Forkhead (Fox) proteins are transcription factors that function in many processes including development, metabolism and cell cycle regulation. This gene family is divided into subfamilies that appear to originate from a common ancestor. I have identified the evolutionary selection pressures acting on individual amino acid positions in the FoxA, FoxC, FoxD, FoxI, FoxO and FoxP subfamilies. The patterns of selection observed allowed for the prediction of residue function and identification of residues that differentiate orthologs and paralogs. The subfamily structure and negative selection found within the subfamilies indicates that after gene duplication, differentiation of subfamilies through amino acid changes and subsequent negative selection on these changes has occurred. Meanwhile, the observed neutral changes and positive selection allow for further protein differentiation. Within the FoxC subfamily, positive selection was identified at one amino acid site in the inhibitory domain. Mutation of this site in FOXC1 alters transactivation activity and the effects of mutants on transactivation activity are different on different reporters. The mutant effects were consistent with those of known disease causing mutations, supporting the predicted positive selection. The inhibitory domain is known to function in reducing FOXC1 transactivation activity and influences protein stability. Here I additionally show that loss of the inhibitory domain and mutation of the positively selected site can reduce FOXC1 DNA binding. Co-transfection of FOXC1 and TLE4, a repressor protein that can potentially bind to the inhibitory domain, was shown to increase FOXC1 transactivation activity. The effects of a novel disease causing FOXC1 inhibitory domain mutation on FOXC1 function were also assessed. The mutation reduced FOXC1 transactivation activity and increased protein half-life both of which may lead to disease. Regulation of FOXC1 activity is critical for normal function and this work has furthered our knowledge of how the inhibitory domain influences FOXC1 activity. I have provided biological evidence for the theory that positive selection acts at the amino acid level to optimize protein function. I have also shown that both changes in transcription factor proteins and the cis-regulatory region of target genes have the potential to contribute to evolutionary adaptation.

The healthy development of a living cell requires precise spatial-temporal gene expression. The code that dictates when and where genes are expressed is stored in a pattern of specific sequence motifs, which can be recognised by transcription factors. Understanding the interaction between these DNA sequence motifs and transcription factors will help to elucidate how genomic sequences build transcriptional control networks. However, the DNA-binding specificities of ~1400 human transcription factors are largely unknown. The in vivo DNA-binding events of transcription factors involve great subtlety, because most transcription factors recognise degenerate sequence motifs and related transcription factors often prefer similar or even identical sequences. Forkhead transcription factors exemplify these challenges. To understand how members within the Forkhead transcription factor family gain their binding and functional specificities, we used chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) to interrogate the genome-wide chromatin binding events of three Forkhead transcription factors: FOXM1, FOXO3 and FOXK2. We find that FOXM1 specifically binds to the promoters of a large array of genes whose activities peak at the G2 and M phases of the cell cycle. The canonical Forkhead consensus GTAAACA is not enriched within the FOXM1 cistrome. It gains its own specific binding events and biological functions by interacting and cooperating with the MMB complex. FOXO3 and FOXK2 are recruited to chromatin by the canonical Forkhead consensus GTAAACA, and they bind both shared and specific regions in the genome. FOXO3 mostly binds to the regions which are also bound by FOXK2, but no competitive or assisted binding between FOXO3 and FOXK2 is detected within those regions. Overall, these results help explain how individual members of the Forkhead transcription factor family gain binding specificity within the genome yet raises new questions of how functional specificity is achieved by other family members.

La dystrophie musculaire de Duchenne est une myopathie héréditaire récessive liée au chromosome X. Elle est causée par l’absence de la dystrophine dans les fibres musculaires. La thérapie cellulaire est l’une des approches thérapeutiques possibles, mais son succès dépend du contrôle du rejet des myoblastes greffés et des fibres musculaires hybrides. À présent, le contrôle du rejet est obtenu par l’administration d’immunosuppresseurs puissants. Notre objectif à long terme est de développer un protocole de tolérance immunologique qui permettrait de prévenir le rejet, sans recours à une immunosuppression soutenue. La première étape du protocole de tolérance immunologique que nous souhaitons développer est d’induire la formation de lymphocytes T régulateurs en utilisant le facteur de transcription Foxp3. Nos travaux nous ont permis de produire, dans des bactéries E. coli, la protéine de fusion Tat-Foxp3. Par des essais in vitro nous avons démontré l’augmentation de l’expression du récepteur CD25 sur les lymphocytes T CD4+ naïfs après transduction de la protéine Tat-Foxp3. Cela suggère que la protéine Tat-Foxp3 pourrait convertir les lymphocytes T CD4+ naïfs en lymphocytes T régulateurs. D’autres travaux seront nécessaires pour confirmer que ces cellules exprimant le CD25 sont vraiment des T régulateurs. / The Duchenne muscular dystrophy is the most common hereditary muscular disease. This disease is inherited as an X-linked recessive trait. It is caused by the absence of dystrophin in muscle fibers. Cell therapy is the potential treatment but, its success depends on the control of the rejection of the transplanted myoblasts and of the hybrid fibers that they formed. At present, the control of the graft rejection is achieved by administration of powerful immunosuppressive drug. Our long-term aim is to develop a protocol for immune tolerance that would prevent the graft rejection without sustained immunosuppression. The first step of this tolerance protocol that we want to develop is to induce the formation of regulatory T cells using the transcription factor Foxp3. In this study we generated, in bacteria E. coli, a fusion protein Tat-Foxp3. By in vitro assays, we demonstrated that Tat-Foxp3 protein up-regulated the expression of CD25 in naïve CD4+ T cells. Additional experiments will be required to confirm that these CD25 expressing cells are Treg.

Forkhead box O transcription factors are a family of proteins involved in cellular processes downstream of the Insulin-PI3K-PKB pathway. In response to extra- or intracellular stresses, for example starvation or oxidative stress, FoxOs are required to direct cell cycle progression and apoptosis. In endothelial cells, they induce apoptosis, and their deregulation is linked to diseases involving the insulin pathway, such as diabetes. FoxOs also exhibit a complex role in tumour transformation: here their main function is to suppress tumorigenesis. In both physiological and cancer contexts, FoxO activation leads to the transcription of some general targets, such as p27kip1 or IGFBP1. The FoxOs can also induce tissue-specific genes, as ANGPT2 and BIM in the endothelium. In endothelial cells, another pathway with a pivotal function is the MEK5/ERK5 MAPK signalling way. Its activation promotes cell survival and proliferation in stressful conditions, e.g., when blood vessels are exposed to the shear forces exerted by the blood stream. Furthermore, recent data described ERK5 as a kinase directing tumour resistance upon therapy-induced stress. Comparing their reported roles in various tumours and in the endothelium, FoxO proteins and the MEK5/ERK5 MAPK cascade appear to exert opposite functions. First non-published data confirmed the hypothesis that FoxO factors are subject to a negative modulation by the MEK5/ERK5 pathway. Hence, one goal of this PhD project was to further characterise this crosstalk at molecular level. The major mechanism of FoxO regulation is the balance among several post translational modifications, such as phosphorylation, acetylation, and ubiquitination. Most importantly, the PKB dependent phosphorylation of FoxOs negatively controls their activity, and it is critical for their subcellular localization. Therefore, the regulation of FoxO localization as mechanism of ERK5 dependent suppression was studied, but the results presented in this thesis argue against this hypothesis. However, additional experiments are required to explore the impact of ERK5 activity on FoxO post-translational modifications. FoxO activity can also be modulated by the interaction with other proteins, which in turn could explain general- and tissue-specific gene expression. Thus, another objective of this work was to investigate FoxO3-interactome in endothelial cells and the impact of MEK5/ERK5 activation on it. As published in (Fusi et al. 2022) and presented here, this analysis unveiled TRRAP as new FoxO bound protein in several cell types. Moreover, the interaction did not rely on the capacity of the FoxOs to bind their consensus DNA sequences at the promoter of target genes. Functional data demonstrated that TRRAP is required for FoxO-dependent gene transcription in endothelial and osteosarcoma cells. In addition, TRRAP expression in the endothelium is important for FoxO induced apoptosis. In summary, the interaction between FoxO factors and TRRAP revealed a new regulatory mechanism of FoxO-dependent gene transcription. It remains to be analysed whether the MEK5/ERK5 cascade may exert its suppressive effect on FoxO activity by interfering with their binding to TRRAP and whether such a mechanism may be relevant for tumorigenesis. / Forkhead-Box-O-Proteine sind eine Familie von Transkriptionsfaktoren, die an verschiedenen zellulären Prozessen stromabwärts des Insulin-PI3K-PKB-Signalwegs beteiligt sind. Als Reaktion auf extra- oder intrazelluläre Stressfaktoren, wie Wachstumsfaktorentzug oder oxidativen Stress, werden die FoxOs benötigt, um Zellzyklusprogression und Apoptose zu regulieren. In Endothelzellen induzieren sie Apoptose und ihre Fehlregulation ist mit Krankheiten, bei denen der Insulinsignalweg involviert ist, wie etwa Diabetes mellitus, verbunden. FoxOs spielen auch eine komplexe Rolle bei der Tumortransformation: Hier besteht ihre Hauptfunktion darin, die Tumorentstehung zu unterdrücken. Sowohl im physiologischen als auch im Kontext von Krebs führt die FoxO-Aktivierung zur Transkription verschiedener allgemeiner Zielgene, wie p27kip1, BIM oder IGFBP1. Die FoxOs können aber auch gewebespezifische Gene, wie zum Beispiel ANGPT2 im Endothel, induzieren. Ein weiterer Signalweg mit wichtiger Funktion in Endothelzellen ist der MEK5/ERK5-MAPK Signalweg. Seine Aktivierung fördert das Überleben und Wachstum von Zellen unter Stressbedingungen, wie z. B. wenn Blutgefäße durch den Blutstrom Schubspannungskräften ausgesetzt sind. Darüber hinaus zeigen neuere Daten, dass ERK5 auch an der Tumorresistenzentwicklung unter therapieinduziertem Stress beteiligt ist. Ein Vergleich der bekannten Rolle beider Signalwege im Endothel und bei der Tumorgenese, impliziert eine mutmaßlich gegensätzliche Funktion von FoxO Proteinen und der MEK5/ERK5-MAPK Kaskade. Erste unveröffentlichte Daten stützen die Hypothese, dass FoxO Faktoren einer Negativregulation durch MEK5/ERK5 unterliegen. Ein Ziel dieses Promotionsprojekts, war es daher diesen Zusammenhang auf molekularer Ebene näher zu charakterisieren. Die FoxO-Regulierung ist primär das Zusammenspiel mehrerer posttranslationaler Modifikationen wie Phosphorylierung, Acetylierung und Ubiquitinierung. Der wichtigste Regulationsmechanismus ist dabei die inhibitorische Phosphorylierung durch die Kinase PKB, welche die transkriptionelle FoxO-Aktivität hemmt und deren subzelluläre Lokalisierung ins Zytoplama fördert. Daher wurde zunächst der Einfluss von ERK5 auf die FoxO-Lokalisierung untersucht. Die Daten dieser Arbeit sprechen gegen einen Einfluss von der ERK5 Aktivität auf FoxO Lokalisation, doch sind zusätzliche Experimente erforderlich, um dessen Wirkung auf das Muster der posttranslationalen Modifikation der FoxOs zu klären. FoxO-Aktivität kann auch durch die Interaktion mit anderen Proteinen moduliert werden, die wiederum auch die allgemeine und gewebespezifische Genexpression steuern könnten. Ein weiteres Ziel dieser Arbeit war es daher, das FoxO3-Interaktom in Endothelzellen und den Einfluss forcierter MEK5/ERK5-Aktivierung darauf zu untersuchen. Wie in (Fusi et al. 2022) gezeigt und hier vorgestellt, führte diese Analyse zur Identifikation von TRRAP als neuem generellen FoxO Bindepartner. Die zelltypunabhängige Interaktion beider Proteine beruhte dabei nicht auf der Fähigkeit der FoxOs direkt an ihre Konsensus-DNA-Sequenzen in den Promotoren ihrer Zielgene zu binden. Funktionelle Daten zeigten nachfolgend, dass TRRAP entscheidend zur FoxO abhängigen Gentranskription in Endothel- und Osteosarkomzellen beiträgt. Darüber hinaus ist TRRAP im Endothel für die effiziente Apoptoseinduktion durch FoxOs wichtig. Zusammenfassend offenbarte die Interaktion zwischen FoxO-Faktoren und TRRAP einen neuen Regulationsmechanismus der FoxO-abhängigen Gentranskription. Es bleibt zu prüfen, ob die MEK5/ERK5 Kaskade FoxOs dadurch hemmt, dass sie die Bindungsfähigkeit von FoxO an TRRAP stört, und ob die beobachtete FoxO-TRRAP Interaktion auch im Kontext der Tumorgenese von Bedeutung ist.

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Thesis (Ph. D.)--University of Washington, 2007. / Vita. Includes bibliographical references (leaves 122-140).

Hcm1, es un factor transcripcional de la familia de los forkhead en Saccharomyces cerevisiae. Los factores forkhead se encuentran evolutivamente conservados, desde levaduras hasta humanos. En mamíferos estos factores regulan diversos procesos, entre ellos el ciclo celular, la supervivencia y la proliferación en respuesta a factores de crecimiento. Además, los factores FoxM, FoxO y sus ortólogos, participan en procesos como el envejecimiento y en enfermedades como el cáncer. Los estudios sobre Hcm1 en S. cerevisiae, indican que este factor es un regulador de la formación del spindle pole y de la expresión del cluster de genes necesarios en la fase S del ciclo celular. En el presente trabajo se estudió la regulación de Hcm1 sobre nuevos procesos celulares. En primer lugar, se demostró que Hcm1 regula positivamente la masa mitocondrial, el número de copias de ADN en esta organela y su actividad metabólica. Además, induce la metabolización de la glucosa favoreciendo el proceso oxidativo sobre la fermentación. Este cambio metabólico inducido por Hcm1, viene acompañado por una mayor resistencia celular al estrés. Además, se demostró que Hcm1 responde al estrés oxidativo aumentando su localización nuclear y su actividad transcripcional. Esta misma respuesta se observó cuando las células eran sometidas a restricción de glucosa o nitrógeno. En esta dirección estudiamos los mecanismos regulatorios de estas respuestas y se determinó que Sir2, una histona deacetilasa NAD+-dependiente relacionada con el envejecimiento y el silenciamiento genético, interacciona con Hcm1 y regula la respuesta a estrés de Hcm1. Paralelamente, analizamos la implicación de las vías AMPK y TOR/Sch9 en la regulación de Hcm1. De esta manera, demostramos que ambas vías son reguladoras de la respuesta de Hcm1 a restricción nutricional, ya que experimentos in vitro indicaron que Snf1 y Sch9 fosforilan Hcm1. El análisis de la expresión génica en la cepa salvaje y en el mutante hcm1, en diferentes puntos de la curva de crecimiento del cultivo, indicó que genes que se inducen durante esta cinética, y que están relacionados con el estrés y el metabolismo, son regulados por este factor. Los resultados obtenidos en este trabajo, permiten concluir que, además de su implicación en el ciclo celular, Hcm1 es un factor clave en la adaptación temprana de las células a la restricción nutricional y en la posterior entrada en fase diáuxica, a través de la inducción de metabolismo oxidativo mitocondrial y la respuesta a estrés. / Hcm1 is a forkhead transcription factor in Saccharomyces cerevisae. The forkhead factors are evolutionary conserved from yeast to human. In mammals, these factors regulate different processes, among them, cell cycle, cell survival and cell proliferation in response to growth factors. Moreover, FoxO, FoxM and their orthologues have been related to the aging process and cancer. Studies on Hcm1 in S. cerevisae indicate that this factor is related to spindle pole dynamics and the regulation of the cluster of genes required during the S phase of the cell cycle. In this work we studied Hcm1 implication on novel cellular processes. First, we demonstrated that Hcm1 positively regulates mitochondrial mass, mtDNA copy and mitochondrial activity. In addition, Hcm1 favours oxidative metabolism of glucose over its fermentation. This metabolic shift, is accompanied by an increase in cellular stress resistance. In response to oxidative stress treatments, Hcm1 shifts to the nucleus and its transcriptional activity is activated. A similar Hcm1 response was observed when the cells were submitted to glucose or nitrogen restriction. Additionally, we analyzed the regulatory mechanisms behind these responses. We demonstrated that Sir2, a NAD+ dependent histone deacetylase involved in aging and genetic silencing, interacts with Hcm1 and regulates its response to oxidative stress. In parallel, we analyzed the role of AMPK and TOR/Sch9 pathways on Hcm1 regulation. In this context, we observed that both pathways regulate Hcm1 in response to nutrient restriction in vivo. Moreover, Snf1 and Sch9 phosphorylate Hcm1 in vitro. Gene expression analysis on wild type cells and in hcm1 mutant at different points along the growth curve, indicated that genes that are upregulated during this kinetic and are related to stress response and metabolism, are regulated by Hcm1. Taken together, our results indicate that Hcm1 not only regulates cell cycle dynamics, but is also a key factor in the early adaptation of the cells to nutrient deficiency and later, to the entry into the diauxic phase. This adaptation is mediated by Hcm1 induction of oxidative metabolism and stress response.

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A família gênica Forkhead P {FOXP) tem sido alvo de muitos estudos envolvendo evolução do cérebro e comportamento animal. Destacam-se particularmente as investigações com o gene FOXP2, que indicam que mudanças neste gene estariam associadas com a evolução da vocalização em algumas espécies de mamíferos, incluindo o Homo sapiens. Recentemente, estudos de desordem intrínseca de proteínas (IDPs) tem ganhado ênfase no contexto evolut ivo, visto que uma correlação posit iva entre regiões de desordem e altas taxas evolutivas tem sido observada. Através de um conjunto de abordagens que inclui predizer o conteúdo de desordem e os motivos lineares de interação, bem como as taxas evolutivas, buscamos desvendar a historia evolutiva dos genes da subfamília FOXP. Concentramos nossas análises sobre regiões desordenadas das proteínas FOXPl, FOXP2, FOXP3 e FOXP4 encontradas em 77 espécies de tetrápodes. Tais regiões proteicas são normalmente negligenciadas em estudos dessa natureza, pois se localizam fora de seus tra dicionais domínios conservados, normalmente associados à função principal da proteína. Sít ios apontados estando sob seleção positiva e relaxamento da restrição seletiva mostraram-se hotspots importantes para mudanças que podem impactar na capacidade de interação das proteínas. Encontramos que os maiores valores de w são mais prevalentes em regiões desordenadas que em ordenadas. Ainda, alto e similar valor de desordem (70%) foi encontrado nas 77 proteínas ortólogas de FOXPl , FOXP2, e FOXP4, indicando a manutenção de um "padrão geral" sobre um longo tempo evolutivo. Portanto, a variabilidade tanto de aminoácidos quanto de motivos lineares dentro das regiões de desordem foi marcante. A proteína FOXP3 apresentou menor nível de desordem (30%), mas signif icante sinal de seleção positiva em alguns sítios. Composição idênt ica de resíduo de aminoácido e/ou motivos lineares em espécies filogeneticamente distantes, indica clara convergência molecular, provavelmente associada a pressões seletivas similares. Sucessivamente, nossos achados mostraram uma clara diferença na composição de motivos lineares entre mamíferos e não mamíferos, dando suporte para a importância dos estudos de evolução da interatividade proteica para as compreensões de características taxa-específicas. / Forkhead Family P (FOXP) has been target of many studies about brain and behavior evo lution among species. FOXP2 receives special attention in academic society, due associations with vocalízation evolution in mammals, including Homo sapiens. Recently, intrinsically disorder proteins studies have gained emphasis in the evolutionary context, as positive correlation between disorder regions and higher evolutionary rate has been observed. Through a set of approaches, including disorder and linear motif predictions, as well as estimate evolutionary rates, we aimed to unveil the evolutionary history of FOXP subfamily genes. We focused our ana lysis over disordered regions of FOXPl, FOXP2, FOXP3 and FOXP4 proteins retrieved in 77 tetrapods. Such protein regions are usually neglected in studies of this nature, for being localized out of the traditional conserved domains, usua lly associated with the main function of the protein. Sites indicated as under relaxation of selective constrains or positive selection have shown to be important hotspots for changes that can impact in protein interaction capability. Higher w va lues are prevalent in disordered regions than in ordered ones. Still, high and similar disorder proportion (~70%) was found among 77 orthologues proteins of FOXPl, FOXP2 and FOXP4, indicating general pattern of disorder maintenance, along tetrapod's evolutionary tree. However, amino acid and linear motifs variability within disordered regions was observed. FOXP3 protein presented lower disorder leveis (~30%), when compared with other paralogues, but signal of positive selection was observed in some sites. ldentical composition of amino acid residues and/or linear motifs is, probably, associated with similar selective pressure. Successively, ou r results showed clear differences in linear motif composition between mammals and non-mammals, supporting the importance of evolutionary studies on protein interaction for the understanding of taxa-specifics characteristics.