<p>A metagenomic gene library prepared from soil found beneath a mummified seal carcass in the Miers Valley, Antarctica, suggests an environment rich in uncharacterised biodiversity including enzymes with possible application to industrial processes. A sequence based gene mining investigation was performed on a clone, which archives a metagenomic sequence from this environment. The sequence was annotated using de novo bioinformatics and molecular biology techniques. A predicted NAD+-dependent DNA ligase, ligDB1 was selected for further characterisation. LigDB1 encodes a gene product that contains all the sequence features of a functional ligase. The protein was overexpressed in a heterologous E. coli host and purified to homogeneity. LigDB1 did not exhibit nick sealing activity, but was able to perform AMP-dependent DNA relaxation in the presence of high concentrations of enzyme. DNA modifying enzymes from cold environments perform optimally at low temperatures and may be of use as molecular tools in biotechnology. Complete characterisation of this enzyme is subject to further investigations.</p>

<p>A metagenomic gene library prepared from soil found beneath a mummified seal carcass in the Miers Valley, Antarctica, suggests an environment rich in uncharacterised biodiversity including enzymes with possible application to industrial processes. A sequence based gene mining investigation was performed on a clone, which archives a metagenomic sequence from this environment. The sequence was annotated using de novo bioinformatics and molecular biology techniques. A predicted NAD+-dependent DNA ligase, ligDB1 was selected for further characterisation. LigDB1 encodes a gene product that contains all the sequence features of a functional ligase. The protein was overexpressed in a heterologous E. coli host and purified to homogeneity. LigDB1 did not exhibit nick sealing activity, but was able to perform AMP-dependent DNA relaxation in the presence of high concentrations of enzyme. DNA modifying enzymes from cold environments perform optimally at low temperatures and may be of use as molecular tools in biotechnology. Complete characterisation of this enzyme is subject to further investigations.</p>

Seed maturation is an important process that is evolutionarily advantageous, allowing for seed dispersal and germination under favourable growth conditions. The B3-domain transcription factor FUSCA3 (FUS3) is a master regulator of seed maturation and controls developmental phase transitions through hormonal regulation in Arabidopsis thaliana. The aim of this study was to determine the post-translational regulation of FUS3 during embryonic and vegetative development. Here, FUS3 was found to interact with the E3 ubiquitin ligase ABI3-INTERACTING PROTEIN2 (AIP2) in yeast two-hybrid, in vitro, and in planta assays. Analysis of transcriptional and translational reporters also showed overlapping spatial and temporal expression patterns of AIP2 and FUS3. Furthermore, in vitro FUS3 degradation was delayed in aip2-1 mutant and increased FUS3-GFP levels were observed during mid-embryogenesis in aip2-1. Finally, double transgenic plants overexpressing AIP2 and FUS3 showed reduced FUS3 levels and reversion of the gain-of-function FUS3 phenotypes back to WT. Together, these results indicate that AIP2 is a negative regulator of FUS3.

A metagenomic gene library prepared from soil found beneath a mummified seal carcass in the Miers Valley, Antarctica, suggests an environment rich in uncharacterised biodiversity including enzymes with possible application to industrial processes. A sequence based gene mining investigation was performed on a clone, which archives a metagenomic sequence from this environment. The sequence was annotated using de novo bioinformatics and molecular biology techniques. A predicted NAD+-dependent DNA ligase, ligDB1 was selected for further characterisation. LigDB1 encodes a gene product that contains all the sequence features of a functional ligase. The protein was overexpressed in a heterologous E. coli host and purified to homogeneity. LigDB1 did not exhibit nick sealing activity, but was able to perform AMP-dependent DNA relaxation in the presence of high concentrations of enzyme. DNA modifying enzymes from cold environments perform optimally at low temperatures and may be of use as molecular tools in biotechnology. Complete characterisation of this enzyme is subject to further investigations. / Magister Scientiae - MSc

A metagenomic gene library prepared from soil found beneath a mummified seal carcass in the Miers Valley, Antarctica, suggests an environment rich in uncharacterised biodiversity including enzymes with possible application to industrial processes. A sequence based gene mining investigation was performed on a clone, which archives a metagenomic sequence from this environment. The sequence was annotated using de novo bioinformatics and molecular biology techniques. A predicted NAD+-dependent DNA ligase, ligDB1 was selected for further characterisation. LigDB1 encodes a gene product that contains all the sequence features of a functional ligase. The protein was overexpressed in a heterologous E.coli host and purified to homogeneity. LigDB1 did not exhibit nick sealing activity, but was able to perform AMP-dependent DNA relaxation in the presence of high concentrations of enzyme. DNA modifying enzymes from cold environments perform optimally at low temperatures and may be of use as molecular tools in biotechnology. Complete characterisation of this enzyme is subject to further investigations. / Magister Scientiae - MSc

Les cellules différenciées peuvent changer de destin cellulaire de manière induite ou naturelle. Afin de comprendre et connaître les acteurs et mécanismes contrôlant les processus de reprogrammation, notre laboratoire étudie le changement d'identité (ou transdifférenciation, Td) naturel d’une cellule épithéliale rectale (nommée Y) en motoneurone (nommé PDA) chez Caenorhabditis elegans. Les travaux préliminaires ont montré qu’il existe une synergie entre les modifications d’histone (jmjd-3.1 et wdr-5.1) et l’ubiquitination (sel-10). SEL-10 est une ubiquitine ligase E3 possédant un domaine Fbox et une répétition de domaines WD40. Dans cette étude, nous avons pu mettre en évidence : i) une implication du domaine Fbox, des indications sur la localisation intracellulaire de SEL-10 et un rôle inattendu du protéasome au sein de la Td. ii) un rôle de SEL-10 dans la robustesse de la Td (résistance aux stress environnementaux). iii) sel-10, jmjd-3.1 et wdr-5.1 agissent sur la transcription de gènes impliqués dans la transdifférenciation (testé par smFISH). Ainsi qu’une caractérisation du motif d’expression marqueur de Td cog-1 au cours de la redifférenciation. / Differentiated cells can change their cellular fate induced or naturally. In order to understand the mechanisms controlling reprogramming processes, our laboratory is studying the natural change in identity (or transdifferentiation, Td) of a rectal epithelial cell (named Y) and motor neuron (named PDA) in Caenorhabditis elegans.Preliminary work has shown that there is a synergy between histone modifications (jmjd-3.1 and wdr-5.1) and ubiquitination (sel-10). SEL-10 is an E3 ubiquitin ligase with a Fbox domain and WD40 repeat domain.In this study, we highlight: i) the Fbox domain involvement in the Td, indications about the intracellular localization of SEL-10 and an unexpected role of the proteasome within TD. ii) a role of SEL-10 in the robustness of the Td. iii) sel-10, jmjd-3.1 and wdr-5.1 act on gene transcription in transdifferentiation. This one was tested by smFISH and allowed the characterization of the cog-1 transdifferentiation marker expression pattern during redifferentiation.

>Magister Scientiae - MSc / A metagenomic gene library prepared from soil found beneath a mummified seal carcass in the Miers Valley, Antarctica, suggests an environment rich in uncharacterised biodiversity including enzymes with possible application to industrial processes. A sequence based gene mining investigation was performed on a clone, which archives a metagenomic sequence from this environment. The sequence was annotated using de novo bioinformatics and molecular biology techniques. A predicted NAD+-dependent DNA ligase, ligDB1 was selected for further characterisation. LigDB1 encodes a gene product that contains all the sequence features of a functional ligase. The protein was overexpressed in a heterologous E. coli host and purified to homogeneity. LigDB1 did not exhibit nick sealing activity, but was able to perform AMP-dependent DNA relaxation in the presence of high concentrations of enzyme. DNA modifying enzymes from cold environments perform optimally at low temperatures and may be of use as molecular tools in biotechnology. Complete characterisation of this enzyme is subject to further investigations

Estudos preliminares através de microarray nos mostraram que a E3 ligase Mdm2 foi regulado positivamente no músculo de animais hipertireoideos. Dessa forma, nós inferimos uma possível relação de Mdm2 com a atrofia causada por T3. Para testar nossa hipótese, ratos foram induzidos ao hipertireoidismo para análises subsequentes. Concomitante com a perda de massa muscular foi confirmado um aumento da expressão de Mdm2 tanto no nível gênico (p<0.05) quanto protéico. Interessantemente, Mdm2 foi preferencialmente expresso em fibras tipo I, mostrando maior sensibilidade dessas fibras ao T3. Além disso, foi observado uma diminuição severa na expressão de Pax7/MyoD associado à superexpressão de Mdm2, sugerindo inatividade das células satélites. Surpreendentemente, a inibição de Mdm2 em miotubos cultivados provocou uma diminuição severa no diâmetro destes (~35%, p<0.05), ou seja, tal inibição foi incapaz de minimizar a proteólise muscular causada por T3. Portanto, nós concluímos que a responsividade de Mdm2 ao T3 agiria como um mecanismo compensatório numa tentativa de minimizar a proteólise muscular causada pelo hipertireoidismo. Esta conclusão é reforçada pela atrofia observada em miotubos durante a inibição de Mdm2 sem a presença de T3. / Previous studies in our lab through microarray assay observed Mdm2, an E3 ligase, up regulated in soleus muscle from hyperthyroid rats. In this sense, we inferred that Mdm2 could be related to muscle atrophy caused by T3. To test our hypothesis, rats were induced to experimental hyperthyroidism for subsequent analysis. Along the muscle mass loss, the increase on Mdm2 gene expression was confirmed (p<0.05) as well as protein expression by RT-PCR and Western Blot, respectively. Interestingly, Mdm2 was expressed predominantly in fiber I type during T3 treatment, demonstrating a higher sensibility when compared to type II fiber. Moreover, it was observed a severe decrease in Pax7/MyoD labeling, associated to an increase on Mdm2 labeling, suggesting that T3 could be associated with inactivation of satellite cells. Surprisingly, Mdm2 inhibition in myotubes have induced severe decrease on myotubes diameter (~35%, p<0.05), in other words, Mdm2 inhibition was not able to decrease muscle proteolysis during high levels of T3. Thus, the increase on Mdm2 levels could be a compensatory effect to reduce the muscle mass loss during T3 treatment. This conclusion is highlighted by the myotubes atrophy observed during the Mdm2 inhibition without T3 treatment.

Une des caractéristiques des cellules tumorales est leur habileté à échapper à la mort cellulaire. Pour y parvenir, elles ont développé une stratégie consistant à éliminer sélectivement les mitochondries endommagées par un processus de mitophagie. L’acteur principal de la mitophagie est l’ubiquitine ligase Parkin ; mais elle est mutée ou absente dans la majorité des cancers. Nous avons découvert qu’une autre ligase, ARIH1, appartenant à la même famille des RBR ligases que Parkin, est capable d’induire la mitophagie en réponse à un stress. Contrairement à Parkin, ARIH1 est surexprimée dans de nombreux cancers, notamment dans les cancers du poumon permettant ainsi une augmentation de la mitophagie conférant ainsi à ces cellules une résistance au stress induit par des agents chimiothérapeutiques. La mort cellulaire la mieux caractérisée est l’apoptose qui est directement liée à l’activation de caspases. Il a pourtant été établi qu’une inhibition des caspases ne permet pas d’empêcher la mort cellulaire car il existe la « mort cellulaire indépendante des caspases » ou CICD. Cependant, sa définition moléculaire précise reste toujours inconnue. Ainsi dans ce but, un criblage siRNA pan génomique a révélé l’importance de la voie ubiquitine/protéasome. Nous avons pu identifier en particulier une enzyme E3 ligase comme étant protectrice de la CICD. Cette enzyme est surexprimée dans de nombreux cancers et pourrait permettre aux cellules cancéreuses de résister à la CICD et favoriser la progression tumorale. En résumé, ce travail a permis de souligner l’importance des ubiquitines ligases dans les mécanismes d’échappement à la mort cellulaire mis en place par les cellules cancéreuses. / One of the hallmarks of tumor cells is their ability to escape cell death.To achieve this, they have developed a strategy of selectively removing damaged mitochondria by a process of mitophagy. The main actor of mitophagy is the ubiquitin ligase Parkin; but it is mutated or absent in the majority of cancers. We have discovered that another ligase, ARIH1, belonging to the same family of RBR ligases as Parkin, is capable of inducing mitophagy in response to stress. In contrast to Parkin, ARIH1 is overexpressed in many cancers, especially in lung cancer, allowing an increase in mitophagy conferring resistance to stress induced by chemotherapeutic agents. The most characterized cell death pathway is apoptosis, which is directly related to caspases activation. However, it has been established, that caspase inhibition does not prevent cell death because there is another type of cell death called "caspase-independent cell death" or CICD. However, its precise molecular definition is still unknown. Thus for this purpose, pan-genomic siRNA screening was performed and revealed the importance of the ubiquitin / proteasome pathway. In particular, we have been able to identify an enzyme E3 ligase as being protective towards CICD. This enzyme is overexpressed in many cancers and could allow cancer cells to resist CICD and promote tumor progression. In summary, this work has highlighted the importance of ubiquitin ligases in the escape mechanisms to cell death implemented by cancer cells.

La GTPase Rac1 est une protéine de signalisation intracellulaire qui joue notamment un rôle clé dans la prolifération cellulaire. Notre laboratoire a montré que la toxine CNF1, produite par les Escherichia coli pathogènes, catalyse l’activation de Rac1. Nous avons également identifié le rôle de la E3 ubiquitine-ligase HACE1, un suppresseur de tumeur avéré, dans la régulation par ubiquitylation de Rac1 actif. S’il est prouvé que la forme activée de Rac1 est une cible d’HACE1, le mode d’interaction de ces deux protéines reste à définir ainsi que le rôle de ces interactions dans l’infection et le cancer. L’objectif de mon travail a été de caractériser les interactions moléculaires entre HACE1 et Rac1. Nous avons testé l’hypothèse que des mutations ponctuelles d’HACE1 identifiées dans les cancers pourraient interférer avec son interaction avec Rac1 et sa capacité de contrôle de la croissance cellulaire. J’ai ainsi pu mettre en évidence que 13 mutations somatiques d’HACE1 issues de tumeurs séquencées altèrent sa fonction de contrôle de la croissance cellulaire. De plus, l’étude de ces mutations nous a permis d’identifier un groupe d’acides aminés, situés sur les ankyrin-repeats 5 à 7 d’HACE1, qui contrôle l’interaction d’HACE1 avec Rac1 et de ce fait son ubiquitylation. Enfin dans cette étude nous précisons le rôle du domaine intermédiaire d’HACE1 (MID) dans la spécificité d’interaction de la ligase avec la forme active de Rac1. In fine, la caractérisation de mutants d’interaction entre HACE1 et Rac1 ainsi que l’effet de la toxine CNF1 sur cet axe de signalisation doit nous renseigner sur l’importance de cette voie de régulation dans le cancer et l’infection. / The small GTPase Rac1 plays a key role in various intracellular signaling pathways including cell proliferation. Our laboratory has shown that the CNF1 toxin, produced by pathogenic Escherichia coli, catalyzes the activation of Rac1. We also identified the role of the E3 ubiquitin-ligase HACE1, a tumor suppressor, in the regulation by ubiquitylation of active Rac1. If the activated form of Rac1 is proved to be a target of HACE1, the mode of interaction between these two proteins remains to be define as well as the role of these interactions in infection and cancer. The aim of my work was to characterize the molecular interactions between HACE1 and Rac1. We tested the hypothesis that HACE1 point mutations identified in cancers could interfere with its interaction with Rac1 and its ability to control cell growth. We showed that 13 cancer-associated somatic mutations of HACE1, led to a defective control of cell proliferation. Moreover, the study of these mutations allowed us to identify a group of amino acids, located on the ankyrin-repeats 5 to 7 of HACE1, which controls the interaction of HACE1 with Rac1 and thus its ubiquitylation. We also identified a role for the intermediate domain of HACE1 (MID) in conferring the specificity of association of HACE1 to the active form of Rac1. Ultimately, the characterization of interaction mutants between HACE1 and Rac1 as well as the effect of the CNF1 toxin on this signaling axis will give us more insight on this regulatory pathway in cancer and infection.