L’ARN polymérase III synthétise de nombreux petits ARN non traduits, dont les ARNt et l’ARNr 5S, essentiels à la croissance de toute cellule. Dans ce travail, nous nous sommes intéressés à la régulation de la transcription par l’ARN polymérase III chez la levure Saccharomyces cerevisiae. Nous avons détecté Sub1 sur les gènes de classe III in vivo. Nous avons également observé que Sub1 est capable de stimuler la transcription par l’ARN III reconstituée in vitro avec les facteurs TFIIIB et TFIIIC recombinants et avec l’ARN Pol III purifiée. Sub1 stimule deux étapes de la transcription : l’initiation et la réinitiation facilitée. Des expériences supplémentaires nous montrent que la protéine interagit directement avec TFIIIB et TFIIIC. Enfin, nous avons pu constater que la délétion de Sub1 dans la levure conduit à une diminution de la transcription par l’ARN Pol III en phase exponentielle de croissance. Par la suite, nous avons cherché à déterminer quel lien pouvait exister entre l’activateur Sub1 et le répresseur Maf1 de la transcription par l’ARN Pol III. Enfin, nous avons également souhaité identifier d’autres éléments pouvant interagir avec la protéine Sub1 au cours de sa fonction de régulateur. / RNA polymerase III synthetizes many small untranslated RNA, including tRNA and 5S rRNA which are essential to cell growth. In this work, we took an interest in RNA polymerase III transcription regulation in the baker’s yeast, Saccharomyces cerevisiae. We have detected Sub1 on all class III genes in vivo. We also observed that Sub1 is able to stimulate RNA polymerase III transcription which has been reconstituted in vitro with TFIIIB et TFIIIC recombinants factors and purified RNA polymerase III. Sub1 stimulates two steps of RNA polymerase III transcription : initiation and facilitated reinitiation. Supplementary experiments established that Sub1 directly interacts with TFIIIB and TFIIIC transcription factors. Finally, we showed that Sub1 deletion in yeast leads to a decrease in RNA polymerase III transcription during exponential phase. Then, we tried to determine which link could exist between Sub1, the activator, and Maf1, the repressor of RNA polymerase III transcription. Furthermore, we attempted to identify other elements which could interact with Sub1 during transcription regulation.

Among the various external signals perceived by yeast cells, nutrient availability is a condition to which these cells show a highly diverse biological response. Diploid cells in response to different nutritional stress conditions shows different developmental outcomes. On nitrogen starvation, cells undergo dimorphic transition whereby a unicellular yeast form transforms to a multicellular pseudohyphal form. While in the complete absence of a nitrogen source and a fermentable carbon source, yeast cells enter into a complex developmental program termed sporulation which culminates in haploid spores. The main objective of this work was to understand the role played by S. cerevisiaeSUB1 in starvation-induced meiotic program of diploid cells, decipher its target in sporulation specific gene expression cascade, study the domain architecture of Sub1 and examine its functional homology to mammalian PC4. Role of Sub1 in induction of sporulation and other stress responses in S. cerevisiae In a previous whole-genome screen for mutants with altered sporulation efficiency in the Saccharomyces cerevisiae S288c strain, SUB1 locus was identified as a negative regulator of sporulation (Deutschbaueret al., 2002). Moreover, genome-wide gene expression analysis in SK1 strain had shown that SUB1 transcript levels are repressed during sporulation (Chu et al., 1998). Many studies in different yeast strain backgrounds implicate more than 1,000 genesout of 6,200 genes in yeast genome as being differentially expressed during the sporulation process (Chu et al., 1998; Primiget al., 2000; Deutschbaueret al., 2002). Interestingly, these studies show the number of regulatory genes that negatively affect sporulation is far lower than those that are activators of sporulation and moreover their mechanism of action is poorly studied. S. cerevisiae.SUB1 is one among negative regulators of sporulation(Deutschbaueret al., 2002). Global transcriptome of diploid yeast cells undergoing sporulation showed SUB1 transcripts are greatly reduced with time progression (Chu et al., 1998). To understand the role of SUB1 in sporulation, we generated deletion of both SUB1 alleles in the diploid S288c strain background and compared the kinetics of asci formation in this strain with that of the wild-type. We observed that cells lacking SUB1 exhibit ~5-fold increase in tetrad asci. Based on Eosin Y and Calcoflour White staining assays, we find no change in spore morphology in the mutant. Thus the increase in sporulation efficiency in sub1/sub1diploids is not accompanied by formation of defective spores. We validated the reduction in SUB1 transcript levels during sporulation in wild-type SK1 strain background. We also examined the Sub1 protein levels by epitope-tagging of the chromosomal SUB1 open reading frame and determining protein levels in this strain. We find that consistent with the data on transcript levels, Sub1-TAP tagged protein levels too decreased gradually on shift to sporulation medium. We created sub1alleles in diploids in the SK1 strain background and using this strain background we investigated Sub1 target genes and chose IME2 (early), SMK1, SPS2 (middle), DIT1, DIT2 (mid-late) and SPS100 (late) genes as representative sporulation genes. We observed that sub1∆/sub1∆cells have a significantly elevated expression of middle genes (SPS2 and SMK1) that followed normal induction kinetics i.e., 5 hours post transfer to sporulation medium. However, the expression levels or timing for other class of sporulation genes did not change in sub1∆strain as compared with the wild-type. In order to confirm these observations, we also studied the effects of over-expression of SUB1 from the GAL1 promoter by transforming the high copy plasmid. This was done in wild-type SK1 cells and the expression of sporulation genes were analyzed. We observed that expression of SMK1 and SPS2middle sporulation genes was reduced on over-expression of SUB1.We used the Sub1-TAP protein to assess if Sub1 directly regulates these genes by Chromatin immunoprecipitation assays. For these studies, we examined the recruitment of Sub1 to these loci through the time course of sporulation. In wild-type SK1 cells, Sub1 was to bound to middle sporulation genes and this was striking in cells at 5th hour post-induction of sporulation. These data establish that Sub1 directly associates with chromatin at these loci co-incident with the time points where expression levels of these changes is altered in cells lacking Sub1. Furthermore, to assess the role of Sub1 in other stress responses, such as pseudohyphae formation in response to nitrogen starvation, pheromone-induced agar invasion and secretory stress, we employed a genetic approach. Genetic interaction studies of SUB1 with RPB4, a subunit of RNA polymerase with functions in stress response and HOS2, a subunit of Set3 complex and a close homolog of mammalian HDAC3, reported to be involved in sporulation and secretory stress, were performed. Based on sporulation frequency and pseudohyphal formation in the double mutants we conclude that SUB1 is downstream of both these genes. Moreover, our results from assays of schmoo formation and pheromone-induced agar invasion suggest that SUB1 functionally interacts with HOS2. Study of domain architecture of Sub1 and homology to human PC4 Comparison of the S. cerevisiae Sub1 protein with its higher eukaryotic homologs showed that the N-terminal region of yeast Sub1 (32-105 aa) is highly conserved (Knauset al., 1996; Henry et al., 1996) with the 106-292 C -terminal amino acids being yeast-specific. We employed deletion analysis to generate partial Sub1 proteins and used them to understand the roles played by these domains in different phenotypes associated with Sub1. Our analysis of the localization of various Sub1-GFP fusion proteins shows that 146-172 aa in the C-terminal domain of Sub1 confers nuclear localization. Sporulation frequency analysis of the different domains of Sub1 suggests that both the N and C terminal domains are necessary for sporulation function of Sub1. The N terminal domain of yeast Sub1 shares homology with human PC4 and not surprisingly possesses ssDNA binding ability first attributed to human PC4 (Kaiser et al., 1995). In order to investigate whether the effects of SUB1 on kinetics of sporulation require its ssDNA binding function, we generated the sub1(Y66A) ssDNA binding mutant (Sikorskiet al., 2011) and over-expressed it in the S288c genetic background. We assessed sporulation efficiency of sub1∆/sub1∆cells over-expressing sub1(Y66A) mutant allele as compared to cells over-expressing wild-type SUB1. Interestingly, cells with over-expression of sub1(Y66A) have reduced sporulation efficiency that is equivalent to the levels achieved on over-expression of wild type SUB1. This data suggests that the ssDNA-binding ability of Sub1 is not important for its role in sporulation. Furthermore, we examined the ability of human PC4 to contribute to yeast sporulation process by complementation analysis. We observed that over-expression of PC4 complemented the phenotypes of sub1∆strain, suggesting that the function of Sub1/PC4 family is evolutionarily conserved. Studies on biochemical interactions of Sub1 with histone proteins Human PC4 is a chromatin-associated protein, present on metaphase chromosomes (Das et al., 2006). The short C-terminal domain of PC4(62-87 aa) interacts with core histones H3 and H2B in vitro and in vivo and this interaction mediates chromatin condensation. The homology between S. cerevisiaeSub1 (32-105 aa) and human PC4 (62-127 aa)is in the domain required for their DNA binding properties and coactivator functions, suggesting possible conservation in their interactions. We tested the interactions of yeast Sub1 with histone proteins by adopting both in vitro and in vivo interaction assays. We find recombinant Sub1 had strong interactions with rat and yeast histone H3in vitro. Moreover,Sub1 was found to interact with histone H2B, but not with H2A, in vivo, a binding specificity also shown by human PC4.Thus, we demonstrate conservation in the interaction of Sub1 with histone proteins.

Le paludisme demeure une des maladies infectieuses les plus meurtrières au monde. Propagé par la piqûre d’un moustique femelle du genre Anopheles, le parasite du paludisme (Plasmodium) migre dans la circulation sanguine et infecte les cellules hépatiques de la victime. Dans le foie, le parasite se différencie et se reproduit par schizogonie à l’intérieur d’une vacuole parasitophore pour compléter la production de plusieurs milliers de mérozoïtes par cellule hépatique infectée. Ces mérozoïtes sont par la suite libérés dans la circulation sanguine où ils infectent les érythrocytes circulants dans lesquels le parasite subit des cycles d’infection, réplication et libération (processus de sortie actif provoqué par le parasite). Ces cycles répétitifs dans le sang sont à l’origine des symptômes cliniques de la maladie.Des études sur Plasmodium falciparum ont montré que P. falciparum SUB1 (PfSUB1), une protéase à sérine de la famille des subtilisines, est relâchée à l’intérieur de la vacuole parasitophore peu avant la libération des mérozoïtes des hématies. A l’intérieur de cette vacuole, la protéase intervient dans la maturation de protéines membres de la famille des SERA (famille de protéines du type papaïne) ainsi qu’un certain nombre de protéines de surface du mérozoïte (famille des MSP). Un grand intérêt a été porté sur cette protéase, car l’inhibition pharmacologique de l’activité de PfSUB1 bloque le processus de sortie et d’invasion des mérozoïtes dans le stade érythrocytaire du parasite in vitro.Le stade hépatique du parasite est une cible idéale pour le développement de traitements prophylactiques antipaludiques, car il précède la phase symptomatique de la maladie. En conséquence, il est important de mieux comprendre les mécanismes de fonctionnement du parasite à ce stade. Le présent projet avait pour but principal d’effectuer une étude du rôle de SUB1 dans le stade hépatique de Plasmodium. Pour ce faire, ce travail s’est effectué sur l’orthologue de PfSUB1 chez le parasite murin P. berghei. Dans un premier temps, l’expression de PbSUB1 dans les stades hépatiques du parasite a été confirmée en utilisant des anticorps spécifiques et en générant une lignée mutante de P. berghei exprimant la protéine endogène fusionnée à un marqueur hémagglutinine. Par la suite, l’enzyme a été exprimée sous forme recombinante et sa fonction et spécificité ont été partiellement caractérisées. Ce travail confirma que la protéase est capable de cliver des peptides basés sur les séquences de PbMSP1 et PbSERA3, substrats potentiels exprimés dans les stades hépatiques du parasite. Finalement, afin de mieux caractériser la fonction de PbSUB1, deux approches récentes permettant d’effectuer un knock-out conditionnel chez P. berghei ont été testées: le système Tet et la mutagenèse conditionnelle Flp/FRT. Afin d’utiliser cette dernière approche, une nouvelle méthode pour insérer des sites de reconnaissances Flp (sites FRT) dans les régions intergéniques de clones (dans ce cas, un clone comprenant pbsub1 et gènes voisins) provenant d’une bibliothèque génomique de P. berghei a été développée. Pour ce faire, plusieurs techniques d’ingénierie moléculaire ont été utilisées. Ces techniques, basées sur les systèmes de recombinaison de la levure (recombinase Flp) et de phages (recombineering) similaire à ceux utilisés par le projet PlasmoGEM (Pfander et al., 2012), surmontent les problèmes rencontrés par les méthodes conventionnelles pour le placement des sites FRT et sont aussi applicables aux longues séquences codantes. Avec ces nouveaux outils, un knock-out conditionnel de pbsub1 a été généré avec succès in vivo où la délétion du gène est accompagnée de l’expression d’un gène rapporteur (GFP) afin de faciliter l’identification des parasites ayant perdu le gène d’intérêt. A la fin de ce travail, une analyse préliminaire de ces parasites déficients en PbSUB1 suggère un rôle essentiel de cette protéase dans le développement de la phase hépatique du parasite. / Malaria remains one of the deadliest infectious diseases in the world. Propagated by the bite of an infected female Anopheles mosquito, the malaria parasite (Plasmodium) enters the bloodstream and infects hepatocytes. In the liver, the parasite differentiates and reproduces by schizogony within a membrane-bound parasitophorous vacuole (PV) resulting in the production of several thousands of merozoites per infected hepatic cell. These parasites are subsequently released into the blood stream where they infect circulating red blood cells and undergo repetitive cycles of infection, replication, and egress (active release of parasites) which are responsible for the clinical symptoms of the disease.Work on P. falciparum, has shown that P. falciparum SUB1 (PfSUB1), a serine protease of the subtilisin-like family, is discharged into the PV just prior to egress from the erythrocyte and mediates the proteolytic maturation of members of the SERA family (a family of papain-like proteins) as well as a number of merozoite surface proteins (MSPs). Pharmacological inhibition of PfSUB1 activity inhibits both egress and invasion of released merozoites in blood stages in vitro.The liver stage of the parasite is an ideal target for development of prophylactic anti-malarial drugs, as it is clinically silent. It is thus of importance to gain more detailed knowledge about parasite development in this stage. The main aim of this project was to study the role of SUB1 in the liver stage of the parasite life cycle. The work was performed on the orthologue of PfSUB1 in the murine malaria species P. berghei. Initially, expression of PbSUB1 in liver stages was confirmed using specific antibodies and by generating a transgenic P. berghei clone expressing epitope-tagged PbSUB1. Next, recombinant enzymatically-active PbSUB1 was expressed in insect cells and partially characterised with respect to its function and substrate specificity. This confirmed that the protease is able to process substrates based on PbMSP1 and PbSERA3, two putative substrates expressed in late hepatic stages of the parasite.Finally, to further study PbSUB1 function, two conditional gene knock-out approaches were applied to study the phenotypic consequences of loss of PbSUB1 expression. Working from a ~10 kb genomic DNA library clone comprising pbsub1 and flanking genes, a method to insert Flp recombinase recognition (FRT) sites into intergenic regions was developed. This was achieved by combining inducible Flp activation in E. coli with recombinase mediated engineering techniques similar to those that underlie the PlasmoGEM project (Pfander et al., 2012). This strategy overcomes challenges of existing techniques and is also suitable for flanking large genes with FRT sites. With these newly generated tools, an inducible knock-out of pbsub1 was successfully generated in vivo, in which stage-specific excision of the gene was accompanied by concomitant induction of GFP expression, facilitating identification of the knock-out parasites. A preliminary analysis of these PbSUB1-deficient parasites suggests an essential role for the protease in the development of liver stage schizonts.

L'ARN polymérase III synthétise de nombreux petits ARN non traduits, dont les ARNt et l'ARNr 5S, essentiels à la croissance de toute cellule. Dans ce travail, nous nous sommes intéressés à la régulation de la transcription par l'ARN polymérase III chez la levure Saccharomyces cerevisiae. Nous avons détecté Sub1 sur les gènes de classe III in vivo. Nous avons également observé que Sub1 est capable de stimuler la transcription par l'ARN III reconstituée in vitro avec les facteurs TFIIIB et TFIIIC recombinants et avec l'ARN Pol III purifiée. Sub1 stimule deux étapes de la transcription : l'initiation et la réinitiation facilitée. Des expériences supplémentaires nous montrent que la protéine interagit directement avec TFIIIB et TFIIIC. Enfin, nous avons pu constater que la délétion de Sub1 dans la levure conduit à une diminution de la transcription par l'ARN Pol III en phase exponentielle de croissance. Par la suite, nous avons cherché à déterminer quel lien pouvait exister entre l'activateur Sub1 et le répresseur Maf1 de la transcription par l'ARN Pol III. Enfin, nous avons également souhaité identifier d'autres éléments pouvant interagir avec la protéine Sub1 au cours de sa fonction de régulateur.