La régénération est un mode de développement, qui suite à un stresse physique permet de reformer à l’identique des structures biologiques initialement développer au cours de l’embryogénèse. De plus ce phénomène, plus ou moins important en fonction des organismes, est néanmoins répandu chez les métazoaires, suggérant ainsi une origine monophylogénique. D’où l’hypothèse d’un lien étroit entre la régénération et l’embryogénèse. En me basant sur cette hypothèse j’ai employé comme modèle pendant ma thèse, l’anémone de mer Nematostella vectensis. Ce modèle cnidaire offre effectivement l’opportunité unique de comparer la régénération d’un corps entier, dite extrême, à l’embryogénèse et ainsi étudier leurs liens au niveau moléculaire. Initialement établie entant que modèle d’embryologie permettant d’étudier l’évolution des réseaux de régulation génétique (RRG) orchestrant les moments clé de l’embryogénèse et s’imposer en tant que modèle d’étude de la régénération extrême. Tout d’abord, au cours de ma thèse j’ai participé à caractérisation tissulaire et cellulaire de la régénération de ce model afin d’en établir un répertoire de référence des étapes clés. En employant ce répertoire et le criblage de 80 d’inhibiteur de kinase, j’ai pu identifier plusieurs voies de signalisation régissant différente étape de la régénération, impliquant les MAPKs, JNK et ERK ainsi que plusieurs récepteurs de facteurs de croissances. Notamment ERK a également été décrit dans le processus de gastrulation chez Nematostella, dont j’ai contribué à l’établissement du RRG associé. C’est donc en me basant sur ce RRG et une base de donnée transcriptomic complète de la régénération de ce modèle, que j’ai pu établir le RRG en aval de ERK associé à la régénération. Par cette approche j’ai pu démontrer la relation au niveau moléculaire entre ces processus développementaux et surtout identifier des aspects spécifiques à la régénération. / Regeneration is a developmental process, which allow to regrow missing structures initially develop during embryogenesis, in response to an injury. Although, this ability to regenerate can be more or less dramatic depending on the organism, it is widely spread among metazoan. As such, suggesting a monophyletic origin and a tight link with embryogenesis has also been hypothesized. Based on this hypothesis, I used during my thesis the sea anemone Nematostella vectensis, a cnidarian model offers the unique opportunity to compare, whole body regeneration and embryogenesis to investigate their molecular links. In fact, Nematostella was established as an embryonic model to investigate evolution of gene regulatory network (GRN) underlying key stages e.g. gastrulation, but recently it has been a rising model to study whole body regeneration. I started to my thesis by carefully characterizing hallmarks of Nematostella regeneration starting from tissular to molecular level, establishing a comprehensive regeneration time line. By taking advantage of this tool, in association to the screening of 80 kinases inhibitors, I have identify several signaling pathways regulating various steps of regeneration in Nematostella, including the MAPK ERK, JNK and growth factor receptors. In parallel I participated to the study of ERK role during Nematostella gastrulation and the underpinning (GRN). Which offered a solid groundwork for the comparison with regeneration at the GRN level. Combining a candidate approach based on the embryonic GRN and a global transcriptomic analysis of regeneration, I have been able to bring evidence on the relationship between embryogenesis and regeneration and additionally to identify regeneration specific aspects.

Life histories unfold within the ecological context of an organism's environment, and thus are intimately linked to organismal fitness. The evolution of alternate life history strategies, either within or between taxa, can profoundly affect ontogeny, ecology, and population dynamics. Many cnidarians (sea anemones, corals, jellyfish, etc.) exhibit complex life histories involving sexual reproduction and multiple modes of asexual reproduction. Sea anemones of the family Edwardsiidae exemplify this complexity, and are therefore an attractive system for studying the developmental and ecological ramifications of life history evolution. I used intra- and interspecific comparisons of two Edwardsiid anemones, Edwardsiella lineata, and Nematostella vectensis to investigate alternative life histories using a multifaceted approach that included field-based ecological surveys, functional genetics, transcriptomics, and phylogenetics. Both anemones are capable of sexual and asexual reproduction. N. vectensis produces a rapidly maturing direct developing larva. By contrast, E. lineata has evolved a new larval stage that parasitizes the ctenophore, Mnemiopsis leidyi. Through fieldwork surveys and laboratory culture, I documented several life history traits, such as a previously un-characterized, pre-parasitic larval stage, and the developmental dynamics of early-stage parasitic infections, that augmented gaps in our knowledge of E. lineata's life history. To better understand how and when E. lineata evolved its novel, parasitic life history, I worked with collaborators in the Finnerty lab to sequence, assemble and annotate the transcriptome. Through a multigene molecular clock approach, enabled by the E. lineata transcriptome assembly, I estimated the divergence date for these two anemones between 215-364 million years ago, thereby establishing an upper bound for the innovation of E. lineata's derived, parasitic life history. Testing a hypothesis that Wnt signaling, which patterns the oral-aboral (OA) axis during embryogenesis, also patterns the OA axis during regeneration, I demonstrated that canonical Wnt signaling is sufficient for oral tissue fate across alternate life histories (embryogenesis and regeneration) of N. vectensis. Taken together, these dissertation research activities constitute an integrative approach to investigating the evolution of life histories, and are a step towards establishing E. lineata and N. vectensis as models for studying the evolutionary developmental mechanisms of parasitism and regeneration.

<p>Heparan sulfates (HSs) are linear, negatively charged polysaccharides composed of alternating hexuronic acid (glucuronic acid or iduronic acid) and glucosamine residues that can be substituted to varying degrees with sulfate groups. HS, localized in the extracellular matrix and on the surface of most cells, interacts with a large number of proteins. The actions of HS largely depend on the amount and distribution of its sulfate groups, that provide binding sites for proteins. </p><p>This thesis focuses on the regulation of the structural diversity in HS, in particular the regulation of its 6-<i>O</i>-sulfation patterns that are generated by the combined action of 6-<i>O</i>-sulfotransferases (6OSTs) during biosynthesis, and 6-<i>O</i>-endosulfatases (Sulfs) after completed biosynthesis. In addition, a new model organism is introduced that offers good prospects for investigating the evolutional aspects of HS structural heterogeneity.</p><p>Our studies showed that the three mouse 6OSTs (6OST1-3) exhibit similar substrate specificities <i>in vitro</i>, with minor differences in target preferences. Overexpression of the 6OSTs in cells resulted in increased 6-<i>O</i>-sulfation of both <i>N</i>-sulfated and <i>N</i>-acetylated glucosamine residues. The changes were independent of enzyme isoform but positively correlated to the level of enzyme expressed.</p><p>Quail Sulf1 and Sulf2 enzymes were shown to be cell surface HS 6-<i>O-</i>endosulfatases with preference towards a subset of trisulfated disaccharides within HS chains. The Sulfs contain a “hydrophilic domain” that was shown to be essential for binding of HS, anchorage to the cell surface and endosulfatase activity. QSulf1 was also shown to promote Wnt-Frizzled signaling in cells. </p><p>An HS-like polysaccharide was isolated from the sea anemone <i>Nematostella vectensis</i> and characterized, and all the enzyme families involved in HS biosynthesis and modification in mammalian model systems were also identified. Our results suggest that <i>Nematostella</i> may be a useful tool for understanding the role of evolution in generating HS structural diversity.</p>

Heparan sulfates (HSs) are linear, negatively charged polysaccharides composed of alternating hexuronic acid (glucuronic acid or iduronic acid) and glucosamine residues that can be substituted to varying degrees with sulfate groups. HS, localized in the extracellular matrix and on the surface of most cells, interacts with a large number of proteins. The actions of HS largely depend on the amount and distribution of its sulfate groups, that provide binding sites for proteins. This thesis focuses on the regulation of the structural diversity in HS, in particular the regulation of its 6-O-sulfation patterns that are generated by the combined action of 6-O-sulfotransferases (6OSTs) during biosynthesis, and 6-O-endosulfatases (Sulfs) after completed biosynthesis. In addition, a new model organism is introduced that offers good prospects for investigating the evolutional aspects of HS structural heterogeneity. Our studies showed that the three mouse 6OSTs (6OST1-3) exhibit similar substrate specificities in vitro, with minor differences in target preferences. Overexpression of the 6OSTs in cells resulted in increased 6-O-sulfation of both N-sulfated and N-acetylated glucosamine residues. The changes were independent of enzyme isoform but positively correlated to the level of enzyme expressed. Quail Sulf1 and Sulf2 enzymes were shown to be cell surface HS 6-O-endosulfatases with preference towards a subset of trisulfated disaccharides within HS chains. The Sulfs contain a “hydrophilic domain” that was shown to be essential for binding of HS, anchorage to the cell surface and endosulfatase activity. QSulf1 was also shown to promote Wnt-Frizzled signaling in cells. An HS-like polysaccharide was isolated from the sea anemone Nematostella vectensis and characterized, and all the enzyme families involved in HS biosynthesis and modification in mammalian model systems were also identified. Our results suggest that Nematostella may be a useful tool for understanding the role of evolution in generating HS structural diversity.

Research in the multidisciplinary science of ecotoxicology is crucial to assess injuries to ecosystem resources from chemical spills or other stressors used to support environmental decision-making. Established guidelines recommend the use of non-standard native species in toxicity investigations. This work focused on the use of native species for aquatic toxicity assessment to make more relevant conclusions on the potential for adverse biological effects to occur as a result to single chemical exposures or exposures to a complex mixture like oil. We apply these studies to investigate petroleum product impacts from the Deepwater Horizon incident and concerns for metal toxicity in estuarine environments using a new model organism. Data generated from comprehensive toxicity testing programs were used in the first probabilistic risk assessment of Deepwater Horizon oil toxicity highlighting a lack of appropriate data and representative phyla. Novel toxicity study methods and a stress-response index were developed and demonstrated sensitivity and success in using the starlet anemone in ecotoxicology studies. Swim performance was used as new method to investigate sublethal indicators of stress resulting in varied responses from sheepshead minnows and Florida pompano. These studies further our ability for better laboratory-to-field extrapolation and for decision-making. The use of native species and complex mixtures like oil presented novel challenges in conducting aquatic toxicity studies. Special emphasis is placed on the necessity to understand the appropriate laboratory conditions for native species not typically held in the laboratory and maintaining study parameters to obtain quality data for more accurate interpretation and replication.

MicroRNAs (miRNAs) sind kurze nicht-kodierende RNAs, die auf posttranskriptionaler Ebene die Genexpression hemmen. Dafür bilden miRNAs Ribonukleoprotein-Komplexe, deren Kernbestandteile aller Bilateria Argonaute (AGO) und GW182 /TNRC6 Proteine sind. GW182 / TNRC6-Proteine rekrutieren CCR4-NOT-Deadenylasen über kurze Tryptophan-reiche Motive (W-Motive), welche additiv wirken und fördern so die translationale Repression und den Abbau von Ziel-mRNAs. Um mehr über die Mechanismen der miRNA-abhängigen Genrepression zu erfahren, habe ich W-Motiv-abhängige Interaktionspartner humaner TNRC6C Proteine bestimmt. Hierzu habe ich, mithilfe von quantitativer Massenspektrometrie, das Interaktom von wildtyp TNRC6C Proteinen mit dem von TNRC6C Proteinen, deren W-Motive mutiert wurden, verglichen. Neben bekannten Interaktionspartnern, wie Untereinheiten des CCR4-NOT Komplexes, habe ich Komponenten von Clathrin-Vesikeln (CCVs), Stoffwechsel assoziierte Enzyme, mitochondriale Proteine, RNA Helikasen, Kinasen und Phosphatasen mit potentiellen Funktionen in der miRNA-assoziierten Repression identifiziert. Die im ersten Teil dieser Studie vorgestellten Ergebnisse legen nahe, dass CCVs die Speicherung oder das Recycling von TNRC6 und AGO Proteinen vermitteln können und somit das miRNA-Silencing modulieren. Der zweite Teil dieser Studie befasst sich mit der Konservierung von miRNA vermitteltem Gen-Silencing in Cnidaria (Nematostella vectensis), welche sich vor 600 Millionen Jahren von der Ahnenreihe der Metazoa abspalteten. Hier zeige ich anhand humaner Zellen, dass Nematostella GW182, ähnlich wie in Bilateria, von AGO rekrutiert wird und nachfolgend in der Repression der mRNA fungiert, was darauf hinweist, dass dieser Mechanismus der miRNA-vermittelten Geninhibition bereits in den letzten gemeinsamen Vorfahren von Cnidaria und Bilateria aktiv war. / MicroRNAs (miRNAs) are short non-coding RNAs that act as post-transcriptional repressors of gene expression. To function miRNAs are assembled in ribonucleoprotein complexes, whose core components in bilaterian animals are Argonaute (AGO) and GW182/TNRC6 proteins. GW182/TNRC6 proteins additively recruit CCR4-NOT deadenylases via short tryptophan-containing motifs (W-motifs), thereby promoting translational repression and the decay of target mRNAs. To gain deeper insights into the mechanisms of miRNA silencing I determined the W-motif-specific interactome of human TNRC6C proteins. Using Stable Isotope Labeling by Amino acids in Cell Culture (SILAC) coupled to affinity purification and Mass Spectrometry (MS) I identified proteins enriched with wild type TNRC6C as compared to two mutants with disrupted W-motifs. Besides known functional interactors, such as subunits of the CCR4-NOT complex, I identified several components of clathrin-coated vesicles (CCVs), metabolic enzymes, mitochondrial proteins, RNA helicases, kinases, and phosphatases with potential functional roles in miRNA-mediated repression. The results presented in the first part of this thesis indicate that CCVs may mediate the storage or recycling of TNRC6 and AGO proteins, thus modulating miRNA silencing. The second part of the thesis addressed the conservation of the mechanisms of miRNA silencing via W-motifs in the cnidarian Nematostella vectensis, separated by 600 million years from other Metazoa. Using cultured human cells, I showed that similarly to bilaterians, GW182 in Nematostella is recruited to the miRNA repression complex via interaction with AGO proteins, and functions downstream to repress mRNA, indicating that this mechanism of miRNA-mediated silencing was already active in the last common ancestor of Cnidaria and Bilateria.