR apresentou maior atividade da PP1 que o A-SHR (1640 ± 107 vs. 940 ± 119 pM/?g, P < 0,01). Além disso, houve uma diminuição na expressão da PP1? no ASHR (32 ± 8 %, P < 0,01) quando comparado ao J-SHR. Os dados sugerem que o NHE3 é diferencialmente regulado antes e após o desenvolvimento da hipertensão em SHR por mecanismos que envolvem modificações pós-transcricionais e distribuição subcelular. Além do mais, a regulação diferencial dos níveis de fosforilação do NHE3 tubular proximal antes e após o desenvolvimento da hipertensão em SHR é devida, provavelmente, a alterações na atividade e na expressão da PP1 / Essential hypertension is characterized by chronic elevation of blood pressure and represents the major risk factor for cardiovascular and renal diseases. The kidney participates in the blood pressure control and intrinsic changes in renal sodium handling play an important role in the pathogenesis of essential hypertension. The renal proximal tubule is responsible for reabsorption of the great majority of sodium that is filtered by the glomerulus and the principal apical membrane mechanism for sodium reabsorption in this nephron is Na+/H+ exchanger isoform 3 (NHE3)- mediated Na+/H+ exchange. However, conflicting data have been reported with regard to NHE3 modulation in experimental models of hypertension. This study aimed to evaluate the possible functional changes of the Na+/H+ exchanger NHE3 in the renal proximal tubule of SHR both at the pre-hypertensive (5 weeks) and at hypertensive (14 weeks) stages and to investigate whether these changes were accompanied by changes in the activity and/or expression of protein kinase A (PKA) and protein phosphatase 1 (PP1). Proximal tubule NHE3 activity was measured by means of stationary microperfusion. Bicarbonate reabsorption was found to be decreased by 62 ± 6 % (P < 0.001) in the transition from youth to adulthood in SHR (Y-SHR to A-SHR), whereas in the transition from Y-WKY to A-WKY it increased by 113 ± 10 % (P < 0.001). Stimulated NHE3 activity in Y-SHR was due to redistribution of NHE3 from intermicrovilar domain (IMV) to microvilar domain (MMV) and to a lower level of serine 552 phosphorylation, a consensus site for PKA. Conversely, during the hypertensive stage, decreased NHE3 activity was due to increased redistribution of NHE3 to the IMV domain and increased phosphorylation at serine 552. To test the hypothesis that the increased levels of NHE3 phosphorylation in the proximal tubule of adult SHR were due to increased PKA activity and/or decreased PP1 activity, it was evaluated both phosphorylation levels and activity of NHE3 in young and adult SHR in response to 6MB-cAMP (an cAMP analog that specifically activates PKA). Y-SHR showed an increase both in the phosphorylation levels at serine 552 (179 ± 14 %, P < 0.001) and in the inhibition of NHE3 transport activity (65 ± 10 %, P < 0.001) compared to Y-SHR in response to 6MB-cAMP. With respect to A-SHR, the phosphorylation of serine 552 was slightly increased (36 ± 4 %, P < 0.01) and NHE3 activity was mildly inhibited (23 ± 9 %, P < 0.05) in response to 6MB-cAMP. Additionally, PKA activity remained unchanged with both age and strain. Nevertheless, Y-SHR exhibited higher PP1 activity than A-SHR (1640 ± 107 vs. 940 ± 119 pM/?g, P < 0.01). Furthermore, PP1? expression was decreased in the renal cortex of A-SHR (32 ± 8 %, P < 0.01) compared to Y-SHR. Taken together, these data suggest that NHE3 is differentially regulated before and after development of hypertension in SHR by mechanisms involving post-translational modifications and subcellular distribution. Moreover, the differential regulation of proximal tubule NHE3 phosphorylation levels before and after development of hypertension in SHR is most likely due to changes on the activity and expression of PP1

A infecção persistente por HPV-16 está fortemente associada ao risco de desenvolvimento de neoplasias do colo do útero, vagina, vulva, pênis, canal anal e orofaringe. O estudo detalhado da variabilidade nucleotídica intra-típica de HPV-16 resultou em importantes achados no que concerne à filogenia e evolução viral, e à história natural das infecções. Variantes Asiático-Americanas (AA) e E-350G de HPV-16 foram associadas com maior risco de persistência da infecção viral e desenvolvimento de câncer de colo de útero quando comparadas à variante Européia protótipo (E-P ou E-350T), embora esta ainda apresente alto risco quando comparada aos outros tipos virais. Mais recentemente, diferenças funcionais entre as proteínas E6/E7 das distintas variantes moleculares de HPV- 16 estão sendo descritas, a fim de explicar as diferenças nas associações epidemiológicas observadas. Dados do nosso grupo apontaram para a transcrição aumentada do gene MEK2 especificamente em queratinócitos humanos primários (PHKs) transduzidos com E6/E7 da variante E-350G. Pelo exposto, objetivou-se: (1) Analisar os níveis de ativação de proteínas efetoras das vias de transdução de sinal mediadas por MAPK e PI3K/AKT em queratinócitos imortalizados por E6/E7 de três variantes moleculares de HPV-16 (AA, E-P, E-350G); (2) Analisar os efeitos das proteínas E6/E7 dessas variantes sob as vias de MAPK quanto à indução de fatores de transcrição; (3) Analisar o potencial transformante de PHKs imortalizados pelas diferentes variantes, e em cooperação com a proteína celular c-MYC; (4) Analisar o potencial de migração e invasão em PHKs imortalizados pelas diferentes variantes de HPV-16, e em cooperação com a proteína celular c-MYC. Neste estudo observou-se que a variante AA de HPV-16 induziu a maior ativação das vias de sinalização estudadas (MAPK, e PI3K/AKT). Ademais, PHKs imortalizados por esta variante apresentaram maior capacidade de migração, de invasão através de uma matriz de colágeno, além de maior potencial transformante. Adicionalmente, as células imortalizadas pela variante AA apresentaram maior expressão da proteína mesenquimal vimentina e diminuição dos níveis da proteína epitelial E-caderina, sugerindo ativação parcial de Transição Epitélio Mesênquima (EMT) nestes queratinócitos. Ademais, quando o oncogene c-MYC foi co-transduzido nas diferentes linhagens infectadas por E6/E7 de HPV-16, foi observado que em PHKs imortalizados pela variante AA também houve maior ativação da via de MAPK-ERK, maior migração, e um potencial transformante semelhante, em relação às células co-transduzidas pela variante E-350G e c-MYC. Em conjunto, estes dados sugerem que a variante AA de HPV-16 possui vantagem seletiva sob as outras variantes em promover transformação celular, migração e invasão, e isto poderia explicar, ao menos em parte, a maior prevalência desta variante no câncer cervical. Os resultados gerados neste estudo são de extrema relevância para avaliar o impacto da variabilidade intra-típica de HPV-16 sobre o potencial oncogênico observado em estudos epidemiológicos / Persistent infection with HPV-16 is strongly associated with risk of developing neoplasia in the uterine cervix, vagina, vulva, penis, anal canal and oropharynx. The detailed study of HPV-16 intra-typical nucleotide variability resulted in important findings regarding phylogeny and viral evolution, and the natural history of infections. Asian-American (AA) and E-350G variants of HPV-16 were associated with increased risk of persistent viral infection and development of cervical cancer compared to the European prototype (E-P or E-350T), although this variant still presents higher risk when compared to other viral types. More recently, functional differences between the E6/E7 proteins of distinct molecular variants of HPV-16 are being described, in order to explain the differences in the epidemiological associations observed. Data from our group pointed to increased transcription of the MEK2 gene specifically in primary human keratinocytes (PHKs) transducing E6/E7 of the E-350G variant. Consequently, the aims of this study were: 1) To examine the activation levels of effector proteins of the signal transduction pathways mediated by MAPK and PI3K/AKT in PHKs immortalized by E6/E7 of three different molecular variants of HPV-16 (AA, E-P, E-350G); (2) To analyze the effects of E6/E7 of different molecular variants of HPV-16 upon MAPK pathways concerning the induction of transcription factors; (3) To analyze the transforming potential of PHKs immortalized by different molecular variants of HPV-16, and in cooperation with the cellular protein c- MYC; (4) To analyze the potential of migration and invasion in PHKs immortalized by different molecular variants of HPV-16, and in cooperation with the cellular protein c- MYC. In this study we observed that the AA variant of HPV-16 induced higher activation of both signaling pathways studied (MAPK, and PI3K/AKT). Furthermore, this variant presented increased migration capacity, higher invasion through a collagen matrix, and greater transforming potential. Moreover, cells immortalized by the AA variant showed higher expression of the mesenchymal protein vimentin and a decrease of the epithelial protein E-cadherin, suggesting partial activation of Epithelial Mesenchymal Transition (EMT). In addition, when the c-MYC oncogene was co-transduced in the different cells lines infected with HPV-16 E6/E7, we observed that in PHKs immortalized by the AA variant there was also an enhanced activation of the MAPK-ERK pathway, a higher ability to migrate, and similar transformation potential in comparison with cells co-transduced with the E-350G variant and c-MYC. Taken together, this data suggest that the AA molecular variant of the HPV-16 has a selective advantage over the other variants to promote cell transformation, migration and invasion, and this could partly explain the higher prevalence of this variant in cervical cancer. The results generated in this study are very important to assess the impact of intra-typical variability of HPV-16 on the oncogenic potential observed in epidemiological studies

A isoforma 3 do trocador Na+ /H+ (NHE3), presente em membrana apical, é a proteína de transporte que medeia a maior parte da reabsorção de NaCl e NaHCO3- em túbulo proximal renal. A fosforilação direta do NHE3 por PKA na serina 552 é um dos mecanismos pelos quais a sua atividade pode ser inibida. A ligação da angiotensina II (Ang II) ao receptor AT1 (AT1R) em túbulo proximal estimula a atividade do NHE3 por diferentes vias de sinalização. Entretanto, não foram ainda bem estabelecidos os efeitos da ativação da via AT1R/Gi, com consequente diminuição nos níveis de cAMP, na regulação do NHE3. A Ang II pode ainda estimular a atividade do NHE3 por promover a sua translocação da base para o corpo das microvilosidades, entretanto, o papel da proteína motora miosina IIA nesta translocação em resposta à Ang II ainda não foi estabelecido. Sendo assim esta tese teve como objetivos: (1) testar a hipótese de que a Ang II diminui os níveis de fosforilação do NHE3 mediados pelo cAMP/PKA na serina 552 aumentando a sua atividade por reduzir os níveis de cAMP e (2) testar a hipótese de que a miosina IIA participa da redistribuição do NHE3 da base para o corpo das microvilosidades em túbulo proximal renal em condições de estímulo da reabsorção de sódio, como ocorre em resposta à Ang II. Visando avaliar os efeitos da ativação da via AT1R/Gi na regulação do NHE3, verificamos, por meio da técnica de recuperação do pH dependente de Na+, que, em condições basais, a Ang II estimulou a atividade do NHE3, mas não alterou a atividade da PKA e nem afetou os níveis de fosforilação do NHE3 na serina 552 em uma linhagem de células de túbulo proximal (OKP). Entretanto, na presença da forskolin (FSK), agente que eleva os níveis intracelulares de cAMP, a Ang II foi capaz de contrapor-se ao efeito inibitório da FSK sobre o NHE3 por promover redução na concentração de cAMP, diminuição da atividade da PKA e, consequentemente, diminuição nos níveis de fosforilação da serina 552. Todos os efeitos da Ang II foram bloqueados quando um pré-tratamento com Losartan, antagonista do receptor AT1, foi feito nas células OKP, destacando a contribuição da via AT1R/proteína Gi no aumento da atividade do NHE3 pela Ang II. Observamos que a inibição da proteína Gi com PTX (toxina pertussis) diminuiu a atividade do NHE3 em células OKP e que a PTX diminuiu a atividade do NHE3 assim como preveniu o efeito estimulatório da Ang II sobre a atividade do NHE3 em túbulo proximal de ratos Wistar. Adicionalmente, com a intenção de avaliar os efeitos da miosina IIA na redistribuição do NHE3, constatamos que a blebistatina, inibidor da miosina IIA, preveniu completamente o aumento de atividade do NHE3 mediado pela Ang II em ratos Wistar e que o uso da blebistatina foi capaz de prevenir o aumento do NHE3 na superfície de células OKP tratadas com Ang II. Em conjunto, nossos resultados sugerem que a Ang II contrapõe-se aos efeitos do cAMP/PKA sobre a fosforilação e a atividade do NHE3 pela ativação da via AT1R/Gi e que a miosina IIA desempenha um papel na mediação da regulação da atividade do NHE3 em túbulo proximal renal de ratos em resposta à Ang II. Sugerem ainda que a desfosforilação do NHE3 na serina 552 pode representar um evento chave na regulação do manuseio de sal tubular proximal pela Ang II na presença de hormônios natriuréticos que promovem o aumento dos níveis de cAMP e da fosforilação do transportador e que a miosina IIA está envolvida na regulação do tráfego do NHE3 em túbulo proximal renal / The Na+/H+ exchanger isoform 3 (NHE3), expressed on the apical membrane, is responsible for most NaCl and NaHCO3 - reabsorption in the renal proximal tubule. Direct phosphorylation of NHE3 by PKA at serine 552 is one of the mechanisms by which its activity is inhibited. Binding of angiotensin II (Ang II) to the AT1 receptor (AT1R) in the proximal tubule stimulates NHE3 activity through multiple signaling pathways. However, the effects of AT1R/Gi activation and subsequent decrease in cAMP accumulation on NHE3 regulation are not well established. Ang II can also stimulate NHE3 activity by promoting its translocations from the base to the body of the microvilli, however, the role of the myosin IIA motor protein in this translocation in response to Ang II is not yet established. Therefore, the aims of this thesis are: (1) to test the hypothesis that Ang II decreases the cAMP/PKA-mediated NHE3 phosphorylation levels at serine 552 increasing its activity by reducing cAMP levels and (2) to test the hypothesis that myosin IIA participates in the NHE3 redistribution from the base to the body of the microvilli in the renal proximal tubule under conditions in which sodium reabsorption is stimulated, such as in response to Ang II. In order to evaluate the effects of AT1R/Gi pathway activation on NHE3 regulation, by means the intracellular pH recovery technique, we verified that under basal conditions, Ang II stimulated NHE3 activity but did not affect PKA-mediated NHE3 phosphorylation at serine 552 in opossum kidney (OKP) cells. However, in the presence of the cAMP-elevating agent forskolin (FSK), Ang II counteracted FSK-induced NHE3 inhibition, reduced intracellular cAMP concentrations, lowered PKA activity, and prevented the FSK-mediated increase in NHE3 serine 552 phosphorylation. All effects of Ang II were blocked by pretreating OKP cells with the AT1R antagonist Losartan, highlighting the contribution of the AT1R/Gi pathway in Ang II-mediated NHE3 upregulation under cAMP-elevating conditions. We also verified that Gi protein inhibition by pertussis toxin treatment decreased NHE3 activity both in vitro and in vivo and, more importantly, prevented the stimulatory effect of Ang II on NHE3 activity in Wistar rat proximal tubules. Additionally, we assessed the effects of myosin IIA on NHE3 redistribution, and found that blebbistatin, a myosin IIA inhibitor, completely prevented the increase of Ang II-mediated NHE3 activity in Wistar rats and that blebbistatin was able to prevent the increase of NHE3 on the Ang II-treated OKP cells surface. Collectively, our results suggest that Ang II counteracts the effects of cAMP/PKA on NHE3 phosphorylation and inhibition by activating the AT1R/Gi pathway and that myosin IIA plays a role in mediating the NHE3 activity regulation in the rat renal proximal tubule in response to Ang II. Furthermore, these findings support the notion that NHE3 dephosphorylation at serine 552 may represent a key event in the regulation of renal proximal tubule sodium handling by Ang II in the presence of natriuretic hormones that promote cAMP accumulation and transporter phosphorylation, and that myosin IIA is involved in NHE3 trafficking regulation in the renal proximal tubule

Cellular response to environmental changes involves a wide repertoire of complex signalling systems often resulting in up and down regulation of various genes. These mechanisms are generally conserved in a variety of organisms. These pathways are also constantly rewired in various organisms, which aid them in maintaining homeostasis and result in species-specific adaptation mechanisms. Protein kinases are central to these mechanisms and orchestrate a multitude of these pathways. This thesis aims to understand the selective forces behind evolution of signalling pathways. More specifically, this thesis focuses on structural and domain architecture differences of protein kinases. Protein kinases are one of the most populated families of proteins in many organisms and it constitutes about 2-3% of proteomes of most of the eukaryotic organisms. These kinases have evolved over ~400 million years and regulate nearly all major signalling pathways. Classification of kinases enables convenient association of kinases to the function and signalling pathway in which they participate. The current scheme of classification is based on the amino acid sequence of the catalytic region, which consists of about 200-300 residues. This scheme proposes division into 7 groups which show gross level similarities in function such as the TK group, which constitutes all tyrosine kinases, or AGC group which constitutes kinases regulated by second messengers. These groups are further divided into ~280 subfamilies providing us insights into function and regulation at a much finer level. This enables ascertaining information about signalling pathways, protein-protein interactions or substrates the kinase phosphorylates. Chapter 1 provides an elaborate introduction to the various types of protein kinases and their roles in signalling processes. This chapter discusses how protein kinases work in a concerted manner with several other players of a signalling pathway to generate a regulated response to external stimuli. Furthermore, it highlights both the evolutionary aspects and dynamical nature of such pathways. The subsequent part of this chapter deals with protein kinases, their evolution, regulation and structural features crucial to catalysis. Protein kinases are regulated in many ways ¬regulation is achieved from within the catalytic domain and also by means of additional domains tethered to the catalytic domain. The regulatory switch is triggered by various cellular and molecular events such as phosphorylation of specific residues, changes in spatial-temporal localization and altered redox states to name a few. The effects of regulatory domains on the overall function have also been discussed. The chapter concludes by highlighting structural analysis carried out to understand the regulatory aspect of kinases and uses this information in rational drug discovery. Chapters 2 and 3 report identification and analysis of a repertoire of protein kinases encoded in the genomes of two of the organisms which are frequently used in comparative genomics. Chapter 2 focuses on the distribution of kinases in Takifugu rubripes, a teleost fish which is a widely used model system for studying human genes. Use of remote homology detection methods identified 519 kinases in fugu. Although the group-wise distribution of kinases shows high similarity to that of human kinases, subfamily distribution shows considerable differences in 22 subfamilies. They are either under or over-represented in fugu. Most noticeable difference is seen for the DYRK subfamily, which is eight times higher in fugu than human. Detailed analysis of the DYRKs revealed interesting insights into and explained partially their high representation in fugu. Only about ten of these kinases classified into these subfamilies showed high sequence similarity and conserved localization signals to the human kinases and kinases commonly found in other eukaryotes such as C.elegans, S.cereviseae and D.melanogaster. Disparity at the level of genome may be attributed to the observation of unique domain architectures characteristic of this genome. A comparison of domain architectures of kinases documented in Pfam with that of the kinases in Takifugu also revealed two kinases with unique domain architectures in fugu; they are associated with Galectin domain and YkyA domains. Despite inconsistencies in the distribution, human and Takifugu kinases subfamilies remarkable similarity is observed in the MAP kinase pathway, which is ubiquitously found across eukaryotic organisms. Nearly 83% of the proteins in this pathway show more than 30% sequence identity between the two organisms thus, validating the use of Takifugu as a model system to study human signalling pathways. While addressing the possibilities of similar expansions of kinases in other teleosts, it was noticed that the Danio rerio genome (zebrafish) had a massively expanded kinome with ~1200 kinases. Chapter 3 explores the possible reasons for the expansion of kinome with kinases specific to Zebrafish. For e.g., the number of kinases from one subfamily (CAMK) is roughly similar to the total number of protein kinases encoded in the human genome. Further, the PIM kinase subfamily is the sole subfamily, which is massively over-represented (~30 times) in this genome. A detailed analysis of PIM kinases of zebrafish revealed that the sequences are divergent from the canonical PIM kinases. Despite this difference, the specific residues, which dictate the functional properties specific to PIM kinases, are highly conserved. These PIM kinases are usually constitutively active, features of which are conserved in PIM kinases of zebrafish as well. Unlike canonical PIM kinases in other eukaryotes, the post-transcriptional regulation of these PIM kinases might be different due to the absence of regulatory regions in the 3'UTR regions of the PIM gene. However, conservation of a S261 phosphorylation site highlights regulation by phosphorylation, which compensates for the constitutively active nature. A massive expansion of the substrate pool of PIM kinases in this genome seems to correlate well with the expansion. Since PIM kinases regulate large number of growth related pathways, we believe that, this might be associated with high regenerative capacity of organs observed in this fish, which makes it an ideal model to study most cancers. While the earlier two chapters primarily focused on the kinase catalytic domain and organism specific changes; the next two chapters address the contribution of domains tethered to the catalytic domain in the overall function of the kinase. Deviations from canonical kinase domain architectures indicate expansion in the functional repertoire of kinases. Chapter 4 is a study on human kinases from the latest revised version of the human genome sequence data. The initial part of the chapter focuses on the differences in the kinase repertoire upon revision of the human genomic data. Seven sequences gleaned from the earlier genomic data are absent and 16 new sequences are added to the kinome dataset according to the latest human genome sequence data. In addition, differences in transcripts for 23 kinases have led to differences in overall length and sub-family classification of these kinases. The identification of the kinome data from this latest version was a mandatory step prior to the study of outlier kinases due to variations in gene transcripts. The domain architectures of the human kinases have been compared with known subfamily-specific domain architectures, in order to identify outliers. Based on the type of domain architecture these outliers have been classified as “rogue” or “hybrid” kinases. Hybrid architecture represent kinases showing high sequence similarity within the kinase domain to a known sub¬family of kinases with the acquisition of non-kinase domains typically found in one of the other subfamilies of kinases. On the other hand rogue architectures belong to kinases with domain architectures not observed in any of the kinase sub-families. A total of 23 outliers have been identified in the human genome-13 hybrids and 10 rogues. The presence of such "hybrid" and "rogue" kinases makes classification of kinases into subfamilies a daunting task and hence necessitates a new method for classification using the full-length sequences. The use of one such alignment-free method, ClaP (Appendix), using full length sequences has been validated for classification of kinases. A similarity metric obtained from full protein sequence comparison further improved the existing methods of classification for 29 kinases, which utilize only the catalytic domain of kinases. Classification based on catalytic domain is incomplete without the knowledge of associated domains, which also have an important role in function. This necessitates a new approach in classification of kinases for function annotation-an integrated one that uses information from the full-length sequence of each kinase. Chapter 5 extends the learning from chapter 4 and aids in identification of 74 "Hybrid" and 18 "Rogue" kinases in other model eukaryotes, Mus musculus, C.elegans, S. Cerevisiae, D. melanogaster and Takifugu rubripes which show significant variations in the overall functions. These sequences due to their hybrid nature might facilitate cross-talk between signalling pathways. Thus annotating the function of each of these 92 outliers has highlighted the use of domain recombination in wiring new pathways and re-wiring existing pathways. Also, these sequences because of their hybrid nature cannot be classified under any of the existing sub-families. Therefore, it has been proposed in this chapter that they be classified as separate sub-family containing sequences with hybrid properties. To validate this, the ClaP method has been extended where the pair-wise distances between two sequences (using full length sequence) has been used to generate phylogenetic trees which have then been subjected to hierarchical clustering to generate sub-family based clusters. Further, a Shannon entropy based score has been used to identify clusters that contain sequences from diverse sub-families grouped together. Upon analysis of these clusters, it was observed that the hybrid and rogue kinases specifically cluster within four clusters with high entropy (constitute large number of sub-families) validating their status as emergent sub-families. In addition, more hybrids and rogues have been identified in these clusters, which have long regions without any domain assignments. Such sequences may contain domain families deviant from those that are currently known and information on their function can be obtained from further genomic studies in future. Lastly, the prevalence of such hybrid and rogue kinases in the genome of a protozoan parasite, P. falciparum has been studied in detail. The role of hybrids and rogues in host-pathogen interaction has been explored. Chapter 6 presents an in-depth analysis of the possible role of charge-neutralization around phosphosites in protein kinases and its substrates. This analysis was a follow up of a study and in collaboration with Dr.Warwicker's group in Manchester, which identified positively charged residues around phosphosites in kinase substrates. The current study not only aims to address the importance of charge neutralization around phosphosites, but also uses this feature for prediction of phosphosites in known structures of kinase substrates. A dataset of phosphosites mapped on a 3-D structure has been used to calculate peak electrostatic potentials around phosphosites based on the solution of a non-linear Poisson-Boltzmann equation. A comparison of peak potentials around phosphosites with that of non-phosphosites reveals a higher positive peak potential at ~10.0 Å radius around the phosphosite. This variation is significantly higher around tyrosine residues in comparison to Ser/Thr residues phosphosites. Further, this distinction in peak potential around the phosphosite is attributed to only certain families like protein kinases and pyruvate kinases. The concept of charge neutralization will therefore show greater success in prediction of phosphosites in such families in comparison to other families with phosphosites. The functional importance of such charge neutralizations has been studied in great detail in the protein kinase domain family due to prior knowledge that certain phosphorylation events contribute to conformational change, which may be correlated to the changes in peak potentials upon phosphorylation. Phosphorylation at certain sites within the kinase catalytic domain often mediates onset of certain signalling events including regulating activity levels of kinases, mediating protein-protein interactions and altering their localization. Therefore, by means of studying conservation patterns of such phosphosites or neutralizing residues, the variations in signalling pathways in homologues with differences in conservation patterns, have been highlighted. Among domain families which do not show clear differences in peak potentials between phosphosites and non-phosphosites, it was noted, in a few cases, that negatively charged ligands bind to the protein in the vicinity of phosphosites, in the un-phosphorylated forms of the protein. Structural studies on a few cases in ligand bound forms indicate a competitive mechanism between phosphorylation and ligand binding which helps in switching between different functional forms. Therefore, the role of phosphorylation as a regulatory mechanism for modulating ligand binding in such domain families has been highlighted. Chapter 7 of the thesis reports a study on disease causing mutations in kinases. So far 180 kinases have been reported to contain disease causing mutations. This chapter particularly focuses on understanding the deleterious effects of non-synonymous missense mutations in kinases. Mutations at certain sites are enriched as seen by the concentration of disease phenotypes upon mutations at these sites in comparison to others. Interactions involving Arginines in sub-domains VIB, VIII, IX and XI are perturbed which affect catalysis. Structural explanation of 10 such mutations, which occur in important sub-domains and not directly implicated in catalysis has been provided. Apart from analyzing the various evolutionary and structural aspects of protein kinases in this thesis an attempt has been made to provide a deeper structural understanding of Msh (MutS Homologues) proteins involved in eukaryotic chromosomal segregation. Chapter 8 deals with Msh4-Msh5 complex, which are eukaryotic homologues of the MutS family of proteins in bacteria. MutS proteins form homodimeric complexes in bacteria that aid in mismatch repair process. There are six MutS homologues in eukaryotes, which form hetero-dimers. Two of the homologues are Msh4 and Msh5, which form hetero-dimeric complexes which is a pre-requisite for its function. They are involved in chromosomal segregation during meiosis-I and aid in resolving Holliday junction DNA. Till date no structure of this complex is available and the exact mode of binding is unclear. In addition, Msh4 and Msh5 display asymmetry in DNA and ATP binding sites. These insights are derived from the severity in phenotypes upon mutation of various residues in these proteins. This work is in collaboration with Dr. Nishant from IISER, Trivandrum. The questions addressed in chapter 8 of the thesis are: What are the structural features that contribute to the asymmetry in function between Msh4 and Msh5 in DNA and ATP binding? Can a structural explanation be provided for each of the 27 mutations causing severe phenotypes (cross-over defects/viability) to predict their role in function of the Msh4-Msh5 complex? Can a prediction be provided for the mode of binding of the Holliday junction DNA? Can residues occurring at interface regions of Msh4 and Msh5 be identified on the basis of the structure which affects the complexation of Msh4 and Msh5? These questions are addressed by homology modelling of the Msh4-Msh5 complex using the Msh2-Msh6 complex as template. Structural explanations have been provided for 23 out of 27 mutations with severe phenotypes. Certain residues in Msh5 are shown to form tighter network of interactions than their counterparts in Msh4 and therefore likely to have a more prominent role in DNA and ATP binding which corroborate with the observed asymmetry in mutant functions. A volume based calculation has been used to suggest a possible mode of binding of the Holliday junction within the cavity of the complex. Finally, the model has been used to predict interface residues that play a crucial role in complexation and function. Experiments are being carried out in Dr. Nishant's laboratory to mutate these residues to validate the model. Chapter 9 summarizes the entire thesis work and also clearly states the chief conclusions from various chapters. Apart from studies embodied in the thesis, the author has been involved in one other study, which is provided as appendix.

Confidentiel / Doctorat en Sciences biomédicales et pharmaceutiques / info:eu-repo/semantics/nonPublished

Abstract Intracellular signalling cascades regulate cardiomyocyte hypertrophic response. Initially hypertrophy of individual myocytes occurs as an adaptive response to increased demands for cardiac work, e.g. during hypertension or after myocardial infarction, but a prolonged hypertrophic response, accompanied by accelerated fibrosis and apoptosis, predisposes the heart to impaired performance and the syndrome of heart failure. The goal of this work was to elucidate some of the main signalling pathways in experimental models of the cardiac hypertrophic response. Mechanical stretching of cultured neonatal rat cardiomyocytes in vitro activates the B-type natriuretic peptide (BNP) gene, a well-established marker of the hypertrophic response, through intracellular signalling cascades mitogen-activated protein kinases (MAPKs) and protein kinase A (PKA) -pathway. Further, transcription factors transcriptional enhancer factor-1 (TEF-1) and activating transcription factor 3 (ATF3) were induced during stretch, and TEF-1 activation was shown to be regulated by extracellular signal-regulated kinase (ERK), while ATF3 activation was modulated by PKA. The BNP gene was also activated by the adenoviral overexpression of the p38 MAPK isoforms p38α and p38β in vitro. Importantly, p38α–induced activation was mediated through activator protein-1 (AP-1) while p38β mediated BNP transcription through GATA-4, which suggests distinct physiological roles for different p38 isoforms. This was further confirmed by quantitative PCR, which demonstrated pro-fibrotic role for the p38α isoform and a pro-hypertrophic role for the p38β isoform. Finally, adenoviral overexpression of ATF3 in vitro and in vivo resulted in activation of cardiac survival factors nuclear factor-κВ and Nkx-2.5, and attenuation of central pro-inflammatory and pro-fibrotic mediators. Together these data suggest a protective role for ATF3 in the heart. Overall this study provides new insights into the role of several signalling molecules involved in cardiac hypertrophic process and suggests potential therapeutic strategies for the diagnosis and treatment of heart failure. / Tiivistelmä Sydämen kammioiden seinämät paksuuntuvat kuormituksen lisääntyessä mm. verenpainetaudissa tai sydäninfarktin jälkeen. Lisääntynyt kuormitus aiheuttaa sydänlihassolujen koon kasvun (hypertrofioitumisen) ohella sidekudoksen kertymistä (fibroosia) ja solukuolemaa. Nämä solutason muutokset lopulta vioittavat sydämen rakennetta niin, että sen toiminta pettää, ja sydän ajautuu vajaatoimintaan. Tätä taudin etenemistä säätelevät molekyylitasolla lukuisat solunsisäiset signaalinvälitysjärjestelmät, joita tässä väitöskirjatyössä tutkittiin eri koemalleissa. Sydämen täyttöpaineen nousun aiheuttama sydänlihassolujen mekaaninen venytys aktivoi natriureettisten peptidien (eteispeptidi, ANP ja B-tyypin natriureettinen peptidi, BNP) synteesiä ja vapautumista verenkiertoon. BNP geenin säätelyä mekaanisen venytyksen aikana tutkittiin rotan sydänlihassoluviljelmissä. Mitogeeni-aktivoituvat proteiinikinaasit (MAPK) sekä proteiinikinaasi A (PKA) säätelivät mekaanisen ärsykkeen aiheuttamaa BNP geenin ekspressiota. Venytys aktivoi myös transkriptiotekijöitä TEF-1 (transcriptional enhancer factor-1) ja ATF3 (activating transcription factor 3). TEF-1 sääteli venytyksen aiheuttamaa BNP:n aktivaatiota ERK:n (extracellular signal-regulated kinase) välityksellä BNP geenin säätelyalueella olevan sitoutumispaikkansa (M-CAT elementti) kautta. ATF3:n säätelyssä PKA:lla oli keskeinen merkitys. Tutkimus osoitti myös, että p38 MAPK:n alatyypeistä p38α lisäsi fibroosiin liittyvien geenien aktiivisuutta, kun taas p38β aiheutti solujen hypertrofioitumista lisäävien geenien ekspressiota. Molemmat alatyypit aktivoivat BNP geenin ekspressiota, mutta aktivaatio tapahtui eri transkriptiotekijöiden kautta. Tutkimuksessa havaittiin myös, että ATF3:n yliekspressio adenovirusvälitteisellä geeninsiirrolla lisäsi kahden sydäntä suojaavan transkriptiotekijän (nuclear factor-κВ ja Nkx-2.5) aktiivisuutta, sekä vähensi sydämen tulehdusvastetta ja fibroosia lisäävien tekijöiden (interleukiini-6 ja plasminogeeniaktivaattorin inhibiittori-1) ekspressiota. Väitöskirjatutkimus antaa uutta tietoa solunsisäisistä signaalinvälitys-järjestelmistä, jotka säätelevät sydänlihaksen kuormitusvastetta sydän- ja verenkiertoelimistön sairauksissa. Näiden solutason mekanismien tunteminen osaltaan edesauttaa jatkossa uusien menetelmien kehittämistä sydämen vajaatoiminnan ehkäisyyn ja hoitoon.

La mycotoxine déoxynivalénol (DON) et son métabolite déépoxy-déoxynivalenol (DOM-1) ont des effets significatifs sur la modification de la fonction des cellules thècales de l’ovaire bovin. L'objectif de cette étude était d'identifier les différentes voies de signalisation impliquées dans le mécanisme d'action de DON et DOM-1 par la spectrométrie de masse. Méthodes: Les cellules thécales de l'ovaire bovin ont été récoltées à partir des vaches adultes, indépendamment du stade du cycle œstral, et ont été cultivées à une densité de 500000 cellules viables dans 1 ml de milieu de McCoy pendant 5 jours. Les cellules ont ensuite été traitées au jour 5 de la culture avec 1 ng/ml de DON ou DOM-1 pendant 30 minutes et des échantillons cellulaires de protéins totales ont été préparés pour spectrométrie de masse. Résultats: la spectrométrie de masse a montré que DON et DOM-1 induisent une surexpression simultanée de ERK1/2, MAPK14 (p38alpha) et MAPK13 (p38delta). La spectrométrie de masse a également indiqué que 94 peptides ont été surexprimés tels que GNGT1, EDN1 et YWHAB. Ils régulent la plupart des voies de prolifération des cellules et sont impliqués dans la biosynthèse des lipides et des glucides. Néanmoins, 255 peptides ont été régulés à la baisse, tels que CALR3, PTGES3, RAD21, ACVR2B et TGFBR1 dont leurs activités sont principalement l'activation ou la désactivation des processus apoptotiques, et le métabolisme du glucose et de la choline. Nos résultats montrent que DON et DOM-1, à une dose de 1 ng/ml, ont le potentiel de stimuler la surexpression de MAPK distinctes et réguler négativement les voies de signalisation spécifiques qui stimulent la prolifération les cellules de la thèque de l’ovaire de bovin. / The mycotoxin deoxynivalenol (DON) and its metabolite deepoxy-DOM-1 have significant effects on bovine ovarian theca cell function. The objective of this study was to identify different signaling pathways involved in the mechanism of action of DON and DOM-1 by mass spectrometry. Methods: bovine ovarian theca cells were harvested from adult cows independently of the stage of the estrous cycle, and were cultured at a density of 500000 viable cells in 1 ml McCoy’s medium for 5 days. The cells were then treated on day 5 of culture with 1 ng/mL DON or DOM-1 for 30 minutes and total cell protein was collected for mass spectrometry. Results from mass spectrometry showed that both DON and DOM-1 induce simultaneous upregulation of ERK1/2 , MAPK14 (p38alpha) and MAPK13 (p38delta). Mass spectrometry also indicated that 94 peptides such as GNGT1, EDN1 and YWHAB were upregulated. They mostly regulate cell proliferation pathways and are involved in biosynthesis of lipid and carbohydrates. Nevertheless, 255 peptides such as CALR3, PTGES3, RAD21, ACVR2B and TGFBR1 were downregulated whose activities are mainly activation or deactivation of apoptotic processes, and glucose and choline metabolism. Our findings show that both DON and DOM-1 at least at a low dose (1 ng/ml) have the potential to stimulate upregulation of distinct MAPKs and downregulate specific signaling pathways that stimulate bovine ovarian theca cell proliferation.

No description available.

La reproduction est un événement crucial pour la vie des plantes. Ce processus nécessite la formation du pollen et des ovules. Les cellules germinales vont subir la méiose puis une succession de mitoses, deux pour le pollen et trois pour l’ovule, ce qui va leur permettre d’acquérir leurs structures finales. Une fois formés, ces deux gamètes doivent se rencontrer. Pour cela, le grain de pollen va germer sur le stigmate puis former le tube pollinique. Le tube pollinique en croissance va traverser les différents tissus femelles et ainsi tracter les deux cellules spermatiques jusqu’à l’ovule, permettant la reproduction. Un important réseau de signalisation cellulaire est nécessaire pour permettre ces événements. Les cascades des Mitogen-Activated Protein Kinases (MAPKs) sont l’un des réseaux de signalisation les plus étudiés chez les plantes. Ces kinases sont impliquées dans de très nombreux processus développementaux tels que la formation de l’embryon ou des stomates. Pour autant, leurs rôles restent encore peu caractérisés pendant de la fécondation. Ce projet a pour objectif de mieux comprendre le rôle que jouent les MAPK lors de la formation des gamètes mâles et femelles ainsi que lors de la croissance des tubes polliniques. Plusieurs membres de la superfamille des MAPKs ont été caractérisés pour leurs rôles dans la reproduction sexuée des végétaux. De précédents travaux dans le laboratoire de Daniel P. Matton, ont démontré l’implication de deux MAPK Kinases Kinases (MAP3K), la Solanum chacoense Fertilization-Related Kinase 1 (ScFRK1) et ScFRK2. Ces deux kinases sont nécessaires pour le développement de l’ovule et du pollen chez S. chacoense, une espèce de pomme de terre sauvage diploïde. Dans un premier temps, nous avons étudié la fonction d’une nouvelle ScFRK, la ScFRK3. Ce troisième membre de la classe des FRKs chez S. chacoense, est, elle aussi, impliquée dans le développement des gamétophytes mâles et femelles. Du patron d’expression jusqu’à l’établissement d’une voie de signalisation potentielle, en passant par la caractérisation phénotypique des mutants, plusieurs expériences ont été réalisées dans le but de comprendre le rôle de ScFRK3 lors de la formation des gamètes chez Solanum chacoense. Nous montrons que la ScFRK3 est impliquée dans la formation du pollen ainsi que celui des ovules. Nous avons ensuite poursuivi nos recherches en affinant le phénotypage du mutant de surexpression ScFRK2. En effet, les précédentes études ont permis de montré que la surexpression de ScFRK2 conduit le primordium ovulaire à la formation de structures carpéloïdes. Pour autant, les ensembles des primordius ovulaires ne sont pas devenu des strutures capéloïde. Nous montrons ici que seulement 10 % des ovules dans l'ovaire sont devenu 4 des carpéloïde. Notre étude montre qu’en plus des structures carpéloïdes, un grand nombre d'ovule n'ont pas de sac embryonnaire à l'anthèse ce qui explique le faible nombre de graines par fruit. L’analyse du développement des sacs embryonnaires monte que la surexpression de ScFRK2 entraine l’arrêt au stade mégaspore fonctionnelle. Ce phénotype est similaire à ce qui a pu être observé dans les lignées ARN interférant pour la ScFRK1 et la ScFRK3. De précédentes études faites chez Arabidopsis thaliana semblent montrer que les membres de la superfamille des MAPK ne sont pas essentiels pour la croissance du tube pollinique. Pour comprendre le rôle que jouent les MAPK dans l’élongation du tube pollinique, nous avons utilisé un inhibiteur des MAP Kinase Kinase (MKK), appelé U0126. La présence de cette drogue dans le milieu de croissance des grains de pollen provoque une diminution de la germination et de l’élongation du tube pollinique. L’utilisation de la méthode semi-in vivo montre une perte de la polarisation de la croissance des tubes polliniques causée par l’inhibition des MKK. La présence de l’inhibiteur conduit à la diminution de la quantité de filaments d’actine ainsi qu’à leur désorganisation à l’apex du tube. L’exocytose est aussi affectée par l’inhibition des MKK. Les cascades MAPK sont nécessaires à la croissance polarisée du tube pollinique chez Arabidopsis thaliana. Pour finir, nous avons voulu identifier certains membres de la superfamille des MAPK impliqués dans la croissance du tube pollinique. Nous nous sommes intéressés en premier lieu aux orthologues de la famille ScFRK chez Arabidopsis thaliana. Les AtMAP3K19-20-21 sont les orthologues les plus proches de ScFRK3. Ces AtMAP3K sont exprimées lors du développement des grains de pollen et lors de l’élongation de tube pollinique. L’analyse du pollen des différentes lignées mutantes montre qu’en leur absence, le pollen ne présente aucun problème de développement contrairement à ScFRK3. Par contre, les doubles mutants et le triple mutant pour les AtMAP3K19-20-21 montrent une diminution de la capacité de germination. L’élongation du tube pollinique est affectée lors de la mutation d’au moins une des AtMAP3K. Ces deux études démontrent que les MAPK sont essentielles dans la formation et l’élongation du tube pollinique. / Reproduction is a crucial event for plant life. This process requires the formation of pollen and ovules. The germ cells will undergo meiosis and then a succession of mitosis, two for the pollen and three for the ovule, which will allow them to acquire their final structures. Once formed, these two gametes must meet each other. For this, the pollen grain will germinate on the stigmas to form the pollen tube. The growth of the pollen tube will pass through the different female tissues and thus pull the two sperm cells to the ovum for reproduction. An important cellular signaling network is necessary to allow these events to occur. The Mitogen-Activated Protein Kinase (MAPKs) cascades are one of the most studied signaling networks in plants. These kinases are involved in a wide range of developmental processes such as embryo formation and stomata. However, their roles remain poorly characterized during fertilization. The aim of this project is to better understand the role played by MAPKs during the formation of male and female gametes as well as during the growth of pollen tubes. Several members of the MAPK superfamily have been characterized for their role in the sexual reproduction of plants. Previous work in Daniel P. Matton's laboratory has demonstrated the involvement of two MAPK Kinases (MAP3K), Solanum chacoense Fertilization-Related Kinase 1 (ScFRK1) and ScFRK2. These two kinases are necessary for egg and pollen development in S. chacoense, a diploid wild potato species. In a first step, we studied the functionality of a new ScFRK, ScFRK3. This third member of the class of FRKs in S. chacoense, is also involved in the development of male and female gametophytes. From the expression pattern to the establishment of a potential signaling pathway, through the phenotypic characterization of mutants, several experiments have been performed in order to understand the role of ScFRK3 in the formation of gametes in S. chacoense. We show that ScFRK3 is involved in the formation of pollen as well as that of the embryonic sac. We then continued our research by refining the phenotyping of the overexpression mutant ScFRK2. Indeed, previous studies have shown that ScFRK2 overexpression leads the ovular primordium to the formation of carpeloid structures. However, the sets of ovular primordia have not become capeloid structures. We show here that only 10% of the eggs in the ovary have become carpeloid. Our study shows that in addition to the carpeloid structures, a large number of ova do not have an embryonic sac in the anthesis, which explains the low number of seeds per fruit. The analysis of the development of the embryonic sacs shows that 7 overexpression of ScFRK2 leads to the cessation of the functional megaspore stage. This phenotype is similar to what has been observed in interfering RNA lines reducing expression of ScFRK1 and ScFRK3. Previous studies in Arabidopsis thaliana suggest that members of the MAPK superfamily are not essential for pollen tube growth. To understand the role that MAPKs play in pollen tube elongation, we used a MAP Kinase Kinase (MKK) inhibitor called U0126. The presence of this drug in the growth medium of pollen grains causes a decrease in germination and elongation of the pollen tube. The use of the semi in vivo method shows a loss of polarization of the pollen tube growth caused by the inhibition of MKK. The presence of the inhibitor leads to a decrease in the number of actin filaments and their disorganization at the apex of the tube. Exocytosis is also affected by MKK inhibition. We show in this chapter that MAPK cascades are necessary for polarized pollen tube growth in Arabidopsis thaliana. Finally, we wanted to identify some members of the MAPK superfamily involved in pollen tube growth. We were first interested in the ScFRK family orthologs in Arabidopsis thaliana. AtMAP3K19-20-21 are the closest orthologs to ScFRK3. These AtMAP3K are expressed during the development of pollen grains and during the elongation of the pollen tube. Pollen analysis of the different mutant lines shows that in their absence the pollen does not present any development problems unlike ScFRK3. On the other hand, double mutants and triple mutant for AtMAP3K19-20-21 show a decrease in germination capacity. Pollen tube elongation is affected when at least one of the AtMAP3Ks is mutated. These two studies demonstrate that MAPKs are essential for the formation and elongation of the pollen tube and that AtMAP3K19-20-21 participate in these biological processes.

No description available.