Dissertations / Theses on the topic 'Branchiostoma'

L’induction neurale est le processus au travers duquel les cellules ectodermiques de l’embryon deviennent neurales. De nombreuses études sur les mécanismes contrôlant ce processus on été réalisées mais du fait de sa complexité, de nombreuses questions restent sans réponse. Au cours de ce travail de thèse, je me suis intéressé à l’étude de l’induction neurale sous une perspective évolutive en étudiant ce processus chez le céphalocordé amphioxus, l’un des plus proches parents des vertébrés. J’ai pu mettre en évidence que, comme les vertébrés, l’amphioxus possède un organisateur. J’ai également confirmé une conservation du rôle des voies de signalisation BMP et FGF respectivement dans l’induction de l’épiderme et la régionalisation du tissu neural. Cependant, au contraire des vertébrés, le signal FGF ne semble pas être un acteur prépondérant de l’induction neurale. Au contraire, un rôle important de la voie de signalisation Activine/Nodal a été mis en évidence.Les résultats obtenus soutiennent d’une part la conservation de certains aspects de ce mécanisme chez tous les chordés, et suggèrent d’autre part l’implication de certains acteurs comme la voie Activine/Nodal jusque là inconnue chez les vertébrés. La position phylogénétique de l’amphioxus et la conservation globale de ce processus entre les céphalochordés et les vertébrés nous permettent de suggérer que l’ancêtre des chordés formait du tissue neurale au travers des mécanismes mis en évidence dans cet étude. Ces résultats nous permettent également de proposer de nouvelles études chez les vertébrés visant à établir un rôle putatif de la voie Activine/Nodal au cours de ce processus, rôle jusque la complètement inconnu<br>Neural induction is the process through which embryonic ectodermal cells become neural. Many studies on the mechanisms controlling this process have been made, but because of its complexity, many questions remain unanswered. In this thesis, I have focused my interest on the study of neural induction in an evolutionary context studying this process in the cephalochordate amphioxus, one of the closest relatives of vertebrates. I have highlighted that amphioxus, as vertebrates, possesses an organizer. I have demonstrated a conservation of the role of BMP and FGF signals in the induction of the epidermis and the regionalization of neural tissue respectively. However, in contrast to vertebrates, FGF signal does not appear to be a major player in neural induction. Instead, an important role of Activin/Nodal signaling pathway has been demonstrated. These results support, first, the conservation of several aspects of this mechanism in all chordates, and second, they suggest the involvement of the Activin/Nodal signaling in this process, something previously unknown in vertebrates. The phylogenetic position of amphioxus and the overall conservation of this process between cephalochordates and vertebrates allow us to suggest that the ancestor of chordates formed its neural tissue through mechanisms highlighted in this study. These results also allow us to propose new studies in vertebrates for establishing a putative role of the Activin/Nodal signaling during this process, a role previously completely unknown

L’induction neurale est le processus au travers duquel les cellules ectodermiques de l’embryon deviennent neurales. De nombreuses études sur les mécanismes contrôlant ce processus on été réalisées mais du fait de sa complexité, de nombreuses questions restent sans réponse. Au cours de ce travail de thèse, je me suis intéressé à l’étude de l’induction neurale sous une perspective évolutive en étudiant ce processus chez le céphalocordé amphioxus, l’un des plus proches parents des vertébrés. J’ai pu mettre en évidence que, comme les vertébrés, l’amphioxus possède un organisateur. J’ai également confirmé une conservation du rôle des voies de signalisation BMP et FGF respectivement dans l’induction de l’épiderme et la régionalisation du tissu neural. Cependant, au contraire des vertébrés, le signal FGF ne semble pas être un acteur prépondérant de l’induction neurale. Au contraire, un rôle important de la voie de signalisation Activine/Nodal a été mis en évidence.Les résultats obtenus soutiennent d’une part la conservation de certains aspects de ce mécanisme chez tous les chordés, et suggèrent d’autre part l’implication de certains acteurs comme la voie Activine/Nodal jusque là inconnue chez les vertébrés. La position phylogénétique de l’amphioxus et la conservation globale de ce processus entre les céphalochordés et les vertébrés nous permettent de suggérer que l’ancêtre des chordés formait du tissue neurale au travers des mécanismes mis en évidence dans cet étude. Ces résultats nous permettent également de proposer de nouvelles études chez les vertébrés visant à établir un rôle putatif de la voie Activine/Nodal au cours de ce processus, rôle jusque la complètement inconnu<br>Neural induction is the process through which embryonic ectodermal cells become neural. Many studies on the mechanisms controlling this process have been made, but because of its complexity, many questions remain unanswered. In this thesis, I have focused my interest on the study of neural induction in an evolutionary context studying this process in the cephalochordate amphioxus, one of the closest relatives of vertebrates. I have highlighted that amphioxus, as vertebrates, possesses an organizer. I have demonstrated a conservation of the role of BMP and FGF signals in the induction of the epidermis and the regionalization of neural tissue respectively. However, in contrast to vertebrates, FGF signal does not appear to be a major player in neural induction. Instead, an important role of Activin/Nodal signaling pathway has been demonstrated. These results support, first, the conservation of several aspects of this mechanism in all chordates, and second, they suggest the involvement of the Activin/Nodal signaling in this process, something previously unknown in vertebrates. The phylogenetic position of amphioxus and the overall conservation of this process between cephalochordates and vertebrates allow us to suggest that the ancestor of chordates formed its neural tissue through mechanisms highlighted in this study. These results also allow us to propose new studies in vertebrates for establishing a putative role of the Activin/Nodal signaling during this process, a role previously completely unknown

The work embodied in this thesis concerns the host defence mechanisms of the hemichordate, <i>Saccoglossus ruber</i> and the cephalochordate, <i>Branchiostoma lanceolatum</i>. Initially the cellular repsonses of these animals towards experimentally introduced foreign particles were examined. <i>S. ruber</i> possesses avidly phagocytic coelomocytes which were studied <i>in vitro</i> and <i>in vivo</i>, and shown by light and electron microscopy to be of a single morphological type. These coelomocytes probably originate from the coelomic lining, but autoradiography failed to substantiate this. The cellular response in <i>B. lanceolatum</i> towards wounding and subcutaneously injected bacteria was very limited. Even after 7 days, a relatively small number of coelomocytes accumulated at the site of injection. These coelomocytes contained phagocytosed bacteria and formed the beginning of nodule-like structures. In the majority of sections, the bacteria were observed surrounded by an unidentifiable amorphous material. Haemagglutinins and antibacterial factors were also detected in whole body homogenates of <i>S. ruber</i> and <i>B. lanceolatum</i>. The haemagglutinins from both animals were proteinaceous and functioned independently of Ca<SUP>++</SUP> and Mg<SUP>++</SUP>. The <i>S. ruber</i> agglutinin showed specificity for D-galactose containing carbohydrates, whereas no clear-cut carbohydrate specificity could be discerned with the <i>B. lanceolatum</i> agglutinin. The <i>S. ruber</i> agglutinin was also associated with the mucus covering the body surface, and the <i>B. lanceolatum</i> agglutinin with mucus in the pharynx. Antibacterial activity in <i>S. ruber</i> was strongest against natural bacterial isolates. The active factor, which may be a bromophenol, was heat stable, dialyzable, bactericidal in its mode of action and also associated with the body surface mucus. The <i>B. lanceolatum</i> antibacterial factor was bacteriostatic, probably proteinaceous, heat labile and operated over a wide temperature range. At a protein concentration above 5 mg ml<SUP>-1</SUP>, the antibacterial proteins aggregated and could be disassociated only at high pH. A role for these humoral factors in the defence systems of the experimental animals is discussed.

The ParaHox cluster is the evolutionary sister of the Hox cluster. Like the Hox cluster, the ParaHox cluster is subject to complex regulatory phenomena such as collinearity. Despite the breakup of the ParaHox cluster within many animals, intact and collinear clusters have now been discovered within the chordate phyla in amphioxus and the vertebrates, and more recently within the hemichordates and echinoderms. The archetypal ParaHox cluster of amphioxus places it in a unique position in which to examine the regulatory mechanisms controlling ParaHox gene expression within the last common ancestor of chordates, and perhaps even the wider Deuterostomia. In this thesis, the genomic and regulatory landscape of the amphioxus ParaHox cluster is characterised in detail. New genomic and transcriptomic resources are used to better characterise the B.floridae ParaHox cluster and surrounding genomic region, and conserved non-coding regions and regulatory motifs are identified across the ParaHox cluster of three species of amphioxus. In conjunction with this, the impact of retrotransposition upon the ParaHox cluster is examined and analyses of transposable elements and the AmphiSCP1 retrogene reveal that the ParaHox cluster may be more insulated from outside influence than previously thought. Finally, the detailed analyses of a regulatory element upstream of AmphiGsx reveals conserved mechanisms regulating Gsx CNS expression within the chordates, and TCF/Lef is likely a direct regulator of AmphiGsx within the CNS. The work in this thesis makes use of new genomic and transcriptomic resources available for amphioxus to better characterise the genomic and regulatory landscape of the amphioxus ParaHox cluster, serving as a basis for the improved identification and characterisation of functional regulatory elements and conserved regulatory mechanisms. This work also highlights the potential of Ciona intestinalis as a ‘living test tube' to allow the detailed characterisation of amphioxus ParaHox regulatory elements.

Nitric Oxide (NO) is a gaseous molecule that acts in a wide range of biological processes. NO can be produced by enzymatic and non-enzymatic pathways and, in this scenario, the enzyme Nitric Oxide Synthase (NOS) has a great importance for its exclusive role in <i>de novo</i> synthesis of NO. In the present study, the role of the NO in the embryonic development was investigated in the cephalochordate <i>Branchiostoma lanceolatum</i> (amphioxus) with the purpose of acquiring further knowledge on the ancestral role of animal <i>Nos</i> and the acquisition of new NO functions during evolution. Amphioxus has three different <i>Nos</i> genes (<i>NosA, NosB</i> and <i>NosC</i>) that are not orthologues of the three <i>Nos</i> of mammals (<i>NosI, NosII</i> and <i>NosIII</i>) deriving from an independent duplication occurred in the common ancestor of cephalochordates. The three amphioxus <i>Nos</i> genes showed a different temporal and spatial expression during development and a different susceptibility to be induced after immune stimulation. The study of the promoter regions of these genes can be very useful to identify possible diversities in regulation that can lead those peculiar expression features. In amphioxus larva, NO was mainly detected in the developing nervous system and in the pharyngeal area, before and after the mouth opening. The inhibition of NOS activity, and as consequence the enzymatic NO production, during amphioxus neurulation, resulted in the alteration of pharyngeal structures formation in the larvae, in particular opening of the mouth resulted compromised. Moreover, an alteration in larva locomotion was observed. Further studies will be necessary to reveal the exactly molecular mechanisms and the pathways in which II NO acts for establishment of the pharyngeal structures and the neuromuscular junctions early in development. For this purpose, a differential transcriptomic analysis of NOS-inhibited embryos was performed but the results are still very preliminary.

Le système nerveux est responsable de l’interconnexion interne des animaux multicellulaires. Il leur permet en effet d’intégrer les activités physiologiques de leurs différentes composantes en une seule entité fonctionnelle, capable d’interagir avec son environnement. L’évolution et le développement des systèmes nerveux complexes comptent parmi les questions les plus fascinantes de la recherche en biologie. Afin de mettre en place une diversité de types de cellules neurales et de connexions neurales, les animaux métazoaires ne déploient qu’un nombre étonnamment réduit de signaux développementaux. C’est l’intermodulation dynamique de ces signaux qui va pouvoir induire un patron spatial d’identités et de comportements cellulaires distincts. L’acide rétinoïque (AR) est une petite molécule diffusible dérivée de la vitamine A qui contribue à la mise en place des axes du système nerveux central des vertébrés et est un régulateur crucial de la différentiation neuronale. D’autre part, il a été montré que les signaux à l’AR affectaient le phénotype de neurotransmetteurs exhibé par des sous-populations neuronales et jouent des rôles divers dans la morphogenèse du système nerveux périphérique issu des placodes crâniennes et des cellules des crêtes neurales. Néanmoins, bien que le rôle de l’AR dans la régionalisation du système nerveux central ait été étudié de manière extensive, nous en savons beaucoup moins au sujet de l’action de l’AR sur le développement du système nerveux périphérique, sur l’établissement des différentes identités de neurotransmetteurs, ou quant à comment ces fonctions ont évolué. Bien qu’initialement considéré comme spécifique aux vertébrés, un volume croissant de données indique désormais que l’AR serait impliqué dans le développement du système nerveux de divers taxons, tels que les cnidaires, les mollusques gastropodes ainsi que les cordés invertébrés. En particulier, l’amphioxus, céphalocordé dont l’évolution est lente, est connu pour posséder un système de signalisation à l’AR semblable à celui des vertébrés. Le génome de l’amphioxus présente un haut degré de conservation de sa synténie par rapport à celui des vertébrés et exhibe relativement peu de pertes ou de duplications indépendantes de ses gènes développementaux. Par conséquent, l’embryogenèse ainsi que la morphologie de l’amphioxus ressemble par bien des points à celles des vertébrés, ce qui facilite l’identification des traits ancestraux et dérivés et en fait donc un modèle approprié à la recherche comparative. Cette étude vise à fournir une description détaillée de différentes populations neurales au sein du système nerveux périphérique de l’amphioxus et d’explorer les rôles joués par l’AR dans ce processus. À cette fin, des analyses d’expression de gènes et d’immunohistochimie ont été utilisées, en vue d’identifier les différentes sous-populations de progéniteurs et les différents types de cellules neurales. De plus, les niveaux de signaux à l’AR ont été altérés pharmacologiquement à différents stades de développement de l’amphioxus, pour déterminer leurs effets sur la formation des populations neurales identifiées, ainsi que sur les patrons de prolifération et d’apoptose. Les résultats inclus dans ce travail révèlent la présence de différentes populations de cellules neurales chez l’amphioxus et mettent en lumière leur vraisemblable relation phylogénétique avec les structures leur correspondant chez les vertébrés. Par ailleurs, différents rôles contexte-dépendants de la signalisation à l’AR on été documentés, incluant la mise en place de frontières discrètes dans le système nerveux central et l’ectoderme de l’embryon d’amphioxus, et la régulation du développement des progéniteurs neuraux tardifs dans le système nerveux périphérique de manière spécifique à leur type cellulaire<br>The nervous system provides internal interconnection to multi-cellular animals. It enables them to integrate the physiological activities of their different components into one functional entity that can successfully interact with its environment. The evolution and development of complex nervous systems is one of the most fascinating questions of biological research. In order to generate a diversity of neural cell types and neural connections, metazoan animals deploy a surprisingly small number of instructive developmental signals, which crosstalk in a dynamic manner to induce a spatial pattern of cell identities and behaviors.Retinoic acid (RA) is a small diffusible signaling molecule derived from vitamin A that contributes to the axial patterning of the vertebrate central nervous system and functions as a crucial regulator of neuronal differentiation. Moreover, RA signals have been shown to affect the neurotransmitter phenotype of specific neuronal subsets and play distinct roles during the morphogenesis of the peripheral nervous system from cranial placodes and neural crest. However, while the role of RA signaling in the regionalization of the central nervous system has been extensively studied, much less is known about its actions in cranial placodes and neural crest derivatives, in the establishment of different neurotransmitter identities, or how these functions might have evolved.Albeit initially believed to be vertebrate-specific, a growing body of evidence now implicates RA signaling in the nervous system development of various distant taxa, such as cnidarians, gastropod mollusks and invertebrate chordates. In particular, the slow evolving cephalochordates, commonly called amphioxus, are known to possess a vertebrate-like RA signaling system. The amphioxus genome has retained a high degree of synteny with vertebrate genomes and exhibits relatively little losses or independent duplications of developmental genes. Accordingly, amphioxus embryogenesis and morphology also display remarkable similarity with vertebrates, which allows the identification of ancestral as well as newly derived traits and makes these animals attractive models for comparative research.This study aims at providing a detailed description of the development of different neural cell populations in the central and peripheral nervous system of amphioxus and explores the roles played by RA signaling during this process. To this end, gene expression analyses and immunohistochemistry were used, in order to identify distinct subsets of neural progenitors and neural cell types. Furthermore, RA signaling levels were manipulated pharmacologically at different stages of amphioxus development, to assess their effects on the formation of identified neural cell populations as well as on proliferation and apoptosis patterns. The results presented in this work reveal the presence of distinct neural cell populations in amphioxus and highlight their likely phylogenetic relationships with corresponding structures in other chordates. In addition, several context-dependent functions of RA signaling were documented, which include the generation of discrete boundaries in the central nervous system and ectoderm of amphioxus embryos as well as the cell type-specific regulation of late neural progenitor development in the peripheral nervous system. The observed roles of RA signaling in the amphioxus neural tube and peripheral nervous system correspond well to those reported for the vertebrate hindbrain and cranial placodes, supporting the current hypothesis of a close evolutionary relationship between these structures and suggesting that the involvement of RA signals in their development is a conserved feature of chordates

Le système nerveux est responsable de l’interconnexion interne des animaux multicellulaires. Il leur permet en effet d’intégrer les activités physiologiques de leurs différentes composantes en une seule entité fonctionnelle, capable d’interagir avec son environnement. L’évolution et le développement des systèmes nerveux complexes comptent parmi les questions les plus fascinantes de la recherche en biologie. Afin de mettre en place une diversité de types de cellules neurales et de connexions neurales, les animaux métazoaires ne déploient qu’un nombre étonnamment réduit de signaux développementaux. C’est l’intermodulation dynamique de ces signaux qui va pouvoir induire un patron spatial d’identités et de comportements cellulaires distincts. L’acide rétinoïque (AR) est une petite molécule diffusible dérivée de la vitamine A qui contribue à la mise en place des axes du système nerveux central des vertébrés et est un régulateur crucial de la différentiation neuronale. D’autre part, il a été montré que les signaux à l’AR affectaient le phénotype de neurotransmetteurs exhibé par des sous-populations neuronales et jouent des rôles divers dans la morphogenèse du système nerveux périphérique issu des placodes crâniennes et des cellules des crêtes neurales. Néanmoins, bien que le rôle de l’AR dans la régionalisation du système nerveux central ait été étudié de manière extensive, nous en savons beaucoup moins au sujet de l’action de l’AR sur le développement du système nerveux périphérique, sur l’établissement des différentes identités de neurotransmetteurs, ou quant à comment ces fonctions ont évolué. Bien qu’initialement considéré comme spécifique aux vertébrés, un volume croissant de données indique désormais que l’AR serait impliqué dans le développement du système nerveux de divers taxons, tels que les cnidaires, les mollusques gastropodes ainsi que les cordés invertébrés. En particulier, l’amphioxus, céphalocordé dont l’évolution est lente, est connu pour posséder un système de signalisation à l’AR semblable à celui des vertébrés. Le génome de l’amphioxus présente un haut degré de conservation de sa synténie par rapport à celui des vertébrés et exhibe relativement peu de pertes ou de duplications indépendantes de ses gènes développementaux. Par conséquent, l’embryogenèse ainsi que la morphologie de l’amphioxus ressemble par bien des points à celles des vertébrés, ce qui facilite l’identification des traits ancestraux et dérivés et en fait donc un modèle approprié à la recherche comparative. Cette étude vise à fournir une description détaillée de différentes populations neurales au sein du système nerveux périphérique de l’amphioxus et d’explorer les rôles joués par l’AR dans ce processus. À cette fin, des analyses d’expression de gènes et d’immunohistochimie ont été utilisées, en vue d’identifier les différentes sous-populations de progéniteurs et les différents types de cellules neurales. De plus, les niveaux de signaux à l’AR ont été altérés pharmacologiquement à différents stades de développement de l’amphioxus, pour déterminer leurs effets sur la formation des populations neurales identifiées, ainsi que sur les patrons de prolifération et d’apoptose. Les résultats inclus dans ce travail révèlent la présence de différentes populations de cellules neurales chez l’amphioxus et mettent en lumière leur vraisemblable relation phylogénétique avec les structures leur correspondant chez les vertébrés. Par ailleurs, différents rôles contexte-dépendants de la signalisation à l’AR on été documentés, incluant la mise en place de frontières discrètes dans le système nerveux central et l’ectoderme de l’embryon d’amphioxus, et la régulation du développement des progéniteurs neuraux tardifs dans le système nerveux périphérique de manière spécifique à leur type cellulaire<br>The nervous system provides internal interconnection to multi-cellular animals. It enables them to integrate the physiological activities of their different components into one functional entity that can successfully interact with its environment. The evolution and development of complex nervous systems is one of the most fascinating questions of biological research. In order to generate a diversity of neural cell types and neural connections, metazoan animals deploy a surprisingly small number of instructive developmental signals, which crosstalk in a dynamic manner to induce a spatial pattern of cell identities and behaviors.Retinoic acid (RA) is a small diffusible signaling molecule derived from vitamin A that contributes to the axial patterning of the vertebrate central nervous system and functions as a crucial regulator of neuronal differentiation. Moreover, RA signals have been shown to affect the neurotransmitter phenotype of specific neuronal subsets and play distinct roles during the morphogenesis of the peripheral nervous system from cranial placodes and neural crest. However, while the role of RA signaling in the regionalization of the central nervous system has been extensively studied, much less is known about its actions in cranial placodes and neural crest derivatives, in the establishment of different neurotransmitter identities, or how these functions might have evolved.Albeit initially believed to be vertebrate-specific, a growing body of evidence now implicates RA signaling in the nervous system development of various distant taxa, such as cnidarians, gastropod mollusks and invertebrate chordates. In particular, the slow evolving cephalochordates, commonly called amphioxus, are known to possess a vertebrate-like RA signaling system. The amphioxus genome has retained a high degree of synteny with vertebrate genomes and exhibits relatively little losses or independent duplications of developmental genes. Accordingly, amphioxus embryogenesis and morphology also display remarkable similarity with vertebrates, which allows the identification of ancestral as well as newly derived traits and makes these animals attractive models for comparative research.This study aims at providing a detailed description of the development of different neural cell populations in the central and peripheral nervous system of amphioxus and explores the roles played by RA signaling during this process. To this end, gene expression analyses and immunohistochemistry were used, in order to identify distinct subsets of neural progenitors and neural cell types. Furthermore, RA signaling levels were manipulated pharmacologically at different stages of amphioxus development, to assess their effects on the formation of identified neural cell populations as well as on proliferation and apoptosis patterns. The results presented in this work reveal the presence of distinct neural cell populations in amphioxus and highlight their likely phylogenetic relationships with corresponding structures in other chordates. In addition, several context-dependent functions of RA signaling were documented, which include the generation of discrete boundaries in the central nervous system and ectoderm of amphioxus embryos as well as the cell type-specific regulation of late neural progenitor development in the peripheral nervous system. The observed roles of RA signaling in the amphioxus neural tube and peripheral nervous system correspond well to those reported for the vertebrate hindbrain and cranial placodes, supporting the current hypothesis of a close evolutionary relationship between these structures and suggesting that the involvement of RA signals in their development is a conserved feature of chordates

Les protéines fluorescentes (PF) homologues d’AvGFP (Green Fluorescent Protein de la méduse Aequorea victoria) sont des outils incontournables de l’imagerie des processus de la cellule vivante. Leurs performances conditionnent la précision de l’analyse quantitative des signaux de fluorescence. Le développement de nouvelles PF demande donc à la fois de parvenir à une forte brillance tout en contrôlant la réponse de la protéine aux variations des paramètres physico-chimiques de la cellule en fonction de la question biologique étudiée. A ce jour, les PF jaunes disponibles montrent une forte sensibilité au pH. Afin d’élaborer des mutants moins sensibles, deux approches ont été considérées : une première consiste à mieux appréhender l’incidence de la dynamique du réseau de liaisons hydrogène entourant le chromophore sur son équilibre acido-basique. La seconde vise à identifier les facteurs structuraux à l’origine de la brillance particulièrement élevée de nouvelles PF jaunes et jaune-vert provenant d’un ver marin, Branchiostoma lanceolatum.J’ai d’abord mis au point un algorithme recherchant l’ensemble des liaisons hydrogène présentes au sein d’une protéine et qui étudie leur dynamique au cours de simulations par dynamique moléculaire. Il permet leur agrégation en réseaux, l’identification des réseaux connectés à un atome d’intérêt ainsi que le suivi de leur dynamique. Pour validation, cet algorithme a été appliqué à la recherche des réseaux de liaisons hydrogène présents au sein de différents mutants d’AvGFP pour lesquels un transfert de proton à l'état excité a été étudié expérimentalement. Cet algorithme pourra également servir à comprendre de façon dynamique le mécanisme d’autres systèmes biologiques dont la fonction repose sur le transfert de protons.D’autre part, j’ai résolu la structure de la protéine fluorescente jaune naturelle lanYFP de Branchiostoma lanceolatum, particulièrement brillante mais à la structure quaternaire tétramérique. Cette protéine a été rendue monomérique par évolution dirigée, ce qui a donné la protéine mNeonGreen à la fluorescence jaune-vert, protéine désormais étalon dans cette gamme spectrale, et dont j’ai également résolu la structure. Mon étude a permis de rationaliser a postériori l’ensemble des mutations introduites au cours de l’évolution. Enfin, j’ai réalisé une étude du dégât d’irradiation spécifique des rayons X permettant de comprendre le changement remarquable de couleur observé sur les cristaux de mNeonGreen après collecte de données de diffraction.L’ensemble des résultats obtenus au cours de ma thèse permet de proposer un cadre de compréhension à la fois théorique et expérimental des déterminants contrôlant les propriétés de fluorescence des PF jaunes<br>Fluorescent Proteins (FPs) homologous to AvGFP (Green Fluorescent Protein from the jellyfish Aequoria victoria) are versatile tools used in live cell imaging. The amount of information that can be derived from the fluorescence signals depends on the spectroscopic performances of the FP. The development of new FPs should focus on both brightness increase and control of the protein response to physicochemical parameter variations within the cell. Current yellow FPs exhibit a strong sensitivity to pH. In order to engineer less sensitive variants, two complementary approaches have been used: the first one consists in studying the influence of the hydrogen bond network dynamics around the chromophore on its protonation state. In the second one, I have sought to identify the structural determinants of the particularly high brightness of newly discovered yellow FPs from a sea worm, Branchiostoma lanceolatum.First, I wrote an algorithm that can identify all hydrogen bonds within a protein and analyse their dynamics along molecular dynamics simulations. It allows for their clustering in networks, the identification of networks connected to a given atom and the monitoring of their dynamics. The method was validated by using the algorithm on various AvGFP mutants for which excited state proton transfer has been experimentally studied. This algorithm should also be useful for the study of other biological systems whose function is based on proton transfer.Besides, I solved the structure of the natural yellow FP lanYFP from Branchiostoma lanceolatum, which is particularly bright, but presents a tetrameric arrangement. This protein was monomerized by directed evolution, which led to the yellow-green FP mNeonGreen, now a benchmark in this spectral range. I also solved the structure of mNeonGreen, which allowed me to rationalize a posteriori the mutations that have been introduced during the evolution process. Finally, I performed a specific radiation damage study in order to explain the remarkable change in colour of mNeonGreen crystals upon X-ray data collection. Altogether, the results of my PhD work provides a theoretical and experimental framework of the determinants that drive the fluorescence properties of yellow FPs

Glycolipids play important roles in the biology of prokaryotes and eukaryotes, including humans, and although theyare found on the cell-membrane surface of all eukaryotic cells, not much is known about their biosynthesis. The aim ofthis project was to characterize two enzymes: glucosylceramide synthase (GCS) which is involved in the biosynthesisof glycolipids such as gangliosides that are abundant in the membranes of nerve cells; and dolicholphosphate mannosesynthase (DPMS), involved in the synthesis precursor for protein glycosylation. Both GCS and DPMS have beenshown play a role in cancer as well as in congenital disorders of glycosylation, and are therefore interesting targets tostudy from a therapeutic perspective.With the goal to identify a suitable expression system for GCS, the genes coding for GCS from lancelet(Branchiostoma floridae) and human (Homo sapiens) were cloned and tested for expression in Escherichia coliBL21(DE3)T1 and C41(DE3) using different vectors. Cloning into three different vectors was successful and initialexpression testing was performed. SDS-PAGE analysis confirmed initial expression of proteins. Although the correctsize of the protein could be confirmed by Western blot, no fluorescence of the GFP-fusion protein could be detected.DPMS from Thermococcus onnurineus (ToDP) was expressed in E. coli C41(DE3) and purified by immobilizedmetal ion affinity chromatography and gel filtration. Crystallization optimization was performed for ToDP producedfrom the vector pNIC28-Bsa4 and plate-like crystals were obtained. X-ray intensity data analysis indicated that thesecrystals contained lipid rather than protein. Crystallization screening for ToDP produced from the vector pNIC-CTHOconstruct was successful. Crystallization screening using the commercially available MemGold-HT96 crystallizationkit resulted in initial crystallization that yielded protein crystals that diffracted to 10 °A resolution.<br>Glykolipider är viktiga biologiska byggstenar hos prokaryoter och eukaryoter, även människor. Trots attglykolipider finns på cellmembranytan hos alla eukaryota celler är inte mycket känt kring syntesen av glykolipider. Målet med detta projekt var att karaktärisera två enzym: glukosylceramidsyntas (GCS) som är involverat i biosyntesenav glykolipider som gangliosider vilka förekommer i cellmembranet hos människors nervceller; och dolikolfosfatmannossyntas (DPMS) som är involverat i syntesen av substrat för proteinglykosylering. Både GCS och DPMS harvisat sig spela en roll i cancer och medfödda glykosyleringssjukdomar och är därför intressanta enzym att studera urett medicinskt perspektiv.Med målet att identifiera ett lämpligt expressionssystem för GCS, klonades gener från lansett (Branschiostomafloridae) och människa (Homo sapiens) och testades för expression i Escherichia coli BL21(DE3)T1 och C41(DE3)med olika vektorer. Kloning av tre olika vektorer lyckades och expressionstester utfördes. Analys med SDS-PAGEbekräftade expression av protein. Trots att korrekt storlek av proteinet kunde bekräftas medWestern blot, detekteradesingen fluorescens från GFP-fusionsproteinet. DPMS från Thermococcus onnurineus (ToDP) i två olika konstrukt uttrycktes i E. coli C41(DE3) och renades med immobiliserad metalljonaffinitetskromatografi och gelfiltrering. Kristalliseringsoptimering utfördes för ToDP uttryckt i vektorn pNIC28-Bsa4 och skivliknande kristaller erhölls. Diffraktionsdata indikerade dockatt kristallerna innehöll lipider och inte protein. Kristallisering av ToDP uttryckt i vektorn pNIC-CTHO lyckadesoch initiala kristallingsförhållanden hittades genom att använda det kommersiellt tillgängliga kristalliseringskitet MemGold-HT96. Diffraktionsdata visade på upplösning ner till 10 Å.

Originally 2A was characterised in foot-and-mouth disease virus. Site directed mutagenesis identified a C-terminus consensus motif [D(V/I)ExNPGP] and it is proposed that 2A interacts with the exit tunnel of the ribosome in a way that a specific peptide bond is skipped between the last glycine of 2A and the proline of 2B, thus providing a discontinuity in translation, resulting in release of discrete proteins from one single ORF. 2A was also identified in other picornaviruses, positive, single and double-stranded RNA insect viruses and mammalian rotaviruses. A motif present at the C-terminus of the 2A oligopeptide [D(V/I)ExNPGP] is very highly, though not completely conserved . The sequence upstream of this motif shows, however, no apparent conservation between 2As of different viruses. In this study, extensive site-directed mutagenesis were performed on several 2A sequences and a series of ‘hybrid' 2As comprising different consensus motifs juxtaposed with different upstream contexts were created as part of a detailed analysis of the mechanism of 2A-mediated ribosome stalling. The results demonstrated that a minimal region of twenty to twenty-three amino acids interacts with the exit tunnel of the ribosome to bring about a pause in processivity, alter the peptidyl transferase centre geometry and restrict the ribosome A site via two distinctive stalling mechanisms. Other molecular analyses tested here will require further optimisations or alternative methods: a visual method to explore the dynamics of re-initiation of translation from proline codon, purification of the translation-regulating factors and structural resolution of 2A sequences. Previously, cellular 2As were identified in non-LTR retrotransposons of trypanosomes. It is reported here as part of two other cellular organisms Saccoglossus kowalevskii (acorn worm) and Branchiostoma floridae (amphioxus). In the acorn worm, the nucleotides sequences corresponding to 2A motifs were part of the untranslated genome. In amphioxus, three 2A elements were identified in hypothetical proteins, and at the N-terminus of twenty non-LTR retrotransposons.

L'acide rétinoïque (AR) est un morphogène dérivé de la vitamine A, qui intervient dans le contrôle de l'organogenèse, de la prolifération et de la différenciation cellulaires chez les Chordés. Dans ce contexte, nous avons étudié les régulations spatio-temporelles de la voie de signalisation de l’AR au cours du développement de l’amphioxus, en mettant l'accent sur l’espèce européenne Branchiostoma lanceolatum.Nous avons tout d'abord inhibé ou activé la voie de signalisation de l’AR lors du développement embryonnaire en traitant des embryons d’amphioxus à des doses variables de composés pharmacologiques interférant avec le métabolisme des rétinoïdes. Grâce à l’utilisation d’outils mathématiques spécifiques, nous avons établi un schéma détaillé des effets des traitements effectués sur le développement du système nerveux central (SNC) et du pharynx chez l’amphioxus en nous basant sur l’expression de gènes marqueurs de tissus spécifiques. À l’issue de cette première analyse, nous avons par la suite étudié les effets d’une perturbation de la signalisation de l’AR à des points clés du développement chez l’amphioxus lors de la régionalisation du SNC et du pharynx. Nous avons ainsi montré que la voie de signalisation de l’AR intervient dans la régionalisation de l’axe antéro-postérieur via le contrôle des gènes hox dès le stade gastrula et jusqu’aux stades larvaires. En outre, nous avons réalisé l'étude préliminaire du gène homologue chez l’amphioxus du gène aldh1a2 des Vertébrés, et avons démontré que la régulation du niveau de synthèse de l’AR au cour du développement est conservée entre l’amphioxus et les Vertébrés. Finalement, nous avons montré que la voie de l’AR participe également à la morphogenèse caudale chez l’amphioxus, et que le mécanisme impliqué semble différent de celui proposé chez les Vertébrés où l’AR contrôle la structuration de la nageoire caudale par le ciblage des tissus mésenchymateux<br>Retinoic acid (RA) is an endogenous vitamin A-derived morphogen. In this context, we studied the spatiotemporal roles of RA signaling in amphioxus development, focusing on the European amphioxus species: Branchiostoma lanceolatum. We first created excess and insufficiency models of RA signaling by exposing amphioxus embryos to series of doses of different pharmacological compounds targeting either the RA receptors or the RA metabolism machinery. By introducing the important mathematical concept of a Cartesian coordinate system founded by René Descartes, we created detailed diagrams of the concentration-dependent defects caused by RA signaling in the central nervous system (CNS) and pharynx of amphioxus by evaluating the statistical significances of tissue-specific marker gene expression in labeled embryos. This analysis yielded a very detailed description of the sensitivities of the developing amphioxus CNS and pharynx to altered RA signaling levels. Following this initial challenge, we correlated the effects of altered RA signaling levels with key amphioxus developmental stages characterized by structural transitions in CNS and pharynx. We show that hox-mediated RA signaling in axial patterning is active beyond the gastrula stage and might be maintained until at least early larval stage, with possible roles in more regionalized axis formation and organ induction. In addition, we carried out a preliminary study on a RA synthesizing gene in amphioxus, called aldh1a, a possible homolog of the vertebrate aldh1a2 gene, demonstrating that the feedback between RA signaling and RA synthesizing levels has emerged before the split of the cephalochordate and vertebrate lineages. Moreover, we are able to show that RA signaling also participates in tail fin morphogenesis in amphioxus by a mechanism that is probably not comparable to that in vertebrates, where RA modulates caudal fin patterning through targeting mesenchymal derivatives

Understanding the mechanisms of transcriptional regulation and the constraints that operate in gene promoter sequences is the key step in understanding the evolutionary conservation of transcriptional regulation. It is well known that regulatory regions with the same expression outputs do not have to share the sequence similarity. The most important elements in regulatory sequences are transcription factor binding sites and their position relocation does not usually influence the expression output. The least complex transcriptional regulation is characteristic for housekeeping genes. For their expression they require only basal core promoter elements (sometimes only CpG islands are sufficient) and general transcription factors, so they can be transcribed easily and immediately whenever they are needed. In this study we focused on transcriptional regulation of invertebrate amphioxus (Branchiostoma floridae) housekeeping genes in vertebrate systems. We prepared a set of constructs with amphioxus regulatory regions for testing their activity in different mammalian cell lines and a set of constructs with the same amphioxus regulatory regions for observing their spatial recognition in developing medaka fish embryo. We found that half of investigated amphioxus regulatory regions are recognized by...

碩士<br>國立臺灣大學<br>海洋研究所<br>101<br>The bHLH-PAS transcription factors are found in both protostomes and deuterostomes. They are involved in many developmental and physiological processes including the regional differentiation of the central nervous system, tube-formation, hypoxia signaling, aromatic hydrocarbon sensing, and circadian rhythm regulation. Although some of their functions are apparently different between model protostomes and vertebrates, little has been known about the evolution of their functions. To understand the evolution of these genes in chordates, I manually annotated bHLH-PAS genes of the basal chordate amphioxus (Branchiostoma floridae) from the draft genome database. My results show that amphioxus has at least 10 bHLH-PAS genes, 9 of which can be assigned to known orthologous families. Moreover, the comparisons of cDNA sequences and gene models show that current amphioxus gene models may not correctly predict the true coding sequence. Finally, I examined the developmental expression patterns of these amphioxus bHLH-PAS genes by quantitative polymerase chain reaction and in situ hybridization. I found that BfArnt, BfNcoa, BfSim, and BfHifα are expressed in similar patterns compared to their vertebrate homologues, suggesting that their functions may be conserved. On the other hand, BfAhr and BfNpas4 are expressed with different patterns between amphioxus and vertebrates. This might imply functional changes after the divergence of cephalochordates and vertebrates. Since vertebrates have multiple bHLH-PAS paralogues that may result from whole genome duplications, I compared the expression patterns and the functions of these paralogues. I suggest that neo- or subfunctionalization of the duplicated paralogues may explain the functional divergence of bHLH-PAS genes in the vertebrate lineage.

The amphioxus Hox cluster is often viewed as “archetypal” for the chordate lineage. Here we present a descriptive account of the 448kb region spanning the Hox cluster of the amphioxus Branchiostoma floridae from Hox14 to Hox1.We provide complete coding sequences of all 14 previously described amphioxus sequences and describe a detailed analysis of the conserved non-coding regulatory sequence elements. We find that the posterior part of the Hox cluster is so highly derived that even the complete genomic sequence is insufficient to decide whether the posterior Hox genes arose by independent duplications or whether they are true orthologs of the corresponding gnathostome paralog groups. In contrast, the anterior region is much better conserved. The amphioxus Hox cluster strongly excludes repetitive elements with the exception of two repeat islands in the posterior region. Repeat exclusion is also observed in gnathostomes, but not protostome Hox clusters. We thus hypothesize that the much shorter vertebrate Hox clusters are the result of extensive resolution of the redundancy of regulatory DNA following the genome duplications rather than the consequence of a selection pressure to remove non-functional sequence from the cluster.

Nitric oxide (NO) is a highly reactive, diffusible gas, essential for many physiological functions including neurotransmission, learning and memory, cardiovascular homeostasis, angiogenesis, host defense through immune response, cell migration, and apoptosis. In vertebrates, NO is produced by the enzymatic conversion of L-arginine by three distinct Nitric Oxide Synthase (NOS) that have been identified as products of different genes with distinct expression patterns, cellular localization, regulation, catalytic properties and inhibitor sensitivity. The pathway of NO formation is one of the oldest bioregulatory systems, highly conserved in metazoan. Comparative studies in different model systems using non-vertebrate organisms, especially basal chordates, are very useful. Because it is likely that the basic primary roles will be evolutionary conserved, the chordate amphioxus is the best available stand-in for the ancestor of the vertebrates. Importantly, amphioxus has a body plan, central nervous system, circulatory system and genome that are vertebrate-like, but simpler. In addition, in comparison to vertebrates, amphioxus has the same spectrum of gene families, but has markedly fewer genes per family (Holland et al., 2008; Putnam et al., 2008). This relative genomic simplicity makes amphioxus an especially favorable prospect for functional studies of signaling networks and other physiological processes. Amphioxus has 3 NOS genes although evolutionary analysis has shown that there is no a direct relationship between the 3 amphioxus NOS and vertebrate eNOS, nNOS and iNOS genes (Andreakis et al., 2011). This indicates that, despite its high conservation, NOS evolution has also been very dynamic in some respects, with recurrent episodes of lineage-specific gene duplications. The study of amphioxus NOS will help to understand the acquisition of new functions of NOS enzymes, but also might illustrate convergent evolution events during NOS evolution. The following thesis project is designed to accomplish the first complete and detailed study of NOS during development. Although much has been published on NOS expression and function in many different organisms, very little is known about its role during the first stages of animal development.

Neural control of reproduction in vertebrates and invertebrates has generated considerable interest due to the presence of common neuropeptides. Gonadotropin-releasing hormone (GnRH), a neuropeptide, is the final integrator of neural regulation governing reproduction in vertebrates by controlling the release of gonadotropins. Little is known about GnRH before the origin of vertebrates or about the biological significance of multiple GnRH forms in a single species. To understand the role of GnRH in invertebrates, I selected a tunicate, Ciona intestinalis, the sister group to vertebrates and amphioxus, Branchiostoina floridae, a group more basal than tunicates. Neural control of reproduction in these chordates was compared with that in the zebrafish, Danio rerio. From the zebrafish, I isolated four GnRH receptor cDNAs that each map to a distinct chromosome and are expressed in a variety of tissues. Each receptor was functional, as shown by its response to physiological doses of native GnRH peptides. Also, two receptors showed selectivity between GnRH1 and GnRH2. Protein localization of each zebrafish GnRH receptor with specific antisera showed that all four receptors are present in the pituitary. However, the most striking localization revealed the presence of GnRH networks in a major motor control centre and fibre tract system in the hindbrain and spinal cord. Both structures are major components in the control of motor movements, such as swimming. Phylogenetic and synteny analysis segregates the four zebrafish GnRH receptors into two distinct phylogenetic groups that are separate gene lineages conserved throughout vertebrate evolution. In Ciona intestinalis, we found two GnRH genes that each encode three GnRH decapeptides in tandem, for six unique GnRH forms from this species. These genes are expressed throughout development. With an immunocytochemical approach, at least one peptide was found in the dorsal strand nerve plexus adjacent to the gonads in adults. Injection near the gonads of gravid Ciona quickly induced spawning, suggesting a novel action for control of reproduction by GnRH. My further studies identified four novel GnRH receptors encoded within the genome of this protochordate, and showed that three receptors responded to Ciona GnRHs by stimulating intracellular accumulation of cAMP. In contrast, only one receptor activated inositol phosphate turnover in response to one of the Ciona GnRHs. My final study involved identifying the GnRH signalling components in amphioxus. I found four novel GnRH receptors, with three displaying sensitivity to the highly conserved vertebrate GnRH2 and one of these showing selectivity for GnRH1. My pharmacological testing showed that the capacity to respond to GnRH1 and GnRH2 is evolutionarily conserved between amphioxus and vertebrates, and that key motifs found to be important in GnRH binding, signalling and activation are present in the amphioxus receptors. Phylogenetic analysis showed that two receptors cluster with the recently identified octopus GnRHR-like sequence; the other two receptors group at the base of the vertebrate GnRHR clade and may represent the proto-vertebrate condition, after which gene duplication and sequence divergence resulted in the four contemporary vertebrate GnRHRs. This work reveals novel and important features of the GnRH signalling axis throughout chordate evolution.