Dissertations / Theses on the topic 'Ribosomal biogenesis'
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1
Verma, Pali. "The Role of NOL6 in Ribosomal Biogenesis." Thesis, Griffith University, 2015. http://hdl.handle.net/10072/365847.
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NOL6 is a nucleolar protein, highly conserved throughout evolution. Previous studies on NOL6 have linked its nucleolar localization to ribosomal biogenesis. In this study, the role of murine NOL6 in ribosome biogenesis and cell cycle progression was explored. Initially, a number of tools were generated to investigate NOL6 function. This involved raising and purifying polyclonal antibodies against NOL6. Additionally, mammalian expression vectors containing the full length Nol6 a and 13 were created. The sub-nucleolar localisation of NOL6 was observed by confocal microscopy in an attempt to study the expression pattern of NOL6 within the nucleolus. Furthermore, ribosomal biogenesis studies by pulse chase analysis were carried out. In these studies, we have shown that loss of NOL6 expression by RNA interference resulted in a significant reduction of the 47/45S precursor rRNA in NIH3T3. We also found that loss of NOL6 expression within these cells resulted in G1 phase arrest and induction of cell death. These findings demonstrate a previously unknown function ofNOL6 in rRNA processing and cell cycle progression.Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
Eskitis Institute for Cell and Molecular Therapies
Science, Environment, Engineering and Technology
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Gartmann, Marco. "Structural characterization of ribosomal complexes involved in ribosome biogenesis and protein folding." Diss., lmu, 2010. http://nbn-resolving.de/urn:nbn:de:bvb:19-120476.
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Ramesh, Madhumitha. "Analysis of Ribosome Biogenesis from Three Standpoints: Investigating the Roles of Ribosomal RNA, Ribosomal Proteins and Assembly Factors." Research Showcase @ CMU, 2016. http://repository.cmu.edu/dissertations/609.
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Ribosomes are ubiquitous and abundant molecular machines composed of ribosomal RNA (rRNA) and ribosomal proteins (r-proteins). They play a central role in the cell by translating the genetic code in mRNA to form polypeptides. Because of their large size and the complexity of molecular interactions within ribosomes, we do not still fully understand how they are synthesized in the cell. Yet, a thorough knowledge of ribosome biogenesis is crucial to understand cellular homeostasis and various disease states including ribosomopathies and cancer. In addition, ribosomes serve as an interesting paradigm to understand the principles that dictate the formation and function of the many different ribonucleoprotein particles that play vital roles in the cell. In addition to the rRNA and r-protein components, trans-acting assembly factors play indispensable roles in synthesizing functional ribosomes. Fundamentally, ribosome biogenesis is driven by a network of molecular interactions that evolve in time and space, as assembly progresses from the nucleolus to the cytoplasm. We sought to gain a deeper understanding of ribosome biogenesis in Saccharomyces cerevisiae by investigating the molecular interactions that drive ribosome assembly. Recent structural studies have revealed a number of such molecular interactions at high resolution. Based on these, our investigation was carried out from the perspectives of all three players that are involved in constructing ribosomes, with a specific emphasis on eukaryote-specific elements of rRNAs and r-proteins. From the standpoint of rRNA, we performed the first systematic study to investigate the potential functions of nearly all of the eukaryotic rRNA expansion segments in the yeast large ribosomal subunit. We showed that most of them are indispensable and play vital roles in ribosome biogenesis. Based on the steps of ribosome biogenesis in which each of them participates, we showed that there is neighborhood-specific functional clustering of rRNA and r-protein interactions that drive ribosome assembly. Further, we found evidence for possible functional co-evolution of eukaryotic rRNA and eukaryote-specific elements of r-protein. From the standpoint of r-protein, we used rpL5 as a paradigm for constantly evolving molecular interactions as assembly progresses. Apart from recapitulating Diamond-Blackfan anemia missense mutations in yeast, we characterized interactions formed by specific regions of rpL5 and propose that these interactions potentially govern the loading of 5S RNP en bloc to the nascent large ribosomal subunit, to ensure proper rotation of the 5S RNP during biogenesis, and to further recruit proteins necessary for the test drive of subunits in the cytoplasm. From the standpoint of assembly factors, we analyzed a so-called group of ITS2 cluster proteins, Nop15, Cic1 and Rlp7 and identified the extensive protein-protein interactions and analyzed protein-RNA interactions that they make. Using our data, we were able to localize Rlp7 to the ITS2 spacer in the pre-rRNA and to identify potential mechanisms for their function. Having identified a network of molecular interactions, we suggest that these proteins orchestrate proper folding of rRNA through this network, and stabilize and facilitate the early steps of assembly. Further, based on their location in the preribosome, these factors might serve to ensure proper progression of early steps of assembly to enable subsequent processing of the ITS2 spacer in the middle steps, possibly by recruiting the ATPase Has1. Thus, we have investigated early nucleolar and late nuclear steps of ribosome assembly in the light of molecular interactions formed by rRNA, r-protein and assembly factors that participate in eukaryotic ribosome assembly. Lessons that emerged from this study and tools developed in the process provide a starting point for further investigations pertaining to the roles of eukaryote-specific segments of molecules that participate in ribosome biogenesis, and serve as a paradigm for how a dynamic network of molecular interactions can drive the assembly of complex macromolecular structures.
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Burlacu, Elena. "Probing ribosomal RNA structural rearrangements : a time lapse of ribosome assembly dynamics." Thesis, University of Edinburgh, 2016. http://hdl.handle.net/1842/17072.
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Ribosome synthesis is a very complex and energy consuming process in which pre-ribosomal RNA (pre-rRNA) processing and folding events, sequential binding of ribosomal proteins and the input of approximately 200 trans-acting ribosome assembly factors need to be tightly coordinated. In the yeast Saccharomyces cerevisiae, ribosome assembly starts in the nucleolus with the formation of a very large 90S-sized complex. This ~2.2MDa pre-ribosomal complex is subsequently processed into the 40S and 60S assembly intermediates (pre-40S and pre-60S), which subsequently mature largely independently. Although we have a fairly complete picture of the protein composition of these pre-ribosomes, still very little is known about the rRNA structural rearrangements that take place during the assembly of the 40S and 60S subunits and the role of the ribosome assembly factors in this process. To address this, the Granneman lab developed a method called ChemModSeq, which made it possible to generate nucleotide resolution maps of RNA flexibility in ribonucleoprotein complexes by combining SHAPE chemical probing, high-throughput sequencing and statistical modelling. By applying ChemModSeq to ribosome assembly intermediates, we were able to obtain nucleotide resolution insights into rRNA structural rearrangements during late (cytoplasmic) stages of 40S assembly and for the early (nucleolar) stages of 60S assembly. The results revealed structurally distinct cytoplasmic pre-40S particles in which rRNA restructuring events coincide with the hierarchical dissociation of assembly factors. These rearrangements are required to trigger stable incorporation of a number of ribosomal proteins and the completion of the head domain. Rps17, one of the ribosomal proteins that fully assembled into pre-40S complexes only at a later assembly stage, was further characterized. Surprisingly, my ChemModSeq analyses of nucleolar pre-60S complexes indicated that most of the rRNA folding steps take place at a very specific stage of maturation. One of the most striking observations was the stabilization of 5.8S pre-rRNA region, which coincided with the dissociation of the assembly factor Rrp5 and stable incorporation of a number of ribosomal proteins.
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Gamalinda, Michael. "Ribosomal Proteins Orchestrate the Biogenesis of Eukaryotic Large Ribosomal Subunits in a Sequential Fashion." Research Showcase @ CMU, 2014. http://repository.cmu.edu/dissertations/441.
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Ribosome biogenesis in eukaryotes involves the transcription, folding, and processing of ribosomal RNA (rRNA), as well as the concomitant assembly of ribosomal proteins. Several hundred trans-acting assembly factors also play a role in the complex process of ribosome biogenesis. Investigations of the construction of ribosomes have focused primarily on the roles of these assembly factors. Little is understood about how ribosomal proteins (r-proteins) function in ribosomal subunit biogenesis in vivo, in either prokaryotes or eukaryotes. I began by focusing on a subset of r-proteins surrounding the polypeptide exit tunnel of the large ribosomal subunit in yeast. R-proteins in this neighborhood, namely L17, L26, L35, and L37, are of importance because they fail to assemble with preribosomes when early pre-rRNA processing steps are blocked. I showed that these rproteins are important for the next pre-rRNA processing, cleavage of the ITS2 spacer sequence in 27SB pre-rRNA. Interestingly, I showed that this biogenesis defect is not due to changes in structure of ITS2. Instead, these r-proteins are required for stable recruitment of key assembly factors that function in this event. I then carried out a global survey of the majority of r-proteins in the 60S subunit. I found that co-transcriptional binding of r-proteins influences post-transcriptional stabilization of 60S subunit structural neighborhoods. This led to a model wherein structural domains of eukaryotic large ribosomal subunits are constructed in a hierarchical fashion. Assembly begins at the convex solvent side, followed by the polypeptide exit tunnel, the intersubunit side, and finally the central protuberance. This hierarchy serves as an initial framework to further understand 60S assembly in vivo. I also showed that pre-ribosomes become more stable as assembly proceeds and that the final steps in 60S maturation occur around regions important for ribosome function. My results also support the hypothesis that the formation of the 3’ end of 27S pre-rRNA is important for early steps of 60S assembly occurring near the 5’ end of pre-rRNA. I also studied the functions of conserved and eukaryote-specific extensions of rproteins that are intrinsically disordered. This revealed distinct roles of extensions in 60S subunit biogenesis and supported a model for the sequential binding of globular and then extended domains of r-proteins during ribosome assembly. My surprising finding for a eukaryote-specific r-protein tail highlights the importance of understanding why several yeast r-proteins have evolved extra sequences that are conserved in higher eukaryotes. Together, these investigations revealed important principles governing ribosome assembly. Furthermore, striking similarities and differences between assembly of bacterial and eukaryotic large ribosomal subunits also emerged, providing insights into how these RNA–protein particles evolved.
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G, C. Keshav. "Investigation of the Role of Bacterial Ribosomal RNA Methyltransferase Enzyme RsmC in Ribosome Biogenesis." Kent State University / OhioLINK, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=kent1621868567263046.
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Leplus, Alexis. "Study of factors implicated in small ribosomal subunit biogenesis under differents growth conditions." Doctoral thesis, Universite Libre de Bruxelles, 2010. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/210189.
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La biogenèse du ribosome est un processus complexe et dynamique qui nécessite de nombreuses étapes de maturation et de modification des ARNr ainsi que l’assemblage et le transport des RNPs précurseurs. Un ribosome mature contient une centaine de pièces, ARN et protéines confondus, mais son assemblage requiert l’intervention de plus de 400 facteurs de synthèse. De part le coût énergétique important de ce processus, plusieurs voies de régulation interviennent pour contrôler la biogenèse des ribosomes en fonction des conditions nutritives. L’une des voies les plus connue est la voie TOR (Target of rapamycin). Cette voie de régulation agît principalement au niveau de la transcription des différents intervenants de la biogenèse :les ARNr, les protéines ribosomiques mais aussi les facteurs de synthèse. Ces facteurs, ayant une action transitoire dans la maturation des ribosomes, sont, par économie, recyclés pour la synthèse de nouveaux ribosomes. Nous nous sommes donc intéressés au devenir de ces facteurs, plus particulièrement de ceux intervenants dans la biogenèse de la petite sous unité, lorsque les conditions environnementales sont inadaptées à la croissance cellulaire. Ainsi, nous avons pu montré, pour quatre facteurs particuliers :Dim2, Rrp12, Hrr25 et Fap7, que leur localisation est dépendante de la synthèse ribosomique. Ainsi, lors de carence en sources nutritives, l’inhibition de la synthèse et de l’activité ribosomique entraîne un confinement de ces facteurs ribosomiques dans le nucléole ou dans des corps cytoplasmiques. En outre, la localisation particulière des facteurs ribosomiques Hrr25 et Fap7 dans les P-bodies en phase de croissance saturée laisse penser que ces corps cytoplasmiques sont le lieu de dégradation des pré-ribosomes lorsque les carences nutritives perdurent.Doctorat en Sciences
info:eu-repo/semantics/nonPublished
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Kim, Sunghan. "Characterization of ribosomal S6 protein phosphorylation and possible control of ribosome biogenesis in arabidopsis cell culture." Connect to this title online, 2004. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1072819298.
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Thesis (Ph. D.)--Ohio State University, 2004.Title from first page of PDF file. Document formatted into pages; contains xvi, 147 p.; also includes graphics. Includes bibliographical references (p. 128-147).
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MIYOSHI, Masaya, Tetsuya OKAJIMA, Tsukasa MATSUDA, Michiko N. FUKUDA, and Daita NADANO. "Bystin in human cancer cells : intracellular localization and function in ribosome biogenesis." Biochemical Society, 2007. http://hdl.handle.net/2237/9306.
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Zakari, Musinu. "The SMC loader Scc2 promotes ncRNA biogenesis and translational fidelity in Saccharomyces cerevisiae." Thesis, Paris 6, 2015. http://www.theses.fr/2015PA066148/document.
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Le complexe Scc2-Scc4 est essentiel pour l’association du complexe cohésine sur l’ADN. Les proteines Cohésine génèrent la cohésion entre les chromatides sœurs, ce qui est essentiel pour la ségrégation des chromosomes. Scc2 (également connu sous le nom NIPBL) est muté chez les patients atteints du syndrome de Cornelia de Lange, une maladie multi-organique caractérisée par des anomalies du développement du visage, de la developpement mental cardiaque et du tractus gastro-intestinal. Comment les mutations localisées au niveau du gène codant pour la proteine Scc2 conduisent à des anomalies du développement chez les patients n’a pas encore été élucidé. Une des hypothèses est que la liaison de Scc2 / cohésine à différentes régions du génome a une incidence sur la transcription. Chez la levure de bière, il a été montre que Scc2 se lie aux genes transcrits par l'ARN Pol III (les ARNt et spliceosomals) , ainsi qu‘aux gènes transcrits par l'ARN Pol II codant pour des petits ARN nucléolaires et nucléaires (snARN et snoARNs ) et des gènes de protéines ribosomiques. Nous rapportons ici que Scc2 est important pour l'expression de ces gènes. Scc2 et le régulateur transcriptionnel Paf1 collaborent pour promouvoir la production de Box H / ACA snoARNs qui guident la pseudouridylation des ARN y compris l'ARN ribosomal. Une mutation de Scc2 a été associée à des défauts dans la production d'ARN ribosomal, la biogenèse des ribosomes, et del’épissage. Alors que le mutant Scc2 n'a pas de défaut général de la synthèse protéique, il montre un déphasage accrue et une réduction de l’utilisation du site interne d'entrée ribosomale (IRES)/ coiffe-indépendante. Ces résultats suggèrent que Scc2 favorise normalement un programme d'expression génétique qui prend en charge la fidélité de la traduction. Nous émettons l'hypothèse que le dysfonctionnement de traduction peut contribuer au syndrome de Cornelia de Lange, qui est causé par des mutations dans Scc2The Scc2-Scc4 complex is essential for loading the cohesin complex onto DNA. Cohesin generates cohesion between sister chromatids, which is critical for chromosome segregation. Scc2 (also known as NIPBL) is mutated in patients with Cornelia de Lange syndrome, a multi-organ disease characterized by developmental defects in head, limb, cognition, heart, and the gastrointestinal tract. How mutations in Scc2 lead to developmental defects in patients is yet to be elucidated. One hypothesis is that the binding of Scc2/cohesin to different regions of the genome will affect transcription. In budding yeast, Scc2 has been shown to bind to RNA Pol III transcribed genes (tRNAs, and spliceosomal), as well as RNA Pol II-transcribed genes encoding small nuclear and nucleolar RNAs (snRNAs and snoRNAs) and ribosomal protein genes. Here, we report that Scc2 is important for gene expression. Scc2 and the transcriptional regulator Paf1 collaborate to promote the production of Box H/ACA snoRNAs which guide pseudouridylation of RNAs including ribosomal RNA. Mutation of Scc2 was associated with defects in the production of ribosomal RNA, ribosome biogenesis, and splicing. While the scc2 mutant does not have a general defect in protein synthesis, it shows increased frameshifting and reduced internal ribosomal entry site (IRES) usage/cap-independent translation. These findings suggest Scc2 normally promotes a gene expression program that supports translational fidelity. We hypothesize that translational dysfunction may contribute to the human disorder Cornelia de Lange syndrome, which is caused by mutations in Scc2
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FUKUDA, Michiko N., Masaya MIYOSHI, and Daita NADANO. "The role of bystin in embryo implantation and in ribosomal biogenesis." Springer, 2007. http://hdl.handle.net/2237/9027.
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Das, Priyanka. "Study of the L13a residues required for ribosomal function." Cleveland State University / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=csu1331762160.
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Weaver, Paul L. "Characterization of a putative RNA helicase, Dbp3p, in ribosomal RNA processing and ribosome biogenesis in Saccharomyces Cerevisiae /." The Ohio State University, 1997. http://rave.ohiolink.edu/etdc/view?acc_num=osu148794750113696.
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Castle, Cathy Lynn. "Protein-Protein interactions involved in the biogenesis of eukaryotic small ribosomal subunits." Thesis, Montana State University, 2008. http://etd.lib.montana.edu/etd/2008/castle/CastleC1208.pdf.
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Ribosome biogenesis is a complicated process involving numerous proteins and modification factors. The process has been well-documented in prokaryotic cells where it is much less complex than the process involved in eukaryotic cells. In eukaryotes, much of what is known about ribosome biogenesis has been learned from studies in the yeast Saccharomyces cerevisiae. Far less has been learned about higher eukaryotes such as humans. However, among organisms in all three domains of life, ribosome structure and function is well conserved. The biogenesis of ribosomal subunits is dynamic, complicated, and, in S. cerevisiae, requires over 200 trans-acting factors for synthesis to occur. The focus of this study is synthesis of the small ribosome subunit in eukaryotes. In order to study this process in higher eukaryotes, a mammalian cell culture method was used. This method involves cloning human ribosomal accessory genes using the Gateway system, a rapid and efficient cloning method that permits parallel construction of numerous plasmids in a modular type of system, each containing the desired gene of interest in a variety of vectors. Proteins were selected based on their activity in yeast with emphasis on the final processing step of the small subunit and the proteins that are involved at that step. These proteins are Nob1p, Enp1p, Tsr1p, Rio2p, Rrp20p, Dim1p, and Hrr25p. The corresponding genes were cloned into vectors containing either the coding region for a full-length fluorescent protein or the C-terminus or N-terminus half of the fluorescent protein. The bimolecular fluorescent complementation assay (BiFC) was then utilized to detect protein-protein interactions. Results of this assay demonstrate binary interactions among pairs of this group of proteins and the location within the cell where these interactions take place.
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Tobin, Christina. "Removal and Replacement of Ribosomal Proteins : Effects on Bacterial Fitness and Ribosome Function." Doctoral thesis, Uppsala universitet, Institutionen för medicinsk biokemi och mikrobiologi, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-150401.
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Protein synthesis is a complex process performed by sophisticated cellular particles known as ribosomes. Although RNA constitutes the major structural and functional component, ribosomes from all kingdoms contain an extensive array of proteins with largely undefined functional roles. The work presented in this thesis addresses ribosomal complexity using mutants of Salmonella typhimurium to examine the physiological effects of ribosomal protein (r-protein) removal and orthologous replacement on bacterial fitness and ribosome function. The results of paper I demonstrate that removal of small subunit protein S20 conferred two independent translation initiation defects: (i) a significant reduction in the rate and extent of mRNA binding and (ii) a drastic decrease in the yield of 70S complexes caused by an impairment in subunit association. The topographical location of S20 in mature 30S subunits suggests that these perturbations are the result of improper orientation of helix 44 of the 16S rRNA when S20 is absent. In paper II we show that the major functional impairment associated with loss of large subunit protein L1 manifested as an increase in free ribosomal subunits at the expense of translationally active 70S particles. Furthermore, the formation of free ribosomal subunits was imbalanced suggesting that L1 is required to suppress degradation or promote formation of 30S subunits. Compensatory evolution revealed that mutations in other large subunit proteins mitigate the cost of L1 removal, in one case seemingly via an increase in 70S complex formation. As shown in paper III, the large fitness costs associated with complete removal of r-proteins is in contrast to the generally mild costs of orthologous protein replacement, even in the absence of a high degree of homology to the native protein. This clearly demonstrates the robustness and plasticity of the ribosome and protein synthesis in general and it also implies that functional constraints are highly conserved between these proteins. The findings of paper III also allowed us to examine the barriers that constrain horizontal gene transfer and we find that increased gene dosage of the sub-optimal heterologous protein may be an initial response to stabilize deleterious transfer events. Overall the results highlight the requirement of r-proteins for the maintenance of ribosomal structural integrity.
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Heuer, André [Verfasser], and Roland [Akademischer Betreuer] Beckmann. "The eukaryotic small ribosomal subunit in the context of translational recycling and ribosome biogenesis / André Heuer ; Betreuer: Roland Beckmann." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2018. http://d-nb.info/1171705166/34.
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Kshetri, Man B. "N-TERMINAL DOMAIN OF rRNA METHYLTRANSFERASE ENZYME RsmC IS IMPORTANT FOR ITS BINDING TO RNA AND RNA CHAPERON ACTIVITY." Kent State University Honors College / OhioLINK, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=ksuhonors1621007414429417.
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Janas, Maja. "Novel Regulation of MicroRNA Biogenesis and Function." Thesis, Harvard University, 2012. http://dissertations.umi.com/gsas.harvard:10121.
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MicroRNAs are small noncoding RNAs that post-transcriptionally reduce protein output from most human mRNAs by mechanisms that are still obscure. This thesis provides insights into three aspects of microRNA biogenesis and function described below. MicroRNA precursors are excised from primary transcripts by the Microprocessor complex containing Drosha and DGCR8. Although most microRNAs are located in introns of protein-coding and noncoding genes, the mechanisms coordinating microprocessing and splicing are unclear. MiR-211 is a microRNA expressed from intron 6 of melastatin, a suspected melanoma tumor suppressor. We demonstrate that miR-211, and not melastatin, is responsible for the tumor suppressive function of this locus, that Drosha-mediated processing of the miR-211 precursor promotes splicing of melastatin exon 6-exon 7 junctions, and that perturbing 5' splice site recognition by the U1 snRNP reduces Drosha recruitment to intron 6 specifically and intronic microRNA levels globally. Thus we identify a novel physical and functional coupling between microprocessing and splicing. Typically, Agos stabilize mature microRNAs and as a complex stoichiometrically bind to complementary mRNAs. We demonstrate an alternative order of events in which Agos bind and repress pre-formed imperfect microRNA-mRNA duplexes in processing bodies of live cells, and cleave pre-formed perfect microRNA-mRNA duplexes in vitro. Our data support a novel catalytic model whereby Agos first deposit microRNAs onto mRNAs and dissociate, thus priming multiple microRNA-mRNA duplexes for concurrent repression by a single Ago. Despite key roles in development and pathogenesis, effectors and regulators of microRNA-mediated repression are still poorly characterized. An RNAi screen revealed that depletion of ribosomal proteins of either small or large ribosomal subunit dissociates microRNA-containing complexes from mRNAs repressed at translation initiation, increasing their polysome association, translation, and stability relative to untargeted mRNAs. Thus ribosomal proteins globally regulate microRNA function. Another RNAi screen revealed that Akt3 phosphorylates Ago2, which negatively regulates cleavage and positively regulates translational repression of microRNA-targeted mRNAs. Thus Ago2 phosphorylation is a molecular switch between its mRNA cleavage and translational repression activities. The following pages will place these novel insights into biological and disease-relevant context, will describe what was known prior to these studies, and will provide perspectives for future studies.
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Dator, Romel P. "Characterization of Ribosomes and Ribosome Assembly Complexes by Mass Spectrometry." University of Cincinnati / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1382373082.
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Inder, Kerry, and n/a. "The Functional Role of NRAP in the Nucleolus." Griffith University. School of Biomolecular and Biomedical Science, 2006. http://www4.gu.edu.au:8080/adt-root/public/adt-QGU20070201.133347.
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The nucleolus is the site for rRNA synthesis, a process requiring the recruitment of many proteins involved in ribosomal biogenesis. Nrap is a novel nucleolar protein found to be present in all eukaryotes. Preliminary characterisation of Nrap suggested it was likely to participate in ribosome biogenesis but as with many other nucleolar proteins, the functional role of Nrap is largely unknown. In this study, the role of mammalian Nrap in the nucleolus and in ribosome biogenesis was explored. Initially, a number of tools were generated to investigate Nrap function. This involved raising and purifying a polyclonal antibody against the N-terminal region of Nrap. The anti-Nrap antibody was found to detect two Nrap bands in mouse fibroblast cells, possibly corresponding to the two mouse Nrap isoforms, and . In addition, mammalian expression vectors containing the full Nrap sequence as well as deletion constructs were created. The subcellular localisation of each construct was observed by fluorescent microscopy. It was revealed that recombinant Nrap did not localise to the nucleolus, possibly because it was exported to undergo degradation by the 26S proteasome. Two putative NLSs were found to be responsible for directing Nrap to the nucleus but a region accountable for nucleolar localisation was not identified. The data indicated that multiple domains working together are likely to direct Nrap to the nucleolus. Nrap was also observed to co-localise with nucleolar proteins B23 and p19ARF. Moreover, it was shown by reciprocal immunoprecipitation that these three nucleolar proteins existed in a complex in unsynchronised mouse fibroblast cells. Recent reports demonstrated a complex relationship between B23 and p19ARF although the functional significance remained unclear. Nrap's in vivo association with B23 and p19ARF indicated a specific functional role in the nucleolus. Nrap knockdown using siRNA significantly increased B23 protein levels in a dose-dependent manner and down-regulated p19ARF protein levels at higher siRNA concentration. Preliminary studies also implicated Nrap in cell proliferation through these novel interactions. Both endogenous and recombinant Nrap were found to be highly unstable suggesting that Nrap might regulate B23 and p19ARF through its own tightly regulated stability. Finally, the role of Nrap in rRNA processing was investigated by northern blot analysis. Nrap knockdown was found to affect the levels of 45S, 32S and 28S rRNAs. The changes found may be a consequence of the concurrent perturbation in the levels of B23 and p19ARF caused by Nrap knockdown. As the results were not consistent with previous reports, it was likely that changes to rRNA processing could be contributed to Nrap loss of function. This study demonstrated for the first time a functional role of Nrap in rRNA processing possibly through its association with B23 and p19ARF.
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Inder, Kerry. "The Functional Role of NRAP in the Nucleolus." Thesis, Griffith University, 2006. http://hdl.handle.net/10072/367738.
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The nucleolus is the site for rRNA synthesis, a process requiring the recruitment of many proteins involved in ribosomal biogenesis. Nrap is a novel nucleolar protein found to be present in all eukaryotes. Preliminary characterisation of Nrap suggested it was likely to participate in ribosome biogenesis but as with many other nucleolar proteins, the functional role of Nrap is largely unknown. In this study, the role of mammalian Nrap in the nucleolus and in ribosome biogenesis was explored. Initially, a number of tools were generated to investigate Nrap function. This involved raising and purifying a polyclonal antibody against the N-terminal region of Nrap. The anti-Nrap antibody was found to detect two Nrap bands in mouse fibroblast cells, possibly corresponding to the two mouse Nrap isoforms, and . In addition, mammalian expression vectors containing the full Nrap sequence as well as deletion constructs were created. The subcellular localisation of each construct was observed by fluorescent microscopy. It was revealed that recombinant Nrap did not localise to the nucleolus, possibly because it was exported to undergo degradation by the 26S proteasome. Two putative NLSs were found to be responsible for directing Nrap to the nucleus but a region accountable for nucleolar localisation was not identified. The data indicated that multiple domains working together are likely to direct Nrap to the nucleolus. Nrap was also observed to co-localise with nucleolar proteins B23 and p19ARF. Moreover, it was shown by reciprocal immunoprecipitation that these three nucleolar proteins existed in a complex in unsynchronised mouse fibroblast cells. Recent reports demonstrated a complex relationship between B23 and p19ARF although the functional significance remained unclear. Nrap's in vivo association with B23 and p19ARF indicated a specific functional role in the nucleolus. Nrap knockdown using siRNA significantly increased B23 protein levels in a dose-dependent manner and down-regulated p19ARF protein levels at higher siRNA concentration. Preliminary studies also implicated Nrap in cell proliferation through these novel interactions. Both endogenous and recombinant Nrap were found to be highly unstable suggesting that Nrap might regulate B23 and p19ARF through its own tightly regulated stability. Finally, the role of Nrap in rRNA processing was investigated by northern blot analysis. Nrap knockdown was found to affect the levels of 45S, 32S and 28S rRNAs. The changes found may be a consequence of the concurrent perturbation in the levels of B23 and p19ARF caused by Nrap knockdown. As the results were not consistent with previous reports, it was likely that changes to rRNA processing could be contributed to Nrap loss of function. This study demonstrated for the first time a functional role of Nrap in rRNA processing possibly through its association with B23 and p19ARF.Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Biomolecular and Biomedical Sciences
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Ho, Hei Ngam Jennifer. "Functional characterization of yeast NMD3 in the biogenesis and transport of the large (60S) ribosomal subunit /." Full text (PDF) from UMI/Dissertation Abstracts International, 2000. http://wwwlib.umi.com/cr/utexas/fullcit?p3004287.
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Herdman, Chelsea. "Relative roles of UBF and RRN3 in the transcription of the ribosomal RNA genes and ribosome biogenesis determined using in vivo mouse models." Doctoral thesis, Université Laval, 2017. http://hdl.handle.net/20.500.11794/28387.
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La biogenèse des ribosomes, aussi appelée la synthèse ribosomale, est un processus cellulaire important se déroulant dans le nucléole et implique la transcription par les trois ARN polymérases nucléaires. L’étape initiale et limitante de ce processus est la transcription des ARNs ribosomaux catalytiques, 28S, 18S and 5.8S, sous la forme d’un long précurseur d’ARN ribosomal (pre-ARNr/47S) par l’ARN polymérase I (RPI). RPI possède un ensemble de facteurs de transcription généraux responsables de son activation. Ces facteurs sont la protéine architecturale UBF, le facteur SL1 qui contient TBP, le facteur d’initiation RRN3 et le facteur de terminaison TTF1. La synthèse de l’ARN ribosomale est finement régulée et correspond à 30-50% de l’ensemble de la transcription de la cellule. De plus, ce processus est lié à la croissance cellulaire, la transformation, la prolifération et à l’activité des facteurs suppresseurs de tumeurs et des oncogènes. UBF et RRN3 sont notamment activés par plusieurs voies de signalisation de croissance cellulaire. Dans les cellules de mammifère, il existe ~200 copies d’ADNr par génome haploïde. Les fragments répétés d’ADN ribosomal sont arrangés en répétition en tandem sur les bras courts des chromosomes acrocentriques. De façon intéressante, dans les cellules somatiques, seulement la moitié des copies d’ADNr sont actives, alors que les autres sont maintenues dans une forme inactive par les modifications épigénétiques et la formation d’hétérochromatine. La raison pour laquelle le génome contient autant de copies et la régulation de leur activité ne sont pas bien comprises. Cette thèse présente l’analyse de l’importance in vivo d’UBF et de RRN3 pour la régulation de la transcription de l’ARNr et pour le maintien de la structure chromatinienne de l’ADNr. Nous avons précédemment analysé la perte de fonction de UBF dans les fibroblastes embryonnaires de souris en utilisant le système de perte de fonction conditionnelle dépendante du tamoxifène. Puisque l’un de nos objectifs était de comparer la fonction de RRN3 dans un modèle similaire, nous avons réanalysé la perte de fonction de RRN3 chez la souris et généré des lignées cellulaires comme préalablement réalisées avec la perte de fonction d’UBF. Nous avons déterminé que RRN3 est essentiel à la préimplantation et le développement est arrêté à E3.5, ce qui contredit les résultats obtenus par un autre groupe qui avait obtenu un arrêt du développement beaucoup plus tardif, à E9.5. Une lignée de fibroblastes embryonnaires de souris inductible au tamoxifène a été créée pour RRN3 de façon similaire à ce qui avait été fait pour UBF. La perte de fonction d’UBF ou de RRN3 inhibe la transcription par RPI. Par contre, nous démontrons que UBF est responsable du recrutement à l’ADNr des autres facteurs associés à RPI et du maintient de l’état ouvert de la chromatine. En comparaison, RRN3 est requis simplement pour le recrutement de RPI. Dans cette étude, nous avons également identifié une région frontalière en amont de l’ADNr formée de H2A.Z, TTF1, CTCF et des modifications d’histones activatrices. Nous avons également découvert que la perte d’UBF entraine une mort cellulaire synchronisée par apoptose, indépendamment de p53 et ce spécifiquement dans les lignées cellulaires transformées. Ce résultat suggère qu’il pourrait être possible de cibler UBF dans le traitement contre le cancer puisque la perte de UBF dans les lignées cellulaires primaires cause un arrêt de prolifération sans entrainer l’apoptose. Finalement, nous avons observé que le niveau d’activité de l’ADNr dans les cellules pluripotentes est différent que dans les cellules différenciées. Des lignées de cellules souches embryonnaires (ESCs) ont été générées à partir des souris conditionnelles pour UBF et RRN3 et nos résultats préliminaires suggèrent que la totalité des gènes de l’ADNr est active dans les cellules pluripotentes. Ce modèle est idéal pour étudier la régulation de l’ADNr ainsi que le rôle de UBF et RRN3 dans cette régulation après l’induction de la différentiation. En résumé, ces résultats permettront de clarifier le rôle in vivo de UBF et RRN3 dans la transcription de l’ARN ribosomal et dans le maintien de l’intégrité de l’ADNr.Ribosome biogenesis, or the synthesis of ribosomes, is an important cell process occurring in the nucleolus that utilizes transcription by all three nuclear RNA polymerases. The initial and rate-limiting step is the transcription of the catalytic ribosomal RNAs 28S, 18S and 5.8S in the form of a precursor ribosomal RNA (pre-rRNA/47S) by RNA polymerase I (RPI, also known as Pol1 and POLR1). RPI has a dedicated set of basal factors responsible for its activation. These are the architectural factor UBF, the TBP containing factor SL1, the initiation factor RRN3, and the termination factor TTF1. Ribosomal RNA synthesis is tightly regulated and accounts for 30-50% of total gene transcription. As such, this process is linked to cell growth, transformation, proliferation and the actions of tumour suppressors and oncogenes. Notably, UBF and RRN3 are activated by many of the same growth signaling pathways. The human and mouse haploid genome contain ~200 copies of the ribosomal RNA genes, the ribosomal DNA (rDNA). These ribosomal DNA copies are arranged in tandem repeats on the short arms of acrocentric chromosomes. Interestingly, only a fraction of the rDNA copies are active, and a significant number are epigenetically silenced and heterochromatic. The reason for having so many copies and their regulation in vivo by silencing is not yet understood, though it has been connected with genome stability. This thesis presents the analysis of the in vivo requirements for UBF and RRN3 in rRNA transcription and rDNA chromatin structure. We had previously analyzed the loss of UBF in mouse embryonic fibroblasts using tamoxifen-dependent conditional knockout. As we wanted to compare the loss of RRN3 in a similar model, we re-analyzed the RRN3 knockout mice and created cell lines as was performed for the UBF knockout. Importantly, we find that RRN3 is essential for preimplantation and its loss arrests development at E3.5, contrary to previous work that showed a late E9.5 developmental arrest. Using mouse embryonic fibroblast (MEF) cell lines conditional for UBF or RRN3, we found that the loss of either factor prevented RPI transcription. However, we found that UBF was essential for the recruitment of the other RPI transcription factors and the formation of the preinitiation complex, as well as to maintain an open rDNA chromatin structure, while RRN3 was required only for RPI recruitment. These studies allowed us to identify an upstream boundary element on the rDNA formed of H2A.Z, TTF1, CTCF and activating histone marks, which is independent of RPI activity. We also found that UBF loss, but not RRN3 loss, led to a synchronous and massive p53-independent apoptosis, specifically in oncogenically transformed cells. This strongly suggests that drug targeting UBF could be a viable cancer treatment. Finally, we have observed that the rDNA activity status in pluripotent cells differs from that of differentiated cells. Embryonic stem cells (ESCs) were also generated from the mice conditional for UBF and RRN3. Preliminary results indicate that, unlike somatic cells, all the rRNA genes in these and other pluripotent cell lines are potentially active. This makes ESCs and their differentiation an ideal model in which to study the establishment of rDNA silencing and the role of UBF and/or RRN3 in this process. Together these data define the in vivo roles of UBF and RRN3 in ribosomal RNA transcription and suggest mechanisms by which they maintain rDNA integrity and may drive cell differentiation.
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Kirby, Tyler. "GLOBAL-SCALE ANALYSIS OF THE DYNAMIC TRANSCRIPTIONAL ADAPTATIONS WITHIN SKELETAL MUSCLE DURING HYPERTROPHIC GROWTH." UKnowledge, 2015. http://uknowledge.uky.edu/physiology_etds/22.
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Skeletal muscle possesses remarkable plasticity in responses to altered mechanical load. An established murine model used to increase mechanical load on a muscle is the surgical removal of the gastrocnemius and soleus muscles, thereby placing a functional overload on the plantaris muscle. As a consequence, there is hypertrophic growth of the plantaris muscle. We used this model to study the molecular mechanisms regulating skeletal muscle hypertrophy.
Aged skeletal muscle demonstrates blunted hypertrophic growth in response to functional overload. We hypothesized that an alteration in gene expression would contribute to the blunted hypertrophic response observed with aging. However, the difference in gene expression was modest, with cluster analysis showing a similar pattern of expression between the two groups. Despite ribosomal protein gene expression being higher in the aged group, ribosome biogenesis was significantly lower in aged compared with young skeletal muscle in response to the hypertrophic stimulus (50% versus 2.5-fold, respectively). The failure to fully up-regulate pre-47S ribosomal RNA (rRNA) expression in old skeletal muscle undergoing hypertrophy indicated ribosomal DNA transcription by RNA polymerase I was impaired. Contrary to our hypothesis, the findings of the study suggest that impaired ribosome biogenesis was a primary factor underlying the blunted hypertrophic response observed in old skeletal muscle rather than dramatic differences in gene expression.
As it appears ribosomal biogenesis may limit muscle hypertrophy, we assessed the dynamic changes in global transcriptional output during muscle hypertrophy, as the majority of global transcription is dedicated to ribosome biogenesis during periods of rapid growth. Metabolic labeling of nascent RNA using 5-ethynyl uridine permitted the assessment of cell type specific changes in global transcription and how this transcription is distributed within the myofiber. Using this approach, we demonstrate that myofibers are the most transcriptionally active cell-type in skeletal muscle, and furthermore, myonuclei are able to dramatically upregulate global transcription during muscle hypertrophy. Interestingly, the myonuclear accretion that occurs with hypertrophy actually results in lower transcriptional output across nuclei within the muscle fiber relative to sham conditions. These findings argue against the notion that nuclear accretion in skeletal muscle is necessary to increase the transcriptional capacity of the cell in order to support a growth response.
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Tiku, Varnesh [Verfasser], Adam [Gutachter] Antebi, and Matthias [Gutachter] Hammerschmidt. "Small Nucleoli and Reduced Ribosomal Biogenesis are Hallmarks of Longevity / Varnesh Tiku ; Gutachter: Adam Antebi, Matthias Hammerschmidt." Köln : Universitäts- und Stadtbibliothek Köln, 2016. http://d-nb.info/1136077839/34.
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Schumacher, Heiko Tobias [Verfasser]. "Involvements of the Plant 3'-5' Exonuclease ERL1 in Chloroplast Ribosomal RNA Biogenesis and RNA Silencing Pathways / Heiko Tobias Schumacher." Kassel : Universitätsbibliothek Kassel, 2009. http://d-nb.info/999715232/34.
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Banerjee, Daipayan. "CHARACTERIZATION OF G-PATCH MOTIF CONTRIBUTION TO PRP43 FUNCTION IN THE PRE-MESSENGER RNA SPLICING AND RIBOSOMAL RNA BIOGENESIS PATHWAYS." UKnowledge, 2013. http://uknowledge.uky.edu/biology_etds/10.
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The DExD/H-box protein Prp43 is essential for two biological processes: nucleoplasmic pre-mRNA splicing and nucleolar rRNA maturation. The biological basis for the temporal and spatial regulation of Prp43 remains elusive. The Spp382/Ntr1, Sqs1/Pfa1 and Pxr1/Gno1 G-patch proteins bind to and activate the Prp43 DExD/H box-helicase in pre-mRNA splicing (Spp382) and rRNA processing (Sqs1, Pxr1). These Prp43-interacting proteins each contain the G-patch domain, a conserved sequence of ~48 amino acids that includes 6 highly conserved glycine (G) residues. Five annotated G-patch proteins in baker’s yeast (i.e., Spp382, Pxr1, Spp2, Sqs1 and Ylr271) and with the possible exception of the uncharacterized Ylr271 protein, all are associated with ribonucleoprotein (RNP) complexes.
Understanding the role of G-patch proteins in modulating the DExD/H box protein Prp43 biological function was the motivation of this thesis. The G-patch domain has been proposed as a protein-protein or a protein-RNA interaction module for RNP proteins. This study found that the three Prp43-associated G-patch domains interact with Prp43 in a yeast 2 hybrid (Y2H) assay but differ in apparent relative affinities. Using a systemic Y2H analysis, I identified the conserved Winged-helix (WH) domain in Prp43 as a major binding site for G-patch motif. Intriguingly, removal of the non-essential N-terminal domain (NTD) of Prp43 (amino acids 2-94), greatly improves G-patch binding, suggesting that the NTD may play a role in modulating enzyme activity by the G-patch effectors. I identify a second site within the Pxr1 that strongly binds Prp43 but, unlike the G-patch, is dispensable for Pxr1 function in vivo.
By constructing chimeric proteins, I demonstrated that individual G-patch peptides differ in the ability to reconstitute Spp382 and Pxr1 function in support of pre-mRNA splicing and rRNA biogenesis, respectively. Through amino acid sequence comparisons and selective mutagenesis I identified several residues within the G-patch motif critical for Prp43-stimulated pre-mRNA splicing without greatly altering its ability to bind Prp43. These data lead me to propose that the G-patch motif is not a simple Prp43 binding interface but may contribute more directly to substrate selection or Prp43 enzyme activation in the biologically distinct pre-mRNA splicing and rRNA processing pathways.
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Trinquier, Aude. "Coupling between transfer RNA maturation and ribosomal RNA processing in Bacillus subtilis." Thesis, Université de Paris (2019-....), 2019. http://www.theses.fr/2019UNIP7066.
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La synthèse des protéines cellulaires requiert à la fois des ribosomes fonctionnels et des ARN de transfert (ARNt) matures comme molécules adaptatrices. Les ribosomes sont de larges complexes ribonucléoprotéiques dont la biogenèse représente la plupart de la transcription cellulaire et consomme une majeure partie de l’énergie de la cellule. Par conséquent, la biogenèse des ribosomes fait l’objet d’une régulation importante afin d’ajuster le nombre de ribosomes aux besoins de la cellule et de dégrader efficacement les particules défectueuses qui pourraient interférer avec la traduction. Les ARNs ribosomiques (ARNr) et les ARNt sont tous deux transcrits sous formes de précurseurs et sont universellement maturés pour devenir fonctionnels pour la traduction. Ce travail de thèse a permis de mettre en évidence un couplage entre la maturation des ARNt et la biogenèse des ribosomes chez la bactérie modèle à Gram positif Bacillus subtilis. Ainsi, l’accumulation d’ARNt immatures lors d’une déplétion en enzymes de maturation, abolit spécifiquement la maturation en 3’ de l’ARNr 16S par l’endoribonucléase YqfG/YbeY, dernière étape dans la formation de la petite sous-unité ribosomique (30S). Nous avons mis en évidence que ce défaut de maturation résultait d’un défaut d’assemblage tardif du 30S coïncidant avec des changements d’expression de plusieurs facteurs d’assemblage du ribosome. Nous avons montré que cette modulation d’expression provenait d’effets transcriptionel et post-transcriptionel. De façon inédite, nos résultats indiquent que l’accumulation d’ARNt immatures est perçue par RelA (le facteur de la réponse stringente), déclenchant la production de (p)ppGpp. Nous avons observé que cette synthèse de (p)ppGpp et la baisse concomitante des niveaux de GTP cellulaire, inhibe la maturation de l’ARNr 16S en 3’, probablement via un blocage des GTPases impliquées dans l’assemblage des ribosomes. L’inhibition de la maturation de l’ARNr 16S côté 3’ est supposée conduire, par la suite, à une dégradation des particules partiellement assemblées par la RNase R. Ainsi, nos résultats supportent un modèle où RelA jouerait un rôle central ; en percevant une déficience de maturation des ARNt et en ajustant, en conséquence, la biogenèse des ribosomes via la production de (p)ppGpp. Ce mécanisme de couplage permettrait de maintenir un équilibre fonctionnel entre ARNt et ARNr, les deux composants majeurs de la machinerie de traductionCellular protein synthesis both requires functional ribosomes and mature transfer RNAs (tRNAs) as adapter molecules. The ribosomes are large essential ribonucleoprotein complexes whose biogenesis accounts for most of cellular transcription and consumes a major portion of the cell’s energy. Ribosome biogenesis is therefore tightly adjusted to the cellular needs and actively surveilled to rapidly degrade defective particles that could interfere with translation. Interestingly, tRNAs and ribosomal RNAs (rRNAs) are both transcribed from longer primary transcripts and universally require processing to become functional for translation. In this thesis, I have characterized a coupling mechanism between tRNA processing and ribosome biogenesis in the Gram-positive model organism Bacillus subtilis. Accumulation of immature tRNAs during tRNA maturase depletion, specifically abolishes 16S rRNA 3’ processing by the endonuclease YqfG/YbeY, the last step in small ribosomal subunit formation. We showed that this maturation deficiency resulted from a late small subunit (30S) assembly defect coinciding with changes in expression of several key 30S assembly cofactors, mediated by both transcriptional and post-transcriptional effects. Interestingly, our results indicate that accumulation of immature tRNAs is sensed by the stringent factor RelA and triggers (p)ppGpp production. We showed that (p)ppGpp synthesis and the accompanying decrease in GTP levels inhibits 16S rRNA 3’ processing, most likely by affecting GTPases involved in ribosome assembly. The inhibition of 16S rRNA 3’ processing is thought to further lead to degradation of partially assembled particles by RNase R. Thus, we propose a model where RelA senses temporary slow-downs in tRNA maturation and this leads to an appropriate readjustment of ribosome biogenesis. This coupling mechanism would maintain the physiological balance between tRNAs and rRNAs, the two major components of the translation machinery
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Punekar, Avinash S. "Ribosomal RNA Modification Enzymes : Structural and functional studies of two methyltransferases for 23S rRNA modification in Escherichia coli." Doctoral thesis, Uppsala universitet, Struktur- och molekylärbiologi, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-212394.
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Escherichia coli ribosomal RNA (rRNA) is post-transcriptionally modified by site-specific enzymes. The role of most modifications is not known and little is known about how these enzymes recognize their target substrates. In this thesis, we have structurally and functionally characterized two S-adenosyl-methionine (SAM) dependent 23S rRNA methyltransferases (MTases) that act during the early stages of ribosome assembly in E. coli. RlmM methylates the 2'O-ribose of C2498 in 23S rRNA. We have solved crystal structures of apo RlmM at 1.9Å resolution and of an RlmM-SAM complex at 2.6Å resolution. The RlmM structure revealed an N-terminal THUMP domain and a C-terminal catalytic Rossmann-fold MTase domain. A continuous patch of conserved positive charge on the RlmM surface is likely used for RNA substrate recognition. The SAM-binding site is open and shallow, suggesting that the RNA substrate may be required for tight cofactor binding. Further, we have shown RlmM MTase activity on in vitro transcribed 23S rRNA and its domain V. RlmJ methylates the exocyclic N6 atom of A2030 in 23S rRNA. The 1.85Å crystal structure of RlmJ revealed a Rossmann-fold MTase domain with an inserted small subdomain unique to the RlmJ family. The 1.95Å structure of the RlmJ-SAH-AMP complex revealed that ligand binding induces structural rearrangements in the four loop regions surrounding the active site. The active site of RlmJ is similar to N6-adenine DNA MTases. We have shown RlmJ MTase activity on in vitro transcribed 23S rRNA and a minimal substrate corresponding to helix 72, specific for adenosine. Mutagenesis experiments show that residues Y4, H6, K18 and D164 are critical for catalytic activity. These findings have furthered our understanding of the structure, evolution, substrate recognition and mechanism of rRNA MTases.
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Saby, Manon Juliette. "Identification de gènes candidats pour l'anémie de Blackfan-Diamond et caractérisation phénotypique." Thesis, Université de Paris (2019-....), 2019. https://theses.md.univ-paris-diderot.fr/SABY_Manon_va2.pdf.
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L’anémie de Blackfan-Diamond (ABD) est une érythroblastopénie congénitale rare secondaire à un blocage de la maturation des cellules érythroïdes entre les stades BFU-e (EPO indépendant) et CFU-e (EPO dépendant). La maladie se manifeste par une anémie arégénérative, le plus souvent macrocytaire. Dans 50% des cas, à l’anémie s’associe un syndrome malformatif affectant l’aire céphalique et les extrémités et incluant un retard de croissance. Bien que très hétérogène tant phénotypiquement que génotypiquement, l'ABD est due à des mutations toujours hétérozygotes dans des gènes de protéines ribosomiques (RP) pour 80% des cas. Le premier gène identifié comme impliqué dans l’ABD est le gène de la RPS19 (RPS19), faisant de l’ABD la première ribosomopathie décrite. A ce jour, 20 gènes de RP ont été identifiés. L'haplo-insuffisance en RP entraîne un défaut de maturation des ARN ribosomiques (ARNr) générant un stress nucléolaire, qui lui-même conduit à la stabilisation de la protéine p53. La p53 stabilisée induit l’apoptose et l'arrêt du cycle cellulaire qui sont responsables en grande partie de l’érythroblastopénie. Plus rarement, l’ABD peut être la conséquence de mutations présentes sur le gène GATA-1 (facteur de transcription majeur de l’érythropoïèse), le gène TSR2 (interagissant avec la protéine RPS26 et intervenant dans la biogenèse des ribosomes) ou encore le gène EPO (cytokine clé de l’érythropoïèse). Cependant, 20% des patients atteints d’ABD ne sont toujours pas génotypiquement diagnostiqués : de nouveaux gènes candidats sont encore à découvrir chez ces patients. Dans cette perspective, l’objectif de ma thèse a donc été de caractériser le rôle fonctionnel de nouveaux gènes candidats afin de confirmer leur lien avec l’ABD. Nous avons procédé à un séquençage d’exomes chez 25 familles ce qui a permis d’identifier 8 gènes candidats. Nous présentons ici quatre de ces gènes dont deux gènes codant pour un chaperon ribosomique : HSPA14 et HEATR3, un gène codant pour une RP : RPL9 et un gène codant un facteur de croissance : CECR1.Les protéines chaperons du ribosome représentent un nouveau groupe de gènes pouvant être associé à la maladie. Mes travaux de thèse ont permis d’étudier la prolifération, la division, l’amplification, la différenciation et la viabilité des cellules primaires érythroïdes issues des patients porteurs de variations alléliques dans ces gènes. Ces expériences ont permis de mettre en évidence un défaut de prolifération érythroïde chez l’ensemble des patients testés accompagné d’une diminution de l’amplification et de la division cellulaire ainsi qu’un retard de différenciation. Ces résultats sont objectivés par la persistance des marqueurs d’immaturité CD34 et IL-3R ainsi que d’un retard d’apparition des marqueurs terminaux tels que la BAND3 ou l’alpha4-intégrine. L’étude transcriptionnelle et protéique met en évidence une stabilisation de p53, conduisant à une activation de ces cibles p21 et de bax. Le travail est finalisé pour HEATR3 (manuscrit en préparation) et en cours de finalisation pour HSPA14.L’étude sur le gène RPL9 grâce à un travail collaboratif a permis de mettre en évidence deux phénotypes différents en fonction du variant allélique identifié : un phénotype ABD pour un variant allélique de la 5’UTR ou un phénotype associé à un risque de cancer. L’étude de la différenciation érythroïde montre un impact sur la différenciation et la prolifération pour le variant lié à l’ABD uniquement. Parallèlement, une étude en collaboration sur le gène RPL13, a permis de confirmer le rôle spécifique de certaines protéines RP dans d’autres pathologies que l’ABD et d’ajouter une nouvelle maladie à la liste des ribosomopathies.Le facteur de croissance CECR1, identifié comme muté chez plusieurs familles du consortium EURODBA, représente un nouveau groupe de gènes pouvant être associés à la maladieDiamond-Blackfan anemia (DBA) is a congenital rare erythroblastopenia due to a blockage in the maturation of erythroid cells between the BFU-e and CFU-e stages. DBA is characterized by an aregenerative, usually macrocytic, anemia, associated with the total absence or less than 5% of erythroid precursors in the bone marrow. In 50% of DBA cases, anemia is associated with congenital malformations affecting the cephalic area and the extremities of the limbs and a growth delay. The DBA phenotype and genotype are heterogeneous, however a mutation in a ribosomal protein (RP) gene, always at heterozygous state, is found in 80% of cases. Up to date, 20 RP genes have been associated with DBA pathophysiology, establishing DBA as the first identified ribosomopathy. Mutations of these RP induce a defect in rRNA maturation. Therefore, for ribosome dysfunction, cell cycle arrest and p53-mediated apoptosis induction are responsible for erythroblastopenia in patients. More rarely, DBA may be the consequence of mutations present on a non-PR gene: the GATA-1 gene (major transcription factor of erythropoiesis), the TSR2 gene (interacting with the RPS26 protein and involved in ribosome biogenesis) or the EPO gene (erythropoiesis key cytokine) have been identified so far. However, 20% of the DBA patients are still not genotypically diagnosed, leaving room for the discovery of new candidate genes. In this perspective, the aim of my PhD was therefore to identify new candidate genes involved in DBA etiology and characterize their functional roles of in order to confirm their link with DBA. For this purpose, we sequenced exomes on 25 families and identified 8 candidate genes. In this manuscript, I will present my work as part of a bigger project to validate four new genes involved in BDA pathophysiology.RPL9 is a RP of the large 60S ribosomal subunit. Mutations in this gene lead to two different phenotypes depending on the allelic variant: a DBA phenotype for an allelic variant of the 5' UTR or a phenotype associated with a cancer risk. As part of a collaborative work that compared the two RPL9 variants, I showed that the DBA variant only has an impact on erythroid differentiation Compared to a healthy individual, patients presenting the DBA variant exhibit a reduced proliferation rate and a delay in the acquisition of erythroid markers. P53-dependent activation of p21 in those cells is most likely responsible for the cell cycle arrest. Activation of caspases sign an induction of apoptosis and is consistent with the reduced viability of erythroid progenitors. A collaborative study on the RPL13 gene confirmed the specific role of certain RP proteins in non-DBA diseases and added a new disease to the list of ribosomopathiesXRibosome chaperone proteins represent a new group of genes that may be associated with DBA. I investigated the proliferation, division, amplification, differentiation and viability of primary erythroid cells from patients with allelic variations in one of these genes: HEATR3. These experiments revealed a lack of erythroid proliferation, with a defect in cell division. The mRNA and protein quantifications showed a stabilization of p53, leading to an activation of its targets: p21, controlling cell cycle, and Bax, involved in apoptosis induction. We also observed a delay in differentiation with the persistence of CD34 and IL-3R immaturity markers and a delay in the appearance of terminal markers such as BAND3 or alpha4-integrin. The role of HSP70 controlling GATA1 localization in early stages of the erythroid differentiation was recently elucidated. In this work, I identified as a new candidate gene for DBA, a HSP70 family member, HSPA14, and I characterized the defects in erythroid differentiation induced by this variant. Furthermore, I was able to identify an association of DBA with a variant in CECR1 gene encoding an adenosine deaminase in several families of the EURODBA consortium
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Larburu, Natacha. "Etude structurale de la biogenèse de la petite sous-unité ribosomique humaine par cryo-microscopie électronique et analyse d'images." Thesis, Toulouse 3, 2015. http://www.theses.fr/2015TOU30336/document.
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La biogenèse des ribosomes eucaryotes est un processus complexe qui implique la production et l'assemblage de 4 ARNr et 80 protéines. La production des deux sous-unités du ribosome, 40S et 60S, débute dans le nucléole par la synthèse d'un long précurseur commun contenant les séquences des ARNr matures et se termine dans le cytoplasme où ont lieu les dernières étapes d'assemblage des protéines ribosomiques et de clivage des ARNr. La production de ribosomes nécessite la participation de plus de 200 co-facteurs, qui catalysent les clivages et modifications des ARNr, coordonnent leur repliement et leur association aux protéines ribosomiques, et assurent des étapes de contrôle-qualité. Ces protéines sont associées aux particules en cours de maturation et absentes des sous-unités matures. Cette voie de synthèse, globalement conservée chez les eucaryotes, a été principalement étudiée chez la levure. Cependant, des études récentes ont montré des différences importantes de ce processus entre levure et mammifères. Un des verrous importants pour comprendre la fonction des co-facteurs, est l'absence de données sur la structure des précurseurs des sous-unités ribosomiques. J'ai donc entrepris une étude structurale de l'assemblage cytoplasmique de la petite sous-unité ribosomique chez l'homme par cryo-microscopie électronique à transmission. Le but de ma thèse était de déterminer la structure 3D des précurseurs de la petite sous-unité ribosomique purifiés à différentes étape de leur maturation. Ce travail a été conduit en collaboration avec l'équipe du Pr. Ulrike Kutay (ETH Zurich) pour la purification des particules pré-40S à partir de cellules humaines. La première structure 3D de particule pré-40S intermédiaire purifiée en étiquetant le co-facteur LTV1 a été déterminée à 19Å de résolution. Dans un deuxième temps, la structure 3D de la particule pré-40S tardive purifiée à via RIO1(KD) a aussi été déterminée à 15Å de résolution. Ces données nous ont permis de proposer un modèle de localisation des co-facteurs sur les précurseurs de la petite sous-unité ribosomique et de montrer une nouvelle différence dans la formation de la petite sous-unité chez l'Homme comparé à la levure, du fait de la présence de la protéine RACK1 sur les particules pré-40S humaines. La comparaison des structures des précurseurs de la petite sous-unité obtenues a permis de mettre en lumière l'existence de remodelages structuraux de la particule pré-40S au cours de sa maturation. Ce travail met en lumière les premières structures 3D de particules pré-40S humaines et pose les fondements méthodologiques d'explorations futures de la dynamique structurale des particules pré-ribosomiquesRibosome biogenesis is a complex process that requires the production and the correct assembly of the 4 rRNAs with 80 ribosomal proteins. In Human, the production of the two subunits, 40S and 60S, is initiated by the transcription of a pre-ribosomal rRNA precursor to the mature 18S, 5.8S, and 28S rRNAs by the RNA polymerase I, which is chemically modified and trimmed by endo- and exoribonuclease, in order to form the mature rRNAs. The nascent pre rRNA associated with ribosomal proteins, small ribonucleoprotein particles (snoRNP) and so called co-factors leading to the assembly of an initial 90S particle. This particle is then split into pre-40S and pre-60S pre-ribosomal particles that fallow independent maturation to form the mature subunit into the cytoplasm. Production of eukaryotic ribosomes implies the transient intervention of more than 200 associated proteins and ribonucleoprotein particles, that are absent from the mature subunits. Synthesis of ribosome, globally conserved in eukaryotes, has been principally studied in yeast. However, recent studies reveal that this process is more complex in human compared in yeast. An important bottleneck in this domain is the lack of structural data concerning the formation of intermediate ribosomal subunits to understand the function of assembly factors. Determination of the structural remodeling of pre-ribosomal particles is crucial to understand the molecular mechanism of this complex process. So I have undertaken a structural study on the assembly of the small ribosomal subunit using cryo-electron microscopy and image analysis. The goal of my thesis is to determine the 3D structures of human pre-40S particles at different maturation stages to see the structural remodeling that occurs during the biogenesis of the small ribosomal subunit. We are collaborating with the group of Pr Ulrike Kutay at ETH Zurich, who purify human pre-40S particles. The 3D structures of human pre-40S particles purified at an intermediate and late maturation stages, has been determined with a resolution of 19 and 15Å respectively. Supplementary densities, compared to the mature subunit, indicate the presence of assembly factors and show the unexpected presence of the RACK1 protein in the precursor of the human small ribosomal subunit in the cytoplasm. The comparison of the 3D structures of human pre-40S particle allows showing the structural remodeling that occur during the maturation of the small ribosomal subunit. This work provides the first 3D structure of human pre-40S particles and laid the methodological foundations for future exploration of the structural dynamics of pre-ribosomal particles
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Quynh, Tran Hoang Thi. "Identification and functional characterization of trans-acting factors required for eukaryotic ribosome synthesis." Doctoral thesis, Universite Libre de Bruxelles, 2008. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/210540.
Full textAbstract:
Eukaryotic ribosome synthesis is a complex process that consumes a lot of energy and involves several hundreds of trans-acting factors that transiently associate with nascent ribosomes. Biogenesis of ribosomal subunits (the small 40S and the large 60S) starts with transcription of a long precursor ribosomal RNA (pre-rRNA) by RNA polymerase I (Pol I) in the nucleolus. This is a key step that globally controls yeast ribosome synthesis. The pre-rRNA, ‘the 35S transcript’, encodes the mature sequence (18S, 5.8S, and 25S) rRNA constituents of both the 40S and 60S subunits. The 35S transcript is subsequently modified, cleaved (processed) and assembled with numerous structural ribosomal proteins and ribosome synthesis factors (trans-acting factors) to form various ribosomal particles (pre-ribosomes, precursors to the 40S and 60S subunits) along ribosome assembly pathway. In the budding yeast Saccharomyces cerevisiae, it has been reported recently that the processing of the 35S nascent transcript and the assembly of pre-ribosomes occur concomitantly with Pol I transcription in the nucleolus. In this process, the growing Pol I transcript gradually assembles with pre-40S structural ribosomal proteins and ribosomal synthesis factors to form the so-called ‘SSU-processome’ or ‘90S pre-ribosome’, the earliest precursor of the 40S subunit. The SSU-processome/90S pre-ribosome localizes to the nucleolus and consists of the 35S pre-rRNA, the U3 small nucleolar (sno) RNA, about a dozen of 40S ribosomal proteins and more than forty ribosome synthesis factors. The U3 snoRNA and pre-40S ribosome synthesis factors are all implicated in the processing of the 35S precursor (at sites A0, A1 and A2) and therefore in the synthesis of the 18S rRNA component of the 40S subunit. Significantly, the association of the U3 snoRNA with the growing 35S transcript is important for pre-40S assembly, whereas its dissociation from the processed transcript (following cleavage at sites A0-A2) is crucial for the overall structural remodeling of the 18S rRNA and for the formation of pre-40S ribosomes from the earliest precursor 90S particles.
This thesis mostly addresses the identification and functional characterization of Esf2 and Bfr2, two novel 40S synthesis factors, components of the SSU-processome/90S pre-ribosome in yeast. Both proteins localize to the nucleolus and their genetic depletions lead to failure in the production of 40S subunits. In the absence of either factor, the 35S pre-rRNA is not processed at sites A0-A2 and the 18S rRNA is not synthesized. Also, pre-ribosome assembly is affected and pre-40S ribosomes fail to mature properly. Strikingly, in the absence of either factor, the U3 snoRNA remains associated with unprocessed 35S transcript within pre-ribosomes indicating that Esf2 and Bfr2 are required to dissociate U3 from pre-ribosomes. This process also involves RNP (ribonucleoprotein particle) unwinding activities of the putative RNA helicase Dbp8.
La biogenèse du ribosome eucaryote est un processus complexe qui consomme beaucoup d’énergie et implique plusieurs centaines de facteurs trans qui s’associent de manière transitoire avec les pré-ribosomes en cours de formation. La biogenèse des sous-unités ribosomiques (la petite sous-unité 40S et la grande sous-unité 60S) débute dans le nucléole par la synthèse d’un long précurseur d’ARN ribosomique (le pré-ARNr, dit 35S chez la levure Saccharomyces cerevisiae) par l’ARN Polymérase I (Pol I). Ceci constitue une étape clé dans le contrôle global de la synthèse du ribosome chez la levure. Le pré-ARNr 35S renferme les séquences des ARNr matures 18S (ARNr de la sous-unité 40S) et 5.8S et 25S (deux des trois ARNr de la sous-unité 60S). Le pré-ARNr 35S subit un long processus de maturation et d’assemblage au cours duquel il est modifié, clivé (on parle du « processing » du pré-ARNr) et s’assemble avec des protéines ribosomiques (« RP », composants structuraux des sous-unités ribosomiques matures) et de nombreux facteurs de synthèse (facteurs trans) pour former différentes particules pré-ribosomiques (précurseurs des sous-unités 40S et 60S).
Chez la levure S. cerevisiae, il a récemment été montré que le processing du pré-ARNr 35S et l’assemblage des pré-ribosomes se produisent de manière concomminante avec la transcription Pol I dans le nucléole. Ainsi, le transcrit Pol I en cours de synthèse s’assemble progressivement avec des facteurs de synthèse ainsi que des RP pour former le « SSU processome » ou « pré-ribosome 90S », tout premier précurseur de la petite sous-unité 40S. Le SSU processome/pré-ribosome 90S est localisé dans le nucléole et est consisté du pré-ARNr 35S naissant, du petit ARN nucléolaire (snoRNA) U3, d’une douzaine de RP de la petite sous-unité 40S et de plus de 40 facteurs de synthèse. Le snoRNA U3 et ces facteurs de synthèse sont tous impliqués dans les clivages du pré-ARNr 35S aux sites A0, A1 et A2, et donc dans la biogenèse de l’ARNr 18S. L’association du snoRNA U3 avec le pré-ARNr 35S naissant est importante pour l’assemblage du SSU processome/pré-ribosome 90S. Par ailleurs, sa dissociation après les clivages aux sites A0-A2 permet un remodelage structural général de l’ARNr 18S et la formation du « pré-ribosome 40S » à partir de la particule précoce 90S.
Au cours de cette thèse, nous avons identifié et caractérisé fonctionnelement chez la levure deux nouveaux facteurs de synthèse de la petite sous-unité 40S et composants du SSU processome/pré-ribosome 90S: Esf2 et Bfr2. Ces deux protéines sont localisées dans le nucléole. Leur déplétion entraîne une incapacité à produire la sous-unité ribosomique 40S. En l’absence d’Esf2 ou Bfr2, le pré-ARNr 35S n’est plus clivé aux sites A0-A2 et l’ARNr 18S mature n’est plus produit. L’assemblage des pré-ribosomes est aussi affecté, notamment la formation du pré-ribosome 40S. De manière importante, en l’absence de l’un ou l’autre de ces facteurs, le snoRNA U3 reste associé au pré-ARNr 35S non clivé au sein des pré-ribosomes, indiquant qu’Esf2 et Bfr2 sont requises pour la dissociation d’U3 des pré-ribosomes. Ce processus implique aussi Dbp8, une hélicase à ARN présumée.
Doctorat en sciences, Spécialisation biologie moléculaire
info:eu-repo/semantics/nonPublished
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Bouffard, Stéphanie. "Study of ribosome biogenesis factors in zebrafish neural progenitors." Thesis, Université Paris-Saclay (ComUE), 2017. http://www.theses.fr/2017SACLS228/document.
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Alors que la biogénèse des ribosomes a étéconsidérée comme un mécanisme ubiquiste, lesétapes de ce processus ont récemment étédémontrées comme étant tissu-spécifiques. Letoit optique (OT) du poisson-zèbre est un modèleapproprié pour étudier la prolifération cellulairepuisque les cellules à différents états dedifférenciation se trouvent dans des domainesséparés.Au cours de mon doctorat, j'ai examiné si lesgènes de la biogenèse des ribosomes peuventavoir des rôles spécifiques dans les cellulesprogénitrices neuroépithéliales (CPNe). Profitantd'une analyse transcriptomique antérieure, j'aid'abord examiné les nouveaux candidatsaccumulés dans les CPNe. J'ai décidé de meconcentrer sur proliferation-associated 2G4(pa2G4/ebp1) qui est exprimé de manièrepréférentielle dans les CPNe.Ce gène favorise ou réprime la proliférationcellulaire dans des organismes normaux oupendant la tumorigénèse. J'ai conçu une stratégiepour l'expression inductible et cellule-spécifiquede ce gène.Fibrillarin (Fbl), une méthyltranférasenucléolaire est également préférentiellementexprimée dans CPNe. Ce gène joue un rôleimportant dans le cancer. J'ai montré que lesmutants fbl présentaient des défauts OTspécifiques,en lien avec une apoptose massive etune absence de différenciation neurale. J'aiégalement démontré une diminution de l'activitéde traduction des ribosomes. En outre, lesmutants fbl montrent une progression de la phaseS altérée. Nos données suggèrent que fbl estessentiel à la prolifération des progéniteursneuronaux du poisson-zèbreWhile ribosome biogenesis has been consideredas an ubiquitous mechanism, steps of thisprocess have recently been shown to be tissuespecific. Zebrafish optic tectum (OT) is asuitable model to study cell proliferation sincecells at different differentiation states arespatially partitioned.During my PhD, I examined whether ribosomebiogenesis genes may have specific roles inneuroepithelial progenitor cells (NePCs).Taking advantage of a previous transcriptomicanalysis, I first screened for new candidatesaccumulated in NePCs. I decided to focus onproliferation-associated 2G4 (pa2g4/ebp1),which was expressed preferentially in NePCs.This gene promotes or represses cellproliferation in normal organisms or duringtumorigenesis. I designed a strategy for theinducible expression and cell specificexpression of this gene.Fibrillarin (Fbl), a small nucleolarmethyltransferase is also preferentiallyexpressed in NePCs. It plays an important rolein cancer. I showed that fbl mutants displayedspecific OT defects linked to a massiveapoptosis and an absence of neuraldifferentiation. I also demonstrated deficienciesin the ribosome translational activity.Additionally, fbl mutants showed impaired Sphaseprogression. Our data suggest that fbl isessential for the proliferation of zebrafishneuronal progenitors
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Deraze, Jérôme. "Epigenetic control of ribosome biogenesis homeostasis." Thesis, Paris 6, 2017. http://www.theses.fr/2017PA066342/document.
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La traduction est une activité cellulaire essentielle, réalisée par les ribosomes. Ces particules sont synthétisées dans le nucléole, ce qui nécessite l'expression coordonnée de 4 ARN ribosomaux, 80 protéines ribosomales, et plus de 200 facteurs d'assemblage. Leur biogenèse est complexe et sollicite plus de la moitié de l'énergie des cellules en prolifération. La quantité de ribosomes varie selon les conditions environnementales et métaboliques et de ce fait, leur synthèse est modulée en réponse à de nombreux stimuli. Plusieurs mécanismes coordonnent la biogenèse des ribosomes avec l'homéostasie cellulaire. L'un d'eux est la capacité des protéines ribosomiques à réguler l'expression des gènes à plusieurs niveaux. Ces fonctions effectuées hors du ribosome sont dites extraribosomales. Notre équipe a mis en évidence l'une de ces fonctions de la protéine ribosomale uL11 chez la Drosophile. Quand sa lysine 3 est triméthylée (uL11K3me3), elle interagit avec Corto, un facteur de transcription de la famille des Enhancers de Trithorax et Polycomb. L'étude de leur fixation à la chromatine montre que ces protéines se répartissent différemment à l'échelle du génome, et que uL11K3me3 est présente au niveau de gènes actifs enrichis en composants du ribosome. Nous avons généré les premiers allèles génétiques du gène uL11 chez la Drosophile, et décrivons la stratégie de crible moléculaire employée pour leur isolation. Finalement, nous avons étudié les allèles de uL11 dont la lysine 3 est mutée. Leurs phénotypes ressemblent à ceux des mutants Minute, suggérant que le domaine N-terminal de uL11 possède une fonction essentielle, mais peut-être indépendante d'une interaction avec CortoTranslation is an essential metabolic activity carried by ribosomes. These complexes are synthetized in the nucleolus, and require the coordinated expression of 4 ribosomal RNA, 80 ribosomal proteins, and more than 200 assembly factors. Indeed, their biogenesis is complex and expensive, consuming more than half of the energy in proliferating cells. As the cellular need for ribosomes varies with environmental or metabolic conditions, their synthesis is tightly regulated in response to a number of cues. Many mechanisms ensure that the intensity of ribosome biogenesis is coupled to cell homeostasis. Such is the ability of ribosomal proteins to regulate gene expression at many levels, from translation specificity to activation or repression of transcription. Many such functions are carried off the ribosome, and are thus termed extraribosomal. Our team discovered a new extraribosomal function of ribosomal protein uL11 in Drosophila. Indeed, when trimethylated on lysine 3 (uL11K3me3), it associates with Corto, a transcription factor of the Enhancers of Trithorax and Polycomb family. By studying their genome-wide binding profile on chromatin, we show that these proteins are distributed along different patterns, and that uL11K3me3 specifically binds a subset of active genes enriched in ribosome biogenesis components. Additionally, we generated the first genetic alleles for Drosophila uL11 and describe the molecular screening method that we employed. Last, we studied the uL11 alleles that delete or replace lysine 3. We describe that their Minute-like phenotypes suggest an essential role for the N-terminal domain of uL11, though it may be independent of its association with Corto
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Therizols, Gabriel. "Rôle des ribosomes et de leur biogenèse dans la tumorigenèse et la réponse aux traitements chimiothérapeutiques." Thesis, Lyon 1, 2014. http://www.theses.fr/2014LYO10083/document.
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Les cellules cancéreuses produisent une grande quantité de ribosomes afin de synthétiser les protéines nécessaires à leur prolifération rapide. Les mécanismes qui conduisent à cette augmentation de la production de ribosome ne sont que partiellement compris, mais ils semblent intimement liés à l'acquisition du phénotype tumoral. De plus, une nouvelle théorie propose que les ribosomes ne sont pas des effecteurs neutres de la traduction, mais qu'ils jouent un rôle direct dans la régulation de l'expression génique. Cette théorie se base sur l'observation que la composition des ribosomes est hétérogène en fonction des types cellulaires et des conditions environnementales. Dans ce contexte, j'ai étudié les liens entre les altérations des signaux qui contrôlent la biogenèse des ribosomes, tant au niveau quantitatif que qualitatif, et le développement du phénotype tumoral. Ce manuscrit rapporte trois études effectuées au cours de mon travail de thèse. Ces études ont permis d'identifier : i) un nouveau régulateur de la quantité de ribosomes, la LN-Nétrine-1 et ii) des modifications de la composition et de la fonction des ribosomes induites par des altérations génétiques (perte d'activité de p53) et par l'utilisation d'une molécule chimiothérapeutique, le 5- Fluorouracile. Ces perturbations de la quantité et de la fonction des ribosomes modifient le contrôle de la traduction des cellules et la croissance, la prolifération et la survie cellulaire. Il ressort de ces résultats que les ribosomes sont des éléments qui participent au contrôle de l'expression génique et qui jouent un rôle dans la pathologie cancéreuse et la réponse au traitement chimiothérapeutiqueCancer cells produce large amounts of ribosomes to synthesize the proteins required for their rapid proliferation. The mechanisms leading to this increase in ribosome production are only partly understood, but they are related to the acquisition of the tumor phenotype. In addition, a new theory proposes that ribosomes are not neutral effectors of translation, but have a direct role in the regulation of gene expression. This theory is based on the observation that ribosome composition is heterogeneous in different cell types and according to environmental conditions. In this context, I have analyzed the relationships between changes in signals that control ribosome biogenesis, both quantitatively and qualitatively, and the development of the tumor phenotype. This manuscript reports three studies made during this PhD program. These studies identified: i) a novel regulator of the amount of ribosomes, the LN-Netrin-1 and ii) changes in the ribosome composition and function induced by genetic alterations (loss of activity of p53) and by the use of a chemotherapeutic molecule, the 5-Fluorouracil. These perturbations of the amount and the function of ribosomes modify the translation control and cell growth, cell proliferation and cell survival. From these results it can be conclude that ribosomes are elements involved in the regulation of gene expression and play a role in cancer pathology and response to chemotherapy
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Sloan, Katherine. "The exosome and human ribosome biogenesis." Thesis, University of Newcastle Upon Tyne, 2012. http://hdl.handle.net/10443/1462.
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Exoribonucleases have many important functions in the cell including RNA processing, turnover and quality control. One of the key 3’-5’ exonucleases is the exosome, a multiprotein complex that has been extensively characterised in yeast. Many substrates that undergo maturation and/or degradation involving the yeast exosome have been identified and these include tRNAs, mRNAs, snRNAs, snoRNAs and rRNAs. By comparison, the human exosome is poorly understood and it is not clear whether functions of the yeast exosome are conserved in higher eukaryotes. We show that the human exosome has degradation functions including the turnover, but not the processing, of snoRNAs and the recycling of excised pre-rRNA fragments. We and others have shown that the human exosome also participates in pre-rRNA processing to form the mature 3’ end of 5.8S rRNA. Here we identify a novel role for the exosome in the processing of the pre-rRNA internal transcribed spacer 1 (ITS1). The small (18S) and large (5.8S and 28S) subunit rRNAs are co-transcribed as a single precursor. Processing of ITS1 is a key step in ribosome biogenesis as it separates 18S from the large subunit rRNAs and in higher eukaryotes it involves an additional processing step compared to yeast. We define alternative ITS1 processing pathways in human cells. In the major pathway, following an endonucleolytic cleavage to separate the small and large subunit rRNAs, the exosome, which is not involved in ITS1 processing in yeast, processes to within 25 nucleotides of the 3’ end of 18S. Our data highlight significant differences between the nucleases involved in ITS1 processing in yeast and humans. However, it appears that the roles of several yeast biogenesis factors are conserved in higher eukaryotes. Further, we have investigated mechanisms by which exonucleolytic processing of ITS1 may be regulated and suggest how this could be coordinated with the final maturation steps of the pre-40S complex.
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Jarzebowski, Léonard. "Unraveling variations in ribosome biogenesis activity in the mouse hematopoietic system at homeostasis in vivo." Thesis, Paris 6, 2016. http://www.theses.fr/2016PA066402/document.
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Les cellules souches (CS) se démarquent des progéniteurs et cellules différenciées à de nombreux égards. Notamment, les CS présentent des caractéristiques particulières dans des processus cellulaires fondamentaux, et il a été récemment proposé que la biogenèse des ribosomes (BiRi) participe à la régulation des CS. Pendant ma thèse, j’ai utilisé diverses approches pour étudier le rôle et la régulation de la BiRi dans des populations de CS, in vivo et ex vivo dans des modèles murins.Grâce à un modèle d’inactivation génétique du facteur de BiRi Notchless (Nle), j’ai participé à l’étude de son rôle dans le lignage hématopoïétique et l’épithélium intestinal adultes, et cours du développement embryonnaire précoce. In vivo, la perte constitutive de Nle entraîne une létalité embryonnaire, et j’ai montré ex vivo que l’inactivation de Nle dans des CS embryonnaires induit une réponse au stress ribosomique médiée par le suppresseur de tumeur p53, et des défauts de prolifération/survie. L’induction de la perte de Nle chez l’adulte active également p53 dans les CS hématopoïétiques et intestinale, entraînant leur rapide élimination.En parallèle, j’ai utilisé plusieurs méthodes pour mesurer l’activité de BiRi des progéniteurs immatures et CS hématopoïétiques (CSH) à l’homéostasie, in vivo chez la souris adulte. J’ai ainsi mis en évidence des variations de l’activité de BiRi dans ces populations, révélant notamment une activité de BiRi des CSH jusqu’ici insoupçonnée du fait de leur quiescence.Dans l’ensemble, mon travail renforce l’idée d’un rôle de la BiRi dans la régulation des CS, et apporte une meilleure compréhension de la régulation de ce processus dans le lignage hématopoïétiqueStem cells (SCs) differ from progenitors and differentiated cells on many aspects. Notably, SCs display particular characteristics in fundamental cellular processes, and ribosome biogenesis (RiBi) has recently been proposed to play an important role in the regulation of SCs. During my thesis, I have used various approaches to study the role and regulation of RiBi in SC populations, using in vivo and ex vivo mouse models.Using genetic inactivation of the RiBi factor Notchless (Nle), I have participated to the analysis of its role in the adult hematopoietic system and intestinal epithelium, and in the establishment of the first cell lineages during early embryogenesis. In vivo, constitutive Nle deficiency causes early embryonic lethality, and I showed ex vivo that Nle inactivation in embryonic SCs induces a ribosomal stress response mediated by the tumor suppressor p53, and proliferation/survival defects. Conditional Nle inactivation in the adult mouse also induces activation of p53 in hematopoietic and intestinal SCs in vivo, leading to their rapid elimination.In parallel, I have used different methods to analyze the RiBi activity of hematopoietic SCs (HSCs) and immature progenitors at homeostasis, in vivo in the adult mouse. Thus, I have unraveled variations in the RiBi activity of these populations, and notably uncovered previously unsuspected RiBi activity in HSCs despite their quiescent state.Altogether, my work supports the hypothesis of a role for RiBi in the regulation of SCs and provides better understanding of the activity of this process during hematopoietic differentiation
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D'Souza, Aaron Raynold. "Protein factors involved in the biogenesis of the mitochondrial ribosome." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/273764.
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The mammalian mitochondria contain their own genome which encodes thirteen polypeptide components of the oxidative phosphorylation (OxPhos) system, and the mitochondrial (mt-) rRNAs and tRNAs required for their translation. The maturation of the mitochondrial ribosome requires both mt-rRNAs to undergo post-transcriptional chemical modifications, folding of the rRNA and assembly of the protein components assisted by numerous biogenesis factors. The post-transcriptional modifications of the mt-rRNAs include base methylations, 2’-O-ribose methylations and pseudouridylation. However, the exact function of these modifications is unknown. Many mitoribosome biogenesis factors still remain to be identified and characterised. This work aims to broaden our understanding of two proteins involved in mitoribosome biogenesis through the study of the function of an rRNA methyltransferase and a novel biogenesis factor. Firstly, we characterised MRM1 (mitochondrial rRNA methyltransferase 1), a highly conserved 2’-O-ribose methyltransferase. We confirmed that MRM1 modifies a guanine in the peptidyl (P) transferase region of the 16S mt-rRNA that specifically interacts with the 3’ end of the tRNA at the ribosomal P-site. In bacteria, the modification is dispensable for ribosomal biogenesis and cell viability under standard conditions. However, in yeast mitochondria, Mrm1p is vital for ribosomal assembly and function. We generated knockout cells lines using programmable nuclease technology, and characterised the possible effects of MRM1 depletion on mitochondrial translation and mitoribosome biogenesis. We demonstrated that neither the enzyme nor the modification is required for human mitoribosomal assembly and translation in our experimental setup. Secondly, we identified a novel mitochondrially-targeted putative RNA endonuclease, YbeY. Using YbeY knockout cell lines, we showed that depletion of YbeY leads to loss of cell viability and OxPhos function as a consequence of a severe decrease in mitochondrial translation. Northern blotting and transcriptomic analysis using next generation RNA-Seq revealed transcript-specific changes to steady state levels. This analysis identified mt-tRNASer as a potential target of YbeY. We investigated the effect of YbeY deficiency on mitoribosomal assembly by quantitative sucrose gradient fractionation and mass spectrometry. This analysis showed that the mt-SSU is depleted in YbeY knockout cells. Further, immunoaffinity purification identified MRPS11 as a key interactor of YbeY. We propose that YbeY is a multifunctional protein that performs endonucleolytic functions in the mitochondria and also acts as a mitochondrial ribosome biogenesis factor, assisting small subunit assembly through its interaction with MRPS11.
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Lee, Chrissie Young. "Multiple mechanisms regulating ribosome biogenesis in Saccharomyces cerevisiae." Diss., Restricted to subscribing institutions, 2008. http://proquest.umi.com/pqdweb?did=1781954291&sid=2&Fmt=2&clientId=1564&RQT=309&VName=PQD.
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Saraf, Kritika. "Functional characterization of the connections between translation and ribosome biogenesis." Doctoral thesis, Universite Libre de Bruxelles, 2019. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/288480.
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Ribosomes are cellular nanomachines responsible for protein production in all living cells. When ribosome biogenesis is compromised, or ribosome function unfaithful, it causes diseases called ribosomopathies. The primary goal of my PhD was to understand the consequences of ribosome biogenesis dysfunction on translation. I have contributed to this understanding through four different projects which were aimed to understand how ribosome function affects the different steps of protein translation in the cell. In my first project, we tested if a ribosomal RNA sugar methylation present on the large ribosomal subunit plays a role in translation. We found that the loss of the modification does not grossly inhibit ribosome production or growth. However, these mutants are resistance towards G418, and make fewer decoding errors as compared to the control cells. In my second project, I studied a methyltransferase called Mtq2, which methylates the translation termination release factor eRF1. We found that Mtq2 is directly involved in late steps of large ribosomal subunit maturation and that the catalytic activity of Mtq2 is required for efficient 60S subunit production and for pre-60S export. In project 3, I studied a natural, plant-derived alkaloid called haemanthamine (HAE). We showed that HAE binds the peptidyl transferase center of the large subunit of the eukaryotic ribosome, where it interacts with the 25S rRNA. We also showed that HAE inhibit early stages of pre-rRNA processing and elicit nucleolar stress response in the cells. In project 4, I studied a long non-coding RNA called SAMMSON. SAMMSON plays a crucial role in melanoma survival. We found that depletion of SAMMSON adversely affects ribosome biogenesis. We also demonstrated that by modulating the binding affinity of a single protein, namely CARF, SAMMSON rewires the RNA-protein network and promotes a synchronized increase in rRNA maturation both in the cytosol and mitochondria, thereby boosting translation in both the cellular compartments.Les ribosomes sont des nanomachines cellulaires responsables de la production de protéines dans toutes les cellules vivantes. Lorsque la biogenèse des ribosomes est compromise ou que la fonction des ribosomes est infidèle, elle provoque des maladies appelées ribosomopathies. L'objectif principal de ma thèse était de comprendre les conséquences du dysfonctionnement de la biogenèse des ribosomes sur la traduction. J'ai contribué à cette compréhension par le biais de quatre projets différents visant à comprendre comment la fonction des ribosomes affecte les différentes étapes de la traduction des protéines dans la cellule. Dans mon premier projet, nous avons voulu determiner si une méthylation sur l’ARN ribosomique d’un sucre présente sur la grande sous-unité ribosomique joue un rôle dans la traduction. Nous avons constaté que la perte de cette modification n'inhibait pas grossièrement la production ou la croissance des ribosomes. Cependant, ces mutants sont résistants à G418 et font moins d’erreurs de décodage par rapport aux cellules contrôles. Dans mon deuxième projet, j'ai étudié une méthyltransférase appelée Mtq2, qui méthyle le facteur de libération de la terminaison de la traduction, eRF1. Nous avons constaté que Mtq2 est directement impliqué dans les dernières étapes de la maturation des grandes sous-unités ribosomiques et que l'activité catalytique de Mtq2 est nécessaire pour une production efficace de sous-unités 60S et pour une exportation antérieure à 60S. Dans le cadre du projet 3, j'ai étudié un alcaloïde naturel d'origine végétale appelé hémanthamine (HAE). Nous avons montré que HAE lie le centre de la peptidyl transférase de la grande sous-unité du ribosome eucaryote, où il interagit avec l'ARNr 25S. Nous avons également montré que HAE inhibe les stades précoces du traitement pré-ARNr et induit une réponse au stress nucléolaire dans les cellules. Dans le projet 4, j'ai étudié un long ARN non codant appelé SAMMSON. SAMMSON joue un rôle crucial dans la survie du mélanome. Nous avons constaté que sa perte d’expression affecte négativement la biogenèse des ribosomes. Nous avons également démontré qu'en modulant l'affinité de liaison d'une protéine unique, à savoir CARF, SAMMSON réarme le réseau ARN-protéine et favorise une augmentation synchronisée de la maturation de l'ARNr à la fois dans le cytosol et les mitochondries, renforçant ainsi la traduction dans les deux compartiments cellulaires.
Doctorat en Sciences
info:eu-repo/semantics/nonPublished
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Lackmann, Fredrik. "Nucleolar Ribosome Assembly." Doctoral thesis, Stockholms universitet, Institutionen för molekylär biovetenskap, Wenner-Grens institut, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-145639.
Full textAbstract:
Ribosomes are macromolecular machines that are responsible for production of every protein in a living cell. Yet we do not know the details about how these machines are formed. The ribosome consists of four RNA strands and roughly 80 proteins that associate with each other in the nucleolus and form pre-ribosomal complexes. Eukaryotes, in contrast to prokaryotes, need more than 200 non-ribosomal factors to assemble ribosomes. These associate with pre-ribosomal complexes at different stages as they travel from the nucleolus to the cytoplasm and are required for pre-rRNA processing. We do however lack knowledge about the molecular function of most of these factors and what enables pre-rRNA processing. Especially, information is missing about how non-ribosomal factors influence folding of the pre-rRNA and to what extent the pre-ribosomal complexes are restructured during their maturation. This thesis aims to obtain a better understanding of the earliest events of ribosome assembly, namely those that take place in the nucleolus. This has been achieved by studying the essential protein Mrd1 by mutational analysis in the yeast Saccharomyces cerevisiae as well as by obtaining structural information of nucleolar pre-ribosomal complexes. Mrd1 has a modular structure consisting of multiple RNA binding domains (RBDs) that we find is conserved throughout eukarya. We show that an evolutionary conserved linker region of Mrd1 is crucial for function of the protein and likely forms an essential module together with adjacent RBDs. By obtaining structural information of pre-ribosomal complexes at different stages, we elucidate what structuring events occur in the nucleolus. We uncover a direct role of Mrd1 in structuring the pre-rRNA in early pre-ribosomal complexes, which provides an explanation for why pre-rRNA cannot be processed in Mrd1 mutants.At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 4: Manuscript.
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Brombin, Alessandro. "Functional study of the role played by nucleolar proteins in the control of neural progenitor homeostasis using zebrafish as a model." Thesis, Paris 11, 2015. http://www.theses.fr/2015PA112237/document.
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L’identité des cellules souches et des progéniteurs neuraux, comme celle de tout type cellulaire, est caractérisée par des signatures moléculaires spécifiques qui dépendent de l’environnement dans lesquelles les cellules se trouvent. Ainsi, il est primordial d’étudier ces cellules dans un contexte in vivo. Le toit optique du poisson zèbre est un modèle idéal pour ce type d’étude. En effet, c’est une large partie du cerveau moyen localisée en position dorsale et qui présente la particularité de croitre de manière orientée tout au long de la vie de l’animal grâce aux cellules neuroépitheliales présentes à sa périphérie (dans la « peripheral midbrain layer », PML). De plus, les progéniteurs neuroépithéliaux, les progéniteurs lents et les cellules post-mitotiques sont localisées dans des domaines adjacents du toit, conséquence de sa croissance orientée. Chaque population cellulaire est marquée par des profils d’expression particuliers. Ainsi, une recherche dans la base de données ZFIN nous a permis d’identifier environ 50 gènes ayant une forte expression dans les cellules de la PML (progéniteurs neuroépithéliaux). De façon intéressante, beaucoup de « gènes PML » codent pour des facteurs de la biogenèse des ribosomes. L’accumulation de ce type de transcrits dans les progéniteurs lents était surprenante. Ainsi, au cours de mon doctorat, j’ai étudié le rôle spécifique des facteurs de la biogenèse des ribosomes dans le maintien des cellules neuroepithéliales de la PML. En effet, bien qu’il soit généralement admis que la biogenèse des ribosomes est un processus essentiel dans toutes les cellules, il a été récemment démontré que plusieurs facteurs nécessaires à la synthèse des ribosomes ont un rôle tissu-spécifique. Par exemple, Notchless est requis pour la survie de la masse cellulaire interne de l’embryon préimplantatoire de souris. Récemment, des expériences de knock-out conditionnel chez la souris ont montré que Notchless était nécessaire au maintien des cellules souches hématopoïétiques et intestinales, mais pas à celui des cellules différenciées. En effet, en absence de Notchless dans les cellules souches, la grosse sous-unité ribosomique (60S) ne peut pas être exportée hors du noyau et s’accumule. Au contraire, dans les cellules différenciées, où Notchless n’est pas indispensable, cette accumulation n’est pas observée. J’ai commencé une étude fonctionnelle basée sur la surexpression conditionnelle de la forme dominante-négative du gène notchless homolog 1 (nle1, homologue poisson zèbre du gène Notchless mammifère). Selon mon hypothèse, les progéniteurs lents de la PML (Slow amplifying progenitors, SAPs) pourraient avoir besoin de Notchless pour la maturation de la sous-unité 60S, contrairement aux cellules différenciées qui pourraient survivre après la délétion de ce gène. Des expériences sont encore en cours, mais nous avons déjà pu démontrer que nle1 joue un rôle crucial dans la survie des progénitéurs neuroépithéliaux de la PML. En parallèle, j’ai étudié des lignées de poisson-zèbre mutantes pour des gènes codants pour des composants du complexe de snoRNP (box C/D small nucleolar ribonucleoprotein : Fibrillarine, Nop56, Nop58). Les trois mutants présentent des phénotypes similaires, en particulier une apoptose massive et une dérégulation du cycle cellulaire dans l’ensemble du toit optique à 48 heures de développement. Étonnamment, ces résultats sont en faveur d’un arrêt du cycle cellulaire à la transition G2/M. Ainsi, cette étude pourrait permettre de mettre en évidence de nouveaux mécanismes d’arrêt du cycle cellulaire lors de défauts de biogenèse des ribosomes. L’ensemble de ces résultats montrent comment les facteurs de la biogenèse des ribosomes (tout comme le processus) contribue à la régulation fine de l’homéostasie cellulaire, et donc à la détermination de l’identité des cellules progénitricesIn neural stem cells (NSCs) and neural progenitors (NPs), as in other cell types, cell identity is characterized by specific molecular signatures that depend on the environment provided by neighboring cells. Thus, it is important to study progenitor cells in vivo. The zebrafish optic tectum (OT) is a suitable model for that purpose. Indeed, this large structure of the dorsal midbrain displays life-long oriented growth supported by neuroepithelial cells present at its periphery (in the peripheral midbrain layer, PML). Moreover, neuroepithelial progenitors, fast-amplifying progenitors and post-mitotic cells are found in adjacent domains of the OT, as a consequence of its oriented growth. Each cell population is marked by concentric gene expression patterns. Interestingly, a datamining of the ZFIN gene expression database allowed us to identify around 50 genes displaying biased expression in PML cells (neuroepithelial progenitors). Interestingly, many “PML genes” code for ribosome biogenesis factors. The accumulation of transcripts for such ubiquitously expressed genes in SAPs was very surprising so during my thesis I examined whether ribosome biogenesis may have specific roles in these neuroepithelial cells, while improving our knowledge. Indeed, although it is generally admitted that ribosome biogenesis is essential in all cells, it has been shown quite recently that several components of the ribosome biogenesis have tissue restricted roles. For example, Notchless is required for the survival of the inner cell mass in the preimplantation mouse embryo. More recently, conditional knock-out experiments in mice showed that Notchless is necessary for the maintenance of hematopoietic stem cells and intestinal stem cells, but not for committed progenitors and differentiated cells. Indeed in the absence of Notchless in stem cells, the immature 60S subunit cannot be exported from the nucleus and accumulates. This does not happen in differentiated cells where Notchless is dispensable. I started a functional study based on the conditional overexpression of a dominant-negative form of the gene notchless homolog 1 (nle1, the zebrafish homolog of the mammalian gene Notchless). My hypothesis was that the PML slow-amplifying progenitors (SAPs) may require Notchless for the maturation of the 60S subunit, but not the differentiated cells which could survive also after the deletion of this gene. Experiments are still underway. So far we could demonstrate that nle1 has a crucial role in SAPs. I studied zebrafish mutants for genes coding for the components of the box C/D small nucleolar ribonucleoprotein (snoRNP) complex (Fibrillarin, Nop56, Nop58). Mutants displayed a similar phenotype with massive apoptosis and a deregulation of the cell cycle in the whole tectum at 48hpf. Our data suggest a cell cycle arrest at the G2/M transition, highlighting novel possible mechanisms of cell cycle arrest upon impaired ribosome biogenesis. All together, these data highlight how ribosome biogenesis factors and the whole ribosome biogenesis contribute to the fine regulation of cell homeostasis thereby contributing to the determination of progenitor cell identity
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Shayan, Azad Seyed Ramtin. "Analyse structurale de la biogenèse de la petite sous-unité ribosomique eucaryote par cryo-microscopie électronique et analyse d'images." Thesis, Toulouse 3, 2019. http://www.theses.fr/2019TOU30128.
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L'assemblage des deux sous-unités ribosomiques (appelées 40S et 60S chez les eucaryotes) est un processus complexe, qui nécessite l'intervention de plus de 200 co-facteurs de maturation (CFM). Pour former des sous-unités ribosomiques matures et fonctionnelles, les CFM sont nécessaires à la maturation des ARN ribosomiques (ARNr), mais également à leur repliement correct et à leur assemblage avec les protéines ribosomiques (Rps). Malgré une identification quasi-exhaustive de ces CFM chez la levure et l'humain, leur fonction moléculaire précise reste à élucider. Par ailleurs, des défauts dans la synthèse des ribosomes ont récemment été associés à une liste croissante de maladies génétiques humaines (appelées ribosomopathies) et de cancers, ce qui nécessite une compréhension précise de chaque étape des mécanismes de biogenèse des ribosomes. De nombreuses études moléculaires et fonctionnelles ont récemment permis de définir plusieurs étapes successives de maturation cytoplasmique des particules pré-40S eucaryotes. Il est maintenant crucial d'intégrer ces descriptions moléculaires très détaillées des événements de maturation des ribosomes dans une vision tridimensionnelle de l'assemblage des ribosomes, et de comprendre le remodelage structural que les particules pré-ribosomiques peuvent subir au cours de leur maturation. Dans ce but j'ai déterminé, par cryo-microscopie électronique en transmission et analyse d'images, la structure 3D de précurseurs de la petite sous-unité ribosomique, purifiés à différentes étapes de maturation, chez l'Homme et la levure. Dans un premier temps, j'ai utilisé le CFM Tsr1 comme appât de purification dans des levures de phénotype sauvage, et déterminé la structure haute résolution de ces particules pré-40S cytoplasmiques. Ceci m'a permis de mettre en évidence trois étapes de maturations successives, commençant par l'autophosphorylation et le relargage du CFM Ltv1 et aboutissant à la flexibilité de la plateforme de la particule pré-40S. Ensuite, en collaboration avec le Dr Brigitte Pertschy (Graz, Autriche) j'ai déterminé la structure de particules pré-40S cytoplasmiques de levure, portant une mutation sur la protéine Rps20.Ceci a permis de mieux caractériser le rôle de Rps20 dans le relargage des CFM Rio2 et Ltv1 lors de l'assemblage de la sous-unité 40S. Enfin, j'ai déterminé la structure 3D des particules pré-40S humaines purifiées à un stade cytoplasmique tardif, à une résolution de 3 Å. Ce travail a été mené en collaboration avec l'équipe du Pr. Ulrike Kutay (ETH Zurich). Cette analyse nous a permis de localiser pour la première fois le CFM RIO1 sur les particules pré-40S cytoplasmiques tardives. En outre, nos résultats nous ont permis de mettre en lumière l'existence de remodelages structuraux inédits dans les dernières étapes de la maturation de la petite sous-unité ribosomique humaineRibosome assembly is a complex process that requires the intervention of more than 200 assembly factors (AFs). These proteins are essential for the processing and modification of ribosomal RNAs, as well as the structural assembly of ribosomal subunits. This mechanism, highly studied in yeast, generally conserved in eukaryotes, but has become more complex with evolution in higher eukaryotes. In addition, defects in ribosome synthesis have recently been associated with a list of human genetic diseases (called ribosomopathies) and cancers, via ribosome biogenesis disease. Numerous molecular and functional studies then made it possible to define several successive stages of cytoplasmic maturation of pre-40S particles in human and yeast. It is now crucial to incorporate these highly detailed molecular descriptions of ribosome maturation events into a three-dimensional view of ribosome assembly and to understand the structural remodeling of pre-ribosomal maturation particles. Using tandem purification methods, coupled with cryo-electron microscopy and isolated particle analysis, I have determined several high-resolution 3D structures of cytoplasmic pre-40S particles, in yeast and human, at different maturation steps. First, i determined the 3D structure of the pre-40S particles, purified using AF Tsr1-FPZ as a bait at 3.1 Å resolution. Structural heterogeneity tests indicated that the beak and platform domains are dynamic zones, and sheds new light on the structural remodeling events occurring during 40S subunit assembly. Moreover, in collaboration with the team of Dr. Brigitte Pertschy, we have determined the 3D structure of yeast cytoplasmic pre-40S particles carrying point mutations on Rps20. Our atomic models have allowed to highlight a close relationship between the correct assembly of Rps20 and the release of AFs Ltv1 and Rio2 from the maturing small ribosomal subunit. Finally, I also determined the 3D structures of human pre-40S particles trapped at a very late cytoplasmic maturation step, with a resolution of ~3 Å. This work was performed in collaboration with Prof. Ulrike Kutay's team (ETH Zurich). These data allowed us to uncover new steps in the cytoplasmic maturation of human pre-40S particles. This structural study allows us to propose new molecular mechanisms underlying the final steps of eukaryotic ribosomal assembly
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Cerezo, Emilie. "Contribution de la signalisation RSK à la synthèse de la petite sous-unité ribosomique humaine." Thesis, Toulouse 3, 2021. http://www.theses.fr/2021TOU30288.
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La biogenèse des ribosomes assure l'approvisionnement en ribosomes dans la cellule pour subvenir aux besoins en synthèse protéique. La production des ribosomes est un processus très couteux en énergie. Elle mobilise les trois ARN polymérases (Pol), la machinerie de traduction, le transport nucléo-cytoplasmique, ainsi qu'une succession complexe d'étapes de maturations qui implique plus de 200 facteurs d'assemblage et de maturation (AMF). Dans les cellules de mammifères en prolifération, le taux de synthèse des ribosomes a été estimé à 7500 sous-unités ribosomiques par minute, ce qui nécessiterait l'apport de ~300 000 protéines ribosomiques (RP), 150 petits ARN nucléolaires (snoARN) par ARN précurseur, et un nombre élevé d'AMF. Ce processus très énergivore est finement régulé par des mécanismes qui coordonnent de manière dynamique les niveaux de production de ribosomes aux besoins de la cellule. Ces régulations permettent notamment d'éviter des pertes importantes en énergie cellulaire qui résulteraient d'une production inutile de ribosomes. Au cours de mon doctorat, j'ai étudié des évènements précis de régulation de la biogenèse des ribosomes orchestrés par la voie de signalisation Ras-MAPK/ERK. Cette voie de signalisation est l'un des principaux acteurs de la croissance et de la prolifération cellulaire. ERK et sa kinase effectrice RSK stimulent trois événements clés de la biogénèse des ribosomes : la transcription Pol I/Pol III, le transport nucléo-cytoplasmique et la traduction. Cependant, aucun substrat de cette voie n'a été clairement identifié dans les étapes post-transcriptionnelles de la biogenèse des ribosomes, à savoir les étapes d'assemblage et de maturation des ribosomes. Mes travaux ont permis d'identifier la kinase atypique RIOK2 comme une nouvelle cible de la kinase effectrice RSK. Nous avons découvert que la phosphorylation de RIOK2 par RSK favorise sa dissociation des particules pré-40S, facilitant ainsi la production de la particule mature 40S. Outre ces résultats, nous avons également identifié et caractérisé des partenaires proches de RIOK2 dans la cellule. Cette analyse ouvre la voie vers de nouvelles connexions entre RIOK2, ou d'autres AMF, et des processus intracellulaires clés autres que la synthèse des ribosomes. Dans l'ensemble, ma thèse aura contribué à la découverte de nouvelles perspectives de recherche dans la régulation des étapes de maturation des ribosomes. L'identification de nouveaux mécanismes de régulation pourrait aider à mieux intégrer les phénotypes associés à des dérégulations de la biogenèse des ribosomes, en conditions physiologiques ou pathologiquesRibosome biogenesis feeds the cellular needs in protein synthesis by synthetizing translation-competent ribosomes. This highly energy-consuming process mobilizes the three RNA polymerases (Pol) and the translational machinery, active import and export through the nucleo-cytoplasmic network, as well as an intricate maturation pathway that involves more than 200 assembly and maturation factors (AMFs). In proliferating mammalian cells, the synthesis rate of ribosomes has been estimated at 7500 ribosomal subunits per minutes, requiring ~300 000 ribosomal proteins (RPs), 150 small nucleolar RNAs (snoRNAs) per pre-rRNA and an even higher number of AMFs. This fuel-consuming cellular process is tightly regulated by mechanisms that dynamically coordinate ribosome levels with cell requirements, thereby preventing energy waste due to production of unnecessary ribosomes. During my thesis, I studied discrete ribosome biogenesis regulatory events orchestrated by the Ras-MAPK/ERK signaling pathway. This signaling pathway is one of the main actor of cell growth and proliferation. ERK and its downstream effector kinase RSK stimulate three key events of ribosome biogenesis: Pol I/Pol III transcription, nucleo-cytoplasmic transport, and translation. However, no substrate of this pathway has been clearly identified in the post-transcriptional steps of ribosome biogenesis, namely ribosome assembly and maturation. My study identified the kinase RIOK2 as a new target of RSK kinase. We found that phosphorylation of RIOK2 by RSK promotes its dissociation from pre-40S particles, thereby facilitating the completion of small ribosomal subunit synthesis. Beside these findings, we have characterized the RIOK2 proximal interactome. Analysis of the proteins spatially close to RIOK2 paves the way to new connections between RIOK2, as well as other AMFs, and key intracellular processes other than ribosome biogenesis. Altogether, my thesis contributed to the discovery of novel insights into the regulation of ribosome maturation steps. Identification of novel regulatory events may help better integrating phenotypes associated with deregulation of ribosome biogenesis, during both physiological changes and diseases
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Kaczanowska, Magdalena. "Study of the link between translation termination and ribosome biogenesis /." Stockholm : Institutionen för genetik, mikrobiologi och toxikologi, Univ, 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-288.
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Knight, John. "Regulation of SIRT1 protein in cancer metabolism and ribosome biogenesis." Thesis, University of York, 2011. http://etheses.whiterose.ac.uk/2214/.
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The deacetylase signalling enzyme SIRT1 has been subject of much research interest, in part due to its ability to promote the survival of cancer cells, and redundancy in non-cancer cell viability. The deacetylation and downregulation of p53 and the FOXO family of tumour suppressors has been identified among the downstream effects of SIRT1 in cancer. Importantly, the regulation of cancer cell survival upstream of SIRT1 has not been well characterised, creating the possibility of targeting SIRT1 via its endogenous regulatory mechanisms for anti-cancer therapeutic gain. This Thesis validates two putative anti-cancer targets that promote SIRT1 activity and have also been implicated in essential processes that are commonly aberrant in cancer: cellular metabolism and translational control. SIRT1 is a sirtuin, which are unique deacetylases due to their requirement for the redox metabolite NAD+ as a co-enzyme. The potential to promote SIRT1 activity via provision of NAD+ is analysed here by targeting the metabolic enzyme lactate dehydrogenase A (LDH-A). LDH-A catalyses NAD+ production and promotes aberrant cancer metabolism by perpetuating the Anaerobic Glycolysis cycle. A link is found between cancer metabolism and SIRT1 activity, with LDH-A observed to suppress cancer cell apoptosis via a mechanism consistent with SIRT1 activation. SIRT1 is also subject to regulation by direct interaction with the protein AROS (Active Regulator Of SIRT1). AROS associates with and promotes SIRT1 pro-survival function in cancer cells. Here, AROS is found to specifically promote cancer cell survival, via a mechanism appearing to involve SIRT1 and downstream substrates. However, AROS regulation of SIRT1 is not as simple as originally thought, varying by cell context and substrate. Further to its role in directing SIRT1 activity, AROS also forms a binding interaction with the ribosomal protein RPS19. The effect of AROS upon RPS19 protein and function is analysed for the first time, revealing a role for AROS in 40S ribosomal subunit biogenesis. Beyond this, AROS is discussed as a regulator of translation, and the functional interplay between RPS19, AROS and SIRT1 is described. This provides a link between cancer associated anti-apoptotic signalling and ribosome biogenesis centred on regulation of SIRT1 activity, which could be exploited by anti-cancer therapeutics.
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Armistead, D. Joy. "Role of EMG1 in Bowen-Conradi syndrome and in ribosome biogenesis." The American Society of Human Genetics, 2009. http://hdl.handle.net/1993/23413.
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Bowen-Conradi syndrome is a lethal autosomal recessive disorder affecting Hutterite infants, characterized by severe growth and psychomotor retardation, and leading to death at an average age of thirteen months. Linkage analysis and sequencing identified an A>G mutation in EMG1 as the probable cause of the disease. This gene is implicated in ribosome biogenesis, and the mutation results in an unstable EMG1 protein. The reduction in available EMG1 causes a transient delay in processing of the ribosomal small subunit 18S rRNA, leading to cell cycle delay at G2/M and a subsequent reduction in cell proliferation rates in patient lymphoblasts. A mouse model of Bowen-Conradi syndrome also displayed severe developmental delay, with prominent effects in the cranial central nervous system. Embryos died prematurely during development, probably due to decreased proliferation rates accompanied by apoptosis. These results shed light on the etiology of Bowen-Conradi syndrome, and open the door for development of treatments.
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Choudhury, Priyanka [Verfasser]. "Functional analyses of RNA helicases in human ribosome biogenesis / Priyanka Choudhury." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2019. http://d-nb.info/1222738171/34.
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Pelava, Andria. "Human ribosome biogenesis and the regulation of the tumour suppressor p53." Thesis, University of Newcastle upon Tyne, 2017. http://hdl.handle.net/10443/3561.
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Ribosome production is an energetically expensive and, therefore, highly regulated process. Defects in ribosome biogenesis lead to genetic diseases called Ribosomopathies, such as Dyskeratosis Congenita (DC), and mutations in ribosomal proteins and ribosome biogenesis factors are linked to multiple types of cancer. During ribosome biogenesis, the ribosomal RNAs (rRNAs) are processed and modified, and defects in ribosome biogenesis lead to the activation of p53. This project aimed to investigate the functions of Dyskerin, mutated in X-linked DC, in human ribosome biogenesis and p53 regulation, and to explore the link between ribosome production and p53 homeostasis. Dyskerin is an rRNA pseudouridine synthase and required for telomere maintenance. There is some debate as to whether DC is the result of telomere maintenance or ribosome biogenesis defects. It is shown here that human Dyskerin is required for the production of both LSU and SSU, and knockdown of Dyskerin leads to p53 activation via inhibition of MDM2 via the 5S RNP, an LSU assembly intermediate which accumulates after ribosome biogenesis defects. My data indicate that p53 activation, due to defects in ribosome biogenesis, may contribute to the clinical symptoms seen in patients suffering with DC. In addition, it is shown that defects in early or late stages of SSU or LSU biogenesis, result in activation of p53 via the 5S RNP-MDM2 pathway, and that p53 is induced in less than 12 hours after ribosome biogenesis defects. SSU defects do not cause any obvious defects in LSU production, but they result in inhibition of export of the pre-LSU in the cytoplasm, suggesting that p53 activation after SSU defects is probably due to defects in pre-LSU export. Finally, there are evidence that RPS27a or RPL40, two ribosomal proteins produced as ubiquitin-fusion precursors in the cell, might be novel regulators of the 5S RNP-MDM2 pathway. In conclusion, this work shows the importance of ribosome biogenesis in the regulation of p53 for the development of Ribosomopathies and cancer.
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Essongue, Aurore Hélène. "Mise en évidence des réponses cellulaires indépendantes de p53 induites par l’inhibition de la biogénèse des ribosomes." Thesis, Paris 5, 2014. http://www.theses.fr/2014PA05T057/document.
Full textAbstract:
La biogénèse des ribosomes consiste à assembler les ARN ribosomiques (ARNr) et les protéines ribosomiques de la petite sous unité (RPSs) ou de la grande sous unité (RPLs) afin de former les sous unités 40S et 60S du ribosome. Ce processus est l’un des plus complexes des cellules dont il utilise une grande quantité des ressources. Un taux élevé de biogénèse des ribosomes est une caractéristique de la prolifération cellulaire dans les conditions physiologiques ou pathologiques. L’inhibition de la biogénèse des ribosomes active un checkpoint du cycle cellulaire qui induit un arrêt du cycle cellulaire, et selon le contexte, l’apoptose. L’activation de ce checkpoint est due au facteur suppresseur de tumeur p53 qui s’accumule lorsque la biogénèse des ribosomes est inhibée grâce à l’inhibition de son facteur de dégradation, l’ubiquitine ligase E3 MDM2. Cette inhibition de MDM2 se fait par la fixation d’un complexe formé par les protéines ribosomiques RPL11 et RPL5 et l’ARNr 5S. Des études ont montré le potentiel thérapeutique de l’activation de ce checkpoint dans des cancers caractérisés par une biogenèse ribosomique élevée. Par contre l’activation de p53 semble avoir un rôle pathologique dans les ribosomopathies, un ensemble de pathologies causées par un défaut dans la biogénèse des ribosomes comme l’anémie macrocytaire de Diamond-Blackfan (ABD). p53 est clairement impliqué dans les effets anti-prolifératifs de l’inhibition de la biogénèse des ribosomes, cependant de nombreuses évidences montrent l’existence de mécanismes indépendants de p53 qui affectent l’homéostasie cellulaire. On observe par exemple dans l’ABD, des mutations de RPL11/RPL5 dont la déplétion in-vitro n’induit pas p53. Mon travail de thèse a consisté à élucider les mécanismes mis en place par les cellules pour répondre à l’inhibition de la biogénèse des ribosomes, dans un modèle in-vitro de lignées cellulaires. Dans ces lignées, nous avons inhibé la biogénèse des ribosomes par déplétion des RPs de la grande ou de la petite sous unité, indépendamment de l’induction ou pas de p53, à savoir, RPs6, RPL7a et RPL11. Nous avons mis en évidence des liens entre l’inhibition de la biogénèse des ribosomes et l’homéostasie du réticulum endoplasmique, ou la régulation de l’expression de gènes du métabolisme tels que l’enzyme oncogénique PHGDHRibosome biogenesis is the process that leads to the assembly of ribosomal RNA (rRNA) and ribosomal proteins of the small (RPS) or the large (RPL) subunit into ribosomal 40S and 60S subunits. This is a highly complex process in the cells which uses a large amount of energy and resources. High rate of ribosome biogenesis is a trait of cell proliferation in physiological or pathogenic conditions. Inhibition of ribosome biogenesis activates a cell cycle checkpoint which induces a cell cycle arrest, and apoptosis. Activation of this checkpoint is due to the inhibition of ubiquitin ligase E3 MDM2, which does not anymore address the tumor suppressor factor p53 to proteasome. The p53 tumor suppressor factor then accumulates in cells and blocks the cell cycle progression. The inhibition of MDM2 is caused by the binding of a complex formed by RPL11, RPL5 and rRNA 5S. Few studies reveal that activation of this checkpoint has a therapeutic effect on cancer cells characterized by high rate of ribosome biogenesis. However, p53 activation seems to have pathogenic effects in ribosomopathies, a set of disorders characterized by ribosome biogenesis impairment, like Diamond-Balckfan macrocytic anemia (DBA). It is clear that p53 has anti-proliferative effects when ribosome biogenesis is inhibited, but evidences show that p53independants mechanisms also exist. In DBA for example, mutations in RPL5 and RPL11 that do not lead to p53 activation are observed. The goal of this study was to investigate the cellular mechanisms induced in response to inhibition of ribosome biogenesis. These investigations have been performed in an in-vitro system of cell lines. In those cell lines, ribosome biogenesis has been inhibited by depletion of RPs of the 40S or 60S ribosomal independently of p53 status. We brought out links between inhibition of ribosome biogenesis and endoplasmic reticulum homeostasis, or metabolic genes expression regulation like oncogene PHGDH