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Les gènes sont les parties du génome qui codent pour les protéines. Les gènes d’une ou plusieurs espèces peuvent être regroupés en "familles", en fonction de leur similarité de séquence. Cependant, pour connaître les relations fonctionnelles entre ces copies de gènes, la similarité de séquence ne suffit pas. Pour cela, il est important d’étudier l’évolution d’une famille par duplications et pertes afin de pouvoir distinguer entre gènes orthologues, des copies ayant évolué par spéciation et susceptibles d’avoir conservé une fonction commune, et gènes paralogues, des copies ayant évolué par duplication qui ont probablement développé des nouvelles fonctions. Étant donnée une famille de gènes présents dans n espèces différentes, un arbre de gènes (obtenu par une méthode phylogénétique classique), et un arbre phylogénétique pour les n espèces, la "réconciliation" est l’approche la plus courante permettant d’inférer une histoire d’évolution de cette famille par duplications, spéciations et pertes. Le degré de confiance accordé à l’histoire inférée est directement relié au degré de confiance accordé à l’arbre de gènes lui-même. Il est donc important de disposer d’une méthode préliminaire de correction d’arbres de gènes. Ce travail introduit une méthodologie permettant de "corriger" un arbre de gènes : supprimer le minimum de feuilles "mal placées" afin d’obtenir un arbre dont les sommets de duplications (inférés par la réconciliation) sont tous des sommets de "duplications apparentes" et obtenir ainsi un arbre de gènes en "accord" avec la phylogénie des espèces. J’introduis un algorithme exact pour des arbres d’une certaine classe, et une heuristique pour le cas général. / Genes are segments of genomes that code for proteins. Genes of one or more species can be grouped into gene families based on their sequence similarity. In order to determine functional relationships among these multiple gene copies of a family, sequence homology is insufficient as no direct information on the evolution of the gene family by duplication, speciation and loss can be inferred directly from a family of homologous genes. And it is precisely this information that allows us to distinguish between orthologous gene copies, that have evolved by speciation and are more likely to preserve the same function and paralogous gene copies that have evolved by duplication and usually acquire new functions. For a given gene family contained within n species, a gene tree (inferred by typical phylogenetic methods) and a phylogenetic tree of the considered species, reconciliation between the gene tree and the species tree is the most commonly used approach to infer a duplication, speciation and loss history for the gene family. The main criticism towards reconciliation methods is that the inferred duplication and loss history for a gene family is strongly dependent on the gene tree considered for this family. Indeed, just a few misplaced leaves in the gene tree can lead to a completely different history, possibly with significantly more duplications and losses. It is therefore important to have a preliminary method for "correcting” the gene tree, i.e. removing potentially misplaced branches. N. El-Mabrouk and C. Chauve introduced "non-apparent duplications" as nodes that are likely to result from the misplacement of one leaf in the gene tree. Simply put, such a node indicates that one or more triplets contradict the phylogeny given by the species tree. In this work, the problem of eliminating non-apparent duplications from a given gene tree by a minimum number of leaf removals is considered. Depending on the disposition of this type of nodes in the gene tree, the algorithm introduced leads to an O(nlogn) performance and an optimal solution in a best case scenario . The general case however is solved using an heuristic method.

Der Endozytoserezeptor Megalin gehört zu einer Gruppe von strukturell und funktionell verwandter Rezeptoren, der LDL R Gen Familie. Es sind zwei Arten von Lipidtransportpartikel beschrieben worden, die durch Megalin in Zellen aufgenommen werden. Zum einen werden Lipoproteine über ihre Apoproteine von Megalin erkannt und endozytiert. Zum anderen nimmt Megalin die hydrophoben Vitamine A und D über ihre Carrierproteine in ihre Zielzellen auf. Es handelt sich um Vitamin D bindendes Protein (DBP) und Retinol bindendes Protein (RBP). Zweck dieser Arbeit war es zu untersuchen, ob die Endozytose von Steroidcarriern durch Megalin ein genereller Mechanismus ist oder ob DBP und RBP Ausnahmen darstellen. Hierzu wurden exemplarisch drei Carrierproteine (24p3, Apo D und CCSP) für Steroide ausgesucht, die in Megalin-exprimierende Gewebe aufgenommen werden. Der (rekombinante) Retinolcarrier 23p3 zeigte bei surface plasmon resonance Analysen keine direkte Bindung an Megalin. Der Progesteron-Carrier Apo D hingegen bindet Megalin, ferner konnte in Zellkulturversuchen Endozytose und lysosomale Degradation von Apo D in Megalin-exprimierende Zellen nachgewiesen werden. Auch der Progesteron-Carrier CCSP wird durch Megalin in Zellen aufgenommen, allerdings ist zur Endozytose von CCSP ein Co-Rezeptor notwendig. Mit dieser Arbeit ist die erste in vivo-Beschreibung eines dualen Rezeptorsystems aus Megalin und einem peripheren Membranprotein namens Cubilin gelungen, welches u.a. im proximalen Tubulus der Niere existiert. Abschließend wurde exemplarisch für ein Steroidhormon-abhängiges Gewebe der murine Uterus hinsichtlich seiner Megalin-Expression untersucht. Es konnte ein bereits bekannter Ligand Megalins, das Glykoprotein Laktoferrin, aus der uterinen, luminalen Flüssigkeit aufgereinigt werden. Ferner konnte gezeigt werden, dass die Expression von Laktoferrin im Uterus strenger hormoneller Kontrolle unterliegt. / The endozytic receptor Megalin belongs to a group of structurally and functionally related receptors called LDL R gene family. Two different types of lipid particles are taken up by Megalin into target cells. The first type, lipoproteins are recognized and internalized by Megalin via their apoproteins. In addition, Megalin mediates the endocytosis of the lipophilic vitamins A and D into target cells by means of their carrier proteins. These proteins are the vitamin D binding protein (DBP) and retinal binding protein (RBP). The aim of the investigations was to determine, if the endocytosis of steroid hormone carriers by Megalin is a common occurrence or restricted only to DBP and RBP. Therefore, three carrier proteins for steroids (24p3, Apo D and CCSP) were chosen as an example. All of them are known to be taken up in Megalin expressing tissues. In surface plasmon resonance analysis recombinant 24p3, a carrier of retinol, showed no affinity to Megalin. Whereas the progesterone carrier Apo D bound to Megalin. Furthermore, it was endozytosed and degraded in lysosomes by Megalin expressing cells. The cellular uptake of the progesterone carrier CCSP is mediated by Megalin as well, however a co-receptor is needed. This work demonstrates for the first time the existence of a dual receptor pathway consisting of Megalin and a peripheral membrane protein named Cubilin in vivo. This systems is functional in addition to other tissues in the proximal tubule of the kidney. Finally, the Megalin expression in the murine uterus as an example of a steroid dependent tissue was investigated. Lactoferrin a known Megalin ligand was purified from the luminal uterine fluid. Furthermore, Lactoferrin expression in the uterus was shown to be under tight hormonal control.

MADS-box genes are important regulators of reproductive development in seed plants, including both flowering plants and conifers. In this thesis the evolution of the AGAMOUS subfamily of MADS-box genes, and what the ancestral function of this group of genes might have been in the early seed plants about 300 million years ago, was addressed by the discovery of two novel conifer genes, both basal to all previously known AGAMOUS subfamily genes. DAL20, the most basal of these genes, was exclusively expressed in roots, unlike all previously known AGAMOUS subfamily genes. I also studied the evolutionary mechanisms leading to functional diversification of duplicated genes in two different subfamilies of MADS-box genes; the AGAMOUS and AGL6 subfamilies. Focus was on studying changes in gene expression pattern, representing changes in the transcriptional regulation between the genes, and on comparing the functional properties of the gene products, representing changes in the protein-coding sequence between the genes. Duplicated genes in the AGL6 subfamily were found to have evolved by both mechanisms. In the AGAMOUS subfamily I found duplicated spruce genes; DAL2 and DAL20, that appear to have functionally diversified mainly by changes in the transcriptional regulation. Conifer AGAMOUS subfamily genes were also used in a comparative developmental-genetics approach to evaluate hypotheses, based on the morphology of fossil and extant conifer seed cones, on the identity of the female reproductive organ, the ovuliferous scale, and the evolution of seed cone morphology in the conifer families Pinaceae, Taxodiaceae and Cupressaceae. Seed cones in these families have been hypothesized to have homologous ovule-bearing organs, but I found substantial differences in the expression patterns of orthologous AGAMOUS subfamily genes in seed cones of these families that are not compatible with this hypothesis, indicating that the evolutionary history of conifer seed cones is more diverse than previously thought.

Les gènes sont les parties du génome qui codent pour les protéines. Les gènes d’une ou plusieurs espèces peuvent être regroupés en "familles", en fonction de leur similarité de séquence. Cependant, pour connaître les relations fonctionnelles entre ces copies de gènes, la similarité de séquence ne suffit pas. Pour cela, il est important d’étudier l’évolution d’une famille par duplications et pertes afin de pouvoir distinguer entre gènes orthologues, des copies ayant évolué par spéciation et susceptibles d’avoir conservé une fonction commune, et gènes paralogues, des copies ayant évolué par duplication qui ont probablement développé des nouvelles fonctions. Étant donnée une famille de gènes présents dans n espèces différentes, un arbre de gènes (obtenu par une méthode phylogénétique classique), et un arbre phylogénétique pour les n espèces, la "réconciliation" est l’approche la plus courante permettant d’inférer une histoire d’évolution de cette famille par duplications, spéciations et pertes. Le degré de confiance accordé à l’histoire inférée est directement relié au degré de confiance accordé à l’arbre de gènes lui-même. Il est donc important de disposer d’une méthode préliminaire de correction d’arbres de gènes. Ce travail introduit une méthodologie permettant de "corriger" un arbre de gènes : supprimer le minimum de feuilles "mal placées" afin d’obtenir un arbre dont les sommets de duplications (inférés par la réconciliation) sont tous des sommets de "duplications apparentes" et obtenir ainsi un arbre de gènes en "accord" avec la phylogénie des espèces. J’introduis un algorithme exact pour des arbres d’une certaine classe, et une heuristique pour le cas général. / Genes are segments of genomes that code for proteins. Genes of one or more species can be grouped into gene families based on their sequence similarity. In order to determine functional relationships among these multiple gene copies of a family, sequence homology is insufficient as no direct information on the evolution of the gene family by duplication, speciation and loss can be inferred directly from a family of homologous genes. And it is precisely this information that allows us to distinguish between orthologous gene copies, that have evolved by speciation and are more likely to preserve the same function and paralogous gene copies that have evolved by duplication and usually acquire new functions. For a given gene family contained within n species, a gene tree (inferred by typical phylogenetic methods) and a phylogenetic tree of the considered species, reconciliation between the gene tree and the species tree is the most commonly used approach to infer a duplication, speciation and loss history for the gene family. The main criticism towards reconciliation methods is that the inferred duplication and loss history for a gene family is strongly dependent on the gene tree considered for this family. Indeed, just a few misplaced leaves in the gene tree can lead to a completely different history, possibly with significantly more duplications and losses. It is therefore important to have a preliminary method for "correcting” the gene tree, i.e. removing potentially misplaced branches. N. El-Mabrouk and C. Chauve introduced "non-apparent duplications" as nodes that are likely to result from the misplacement of one leaf in the gene tree. Simply put, such a node indicates that one or more triplets contradict the phylogeny given by the species tree. In this work, the problem of eliminating non-apparent duplications from a given gene tree by a minimum number of leaf removals is considered. Depending on the disposition of this type of nodes in the gene tree, the algorithm introduced leads to an O(nlogn) performance and an optimal solution in a best case scenario . The general case however is solved using an heuristic method.

In the present study, we have approached the molecular characterization of the HCMV specific UL1. To this end a HCMV (AD169-derived HB5 background) recombinant with an HA-epitope tagged UL1 and a mutant with a full UL1 deletion in the endotheliotropic HCMV TB40/E strain were generated. Our data reveal that the UL1 is transcribed with late kinetics. pUL1 is glycosylated and localizes at the site of virus assembly and secondary envelopment in infected cells forming part of the envelope of HCMV virions. A HCMV mutant with a targeted deletion of UL1 exhibits a growth defect phenotype in retinal pigment epithelium cells but not in fibroblasts, indicating that this ORF encodes a cell-type specific tropism factor. / En aquest treball hem investigat la pauta oberta de lectura de UL1 del Cytomegalovirus humà (HCMV), el gen UL1 es específic del HCMV. Hem caracteritzat la proteïna UL1 modificada amb un epítop HA en la soca HB5, derivada de AD169. L'UL1 s’expressa com una glicoproteïna que es pot detectar a les 48 i 72h post-infecció. En fibroblasts humans infectats, UL1 co-localitza al citoplasma, al lloc d’assemblatge del virió, amb proteïnes estructurals del virus. A més a més, els anàlisis de virions AD169 purificats que contenen UL1-HA mostren que UL1 és un nou constituent de l’envolta del HCMV. La delecció de UL1 en el context de la soca TB40/E del HCMV disminueix el creixement viral de manera selectiva en determinats tipus cel•lulars, suggerint que UL1 podria estar involucrat en la regulació del tropisme cel•lular del HCMV.

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AsymmeTree is a flexible and easy-to-use Python package for the simulation of gene family histories. It simulates species trees and considers the joint action of gene duplication, loss, conversion, and horizontal transfer to evolve gene families along the species tree. To generate realistic scenarios, evolution rate heterogeneity from various sources is modeled. Finally, nucleotide or amino acid sequences (optionally with indels, among-site rate heterogeneity, and invariant sites) can be simulated along the gene phylogenies. For all steps, users can choose from a spectrum of alternative methods and parameters. These choices include most options that are commonly used in comparable tools but also some that are usually not found, such as the innovation model for species evolution. While output files for each individual step can be generated, AsymmeTree is primarily intended to be integrated in complex Python pipelines designed to assess the performance of data analysis methods. It allows the user to interact with, analyze, and possibly manipulate the simulated scenarios. AsymmeTree is freely available on GitHub.

[Français] Une fraction importante des génomes eucaryotes est constituée de Gènes Répétés en Tandem (GRT). Un mécanisme fondamental dans l’évolution des GRT est la recombinaison inégale durant la méiose, entrainant la duplication locale (en tandem) de segments chromosomiques contenant un ou plusieurs gènes adjacents. Différents algorithmes ont été proposés pour inférer une histoire de duplication en tandem pour un cluster de GRT. Cependant, leur utilisation est limitée dans la pratique, car ils ne tiennent pas compte d’autres événements évolutifs pourtant fréquents, comme les inversions, les duplications inversées et les délétions. Cette thèse propose différentes approches algorithmiques permettant d’intégrer ces événements dans le modèle de duplication en tandem classique. Nos contributions sont les suivantes: • Intégrer les inversions dans un modèle de duplication en tandem simple (duplication d’un gène à la fois) et proposer un algorithme exact permettant de calculer le nombre minimal d’inversions s’étant produites dans l’évolution d’un cluster de GRT. • Généraliser ce modèle pour l’étude d’un ensemble de clusters orthologues dans plusieurs espèces. • Proposer un algorithme permettant d’inférer l’histoire évolutive d’un cluster de GRT en tenant compte des duplications en tandem, duplications inversées, inversions et délétions de segments chromosomiques contenant un ou plusieurs gènes adjacents. / [English] Tandemly arrayed genes (TAGs) represent an important fraction of most genomes. A fundamental mechanism at the origin of TAG clusters is unequal crossing-over during meiosis, leading to the duplication of chromosomal segments containing one or many adjacent genes. Such duplications are called tandem duplications, as the duplicated segment is placed next to the original one on the chromosome. Different algorithms have been proposed to infer the tandem duplication history of a TAG cluster. However, their applicability is limited in practice since they do not take into account other frequent evolutionary events such as inversion, inverted duplication and deletion. In this thesis, we propose different algorithmic approaches allowing to integrate these evolutionary events in the original tandem duplication model of evolution. Our contributions are summarized as follows: • We integrate inversion events in a tandem duplication model restricted to single gene duplications, and we propose an exact algorithm allowing to compute the minimum number of inversions explaining the evolution of a TAG cluster. • We generalize this model to the study of orthologous TAG clusters in different species. • We propose an algorithm allowing to infer the evolutionary history of a TAG cluster through tandem duplication, inverted duplication, inversion and deletion of chromosomal segments containing one or many adjacent genes.