Les cellules souches ont attiré l’attention du public ces dernières années, grâce non-seulement à leur utilisation comme thérapies visant à s’attaquer à certains types de cancers, mais aussi en relation avec leur potentiel dans le domaine de la médecine regénérative. Il est établi que le destin cellulaire des cellules souches embryonnaires (ESC) est régulé de façon intensive par un groupe de facteur clés agissant sur leur pluripotence. Il est néanmoins envisageable que certains déterminants influençant l’auto-renouvellement et la différenciation de ces cellules soient toujours inconnus. Afin de tester cette hypothèse, nous avons généré, en utilisant une méthode par infections virales, une collection de ESC contenant des délétions chromosomales chevauchantes que nous avons baptisée DelES (Deletion in ES cells). Cette librairie contient plus de 1000 clones indépendants dont les régions délétées couvrent environ 25% du génome murin. À l’aide de cette ressource, nous avons conduit un criblage de formation de corps embryoïdes (EB), démontrant que plusieurs clones délétés avaient un phénotype de différenciation anormal. Nos études de complémentation sur un groupe de clones ont par la suite permis l’identification de Rps14 - un gène codant pour une protéine ribosomale (RP) comme étant haploinsuffisant pour la formation de EB. Dans un deuxième temps, l’analyse approfondie des résultats de notre crible a permis d’identifier un groupe de gènes codants pour des RP qui semblent essentiels pour la différenciation des ESC, mais dispensables pour leur auto-renouvellement. De manière intéressante, les phénotypes anormaux de formation en EB les plus marqués sont associés à des délétions de RP qui se retrouvent au site de sortie des ARN messagers (ARNm) du ribosome, soit Rps5, Rps14 et Rps28. Étonnament, alors qu’un débalancement des RP conduit généralement à une réponse de type p53, l’haploinsuffisance de ces trois gènes ne peut être renversée par une simple réduction des niveaux d’expression de ce gène suppresseur de tumeurs. Finalement, nos études de profilage polysomal et de séquençage à haut-débit montrent une signature spécifique de gènes liés au mésoderme chez un clone hétérozygote pour Rps5, suggérant ainsi une explication au phénotype de différenciation p53-indépendant identifié chez ces ESC. Nos travaux rapportent donc la création d’une ressource intéressante de génomique fonctionnelle qui a permis de mettre à jour le rôle essentiel que jouent les RP dans le processus de formation de EB. Nos résultats permettent aussi de documenter une réponse p53-indépendante suite à un débalancement de RP dans un contexte opposant l’auto-renouvellement et la différenciation des ESC. / Stem cells have captured public’s attention in the last years, thanks to their involvement in cancer therapies and also their huge theoretical potential in the regenerative medicine field. In order to translate this new technology to the clinic, a better understanding of their regulatory mechanisms is still needed. It is well established that mouse embryonic stem cell (ESC) fate is highly regulated by core pluripotency factors. However, it is conceivable that novel self-renewal or differentiation regulators are not yet described. To investigate this possibility, we used a viral-based approach to generate a collection of ESC with nested chromosomal deletions called DelES (Deletion in ES cells). This library contains more than a thousand independent ESC clones highly enriched in chromosomal deletions which together cover ~25% of the mouse genome. Using this resource, we conducted an embryoid body (EB) differentiation screen and showed that several clones were having an abnormal EB formation phenotype. Complementation studies later identified Rps14-a ribosomal protein (RP) coding gene- as a novel haploinsufficient gene in EB formation from undifferentiated ESC. Further analyses of our screen results showed a strong bias for a subset of small subunit ribosomal protein genes which are critical for ESC differentiation but not for their self-renewal activity. Interestingly, the most severe differentiation phenotypes were found with ribosomal proteins associated to the ribosome’s mRNA exit site, namely Rps5, Rps14 and Rps28. While RP gene imbalance often leads to a p53 response that can be corrected by p53 suppression, ESC clones with decreased expression of mRNA exit site RP genes were surprisingly insensitive to p53 reduction, but were rescued by BAC or cDNA complementation, thus confirming the causative nature of these genes in the ESC phenotype. Finally, polysomal profiling and RNA-Seq studies showed that Rps5 deleted ESC exhibit an abnormal mesodermal gene signature. Together, our work presents a highly valuable resource for functional genomic studies in ESC and also highlights a novel p53-independent role linked to RP gene imbalance. Our results shed light on the relevance of these subunits for the developmental transition of ESC from a pluripotent to a differentiated state.

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.

With age comes a decline in the dynamic regulation of a balanced and functional mitochondrial proteome (proteostasis) that leads to an increase in oxidative stress and macromolecule damage, with a decline in ATP production. Compromised protein networks and reduced available energy leaves an organism susceptible to accelerated aging and the onset of age-related disease. Since mitochondrial respiratory complexes are composed of protein subunits from both mitochondria and nuclear genomes, their assembly relies on the coordination of mitochondrial and cytoplasmic translation machinery. Disruption of mitochondrial translation generates an imbalance in the ratio of mitochondrial (mtDNA) to nuclear DNA (nDNA) encoded proteins, which is called a mitonuclear protein imbalance. In response to the protein imbalance, a retrograde stress signal is sent from the mitochondria to the nucleus, invoking the mitochondrial unfolded protein response (UPRᵐᵗ) to resolve the mitoproteostatic stress. In a young healthy cell, the UPRᵐᵗ upregulates protein folding chaperones and proteases to resolve the consequences of a mitonuclear protein imbalance. In the early stages of aging, the UPRᵐᵗ appears to be upregulated in response to age-related mitochondrial proteostatic stress. In aged senescent cells however, the UPRᵐᵗ response is blunted. There is cross-species evidence that induction of the UPRᵐᵗ through moderate-intensity exercise or through genetic disruption of the mitochondrial translation machinery will act as a hormetic - resulting in health benefits in the long term. Caenorhabditis elegans longevity models demonstrate that a reduction in mitochondrial ribosomal protein (Mrp) gene expression or disturbed mitochondrial translation will function as a hormetic. The disruption of the mitochondrial ribosome leads to a mitonuclear protein imbalance, invokes the nematode UPRᵐᵗ, which then robustly extends C. elegans lifespan and health span. To determine whether the hormetic effects of mild mitochondrial ribosome disruption can be recapitulated in a mammalian model, this thesis tests a C57/BL6/NTaconic mouse model altered in the germline to have reduced Mrpl54 expression through heterozygous mutation. Mice were metabolically tested at ages 6-, 18-, and 24-months and followed through their natural lifespan to determine whether reduction in the expression of a critical Mrp (Mrpl54) impacts lifespan or metabolic health span. While Mrpl54 mRNA expression was ~50% of wildtype in all Mrpl54⁺ᐟ⁻ tissues tested, there were no differences observed in metabolic health with age or lifespan in either male or female mice. Cultured Mrpl54⁺ᐟ⁻ primary myoblasts had lower absolute levels of nDNA- and mtDNA-encoded respiratory complex subunits relative to wildtype; however, the ratio between nDNA- and mtDNA-encoded protein subunits remained like wildtype. Further testing of the model revealed that Mrpl54⁺ᐟ⁻ males had weaker grip strength by age 12-months, which was also found in the data from multiple heterozygous Mrp (Mrp⁺ᐟ⁻) mouse models available at the International Mouse Phenotyping Consortium. 12-month-old Mrpl54⁺ᐟ⁻ males displayed reduced tetanic force and better fatigue recovery in ex vivo skeletal muscles, and the transmission electron micrographs of skeletal muscle sarcomeres revealed an early aging phenotype. Unlike the C. elegans reduced Mrp longevity model, reduced expression of a critical Mrp did not result in lifespan or metabolic health span benefits in a mouse model. In contrast, the Mrpl54⁺ᐟ⁻ male model showed evidence of premature skeletal muscle aging. While the results of this research do not support the role of Mrpl54 reduced expression in mammalian lifespan or health span extension, they do point to a premature aging phenotype for certain muscle parameters that may be relevant to people living with heterozygous mitochondrial protein mutations. Typically, these individuals are regarded as carriers and free of phenotype associated with their mitochondrial protein mutation. The results in this thesis suggest that those with a heterozygous mitochondrial protein gene mutation may manifest a phenotype as they grow older and are less resilient to external or internal challenges.

No description available.

Submitted by Angela Maria de Oliveira (amolivei@uepg.br) on 2017-11-30T10:57:51Z No. of bitstreams: 2 license_rdf: 811 bytes, checksum: e39d27027a6cc9cb039ad269a5db8e34 (MD5) Douglas Tomachewski.pdf: 4287227 bytes, checksum: 4ee4e1b519755860efa6f01d55b3569f (MD5) / Made available in DSpace on 2017-11-30T10:57:51Z (GMT). No. of bitstreams: 2 license_rdf: 811 bytes, checksum: e39d27027a6cc9cb039ad269a5db8e34 (MD5) Douglas Tomachewski.pdf: 4287227 bytes, checksum: 4ee4e1b519755860efa6f01d55b3569f (MD5) Previous issue date: 2017-09-04 / A identificação de microrganismos, nas áreas da saúde e agricultura, é essencial para compreender a composição e o desenvolvimento do meio. Novas técnicas estão buscando identificar estes microrganismos com mais acurácia, rapidez e com menor custo. Uma técnica cada vez mais estudada e utilizada atualmente é a identificação de microrganismos através de espectros de massa, gerados por uma espectrometria de massa. Os espectros de massa são capazes de gerar um perfil para reconhecimento de um microrganismo, utilizando os picos referentes às mais abundantes massas moleculares registradas nos espectros. Analisando os picos pode-se designar um padrão, como uma impressão digital, para reconhecer um microrganismo, esta técnica é conhecida como PMF, do inglês Peptide Mass Fingerprint. Outra forma de identificar um espectro de massa, é através dos picos que são esperados que se apresentem no espectro, modelo qual este trabalho utilizou. Para prever os picos esperados no espectro, foram calculados os pesos moleculares estimados de proteínas ribossomais. Essas proteínas são denominadas house keeping, ou seja são presentes para o próprio funcionamento celular. Além de apresentarem grande abundância no conteúdo procariótico, elas são altamente conservadas, não alterando sua fisiologia para diferentes meios ou estágios celulares. Os pesos estimados formaram uma base de dados presumida, contendo todas as informações obtidas do repositório do NCBI. Esta base de dados presumida foi generalizada para taxonomia a nível de espécie, e posteriormente submetida à um aprendizado de máquina. Com isso foi possível obter um modelo classificatório de microrganismos baseado em valores de proteínas ribossomais. Utilizando o modelo gerado pelo aprendizado de máquina, foi desenvolvido um software chamado Ribopeaks, capaz classificar os microrganismos a nível de espécie com acurácia de 94.83%, considerando as espécies correlatas. Também foram observados os resultados a nível taxonômico de gênero, que obteve 98.69% de assertividade. Valores de massas moleculares ribossomais biológicas retiradas da literatura também foram testadas no modelo obtido, obtendo uma assertividade total de 84,48% para acertos em nível de espécie, e 90,51% de acerto em nível de gênero. / Identification of microorganisms in health and agriculture areas is essential to understand the composition and development of the environment. New techniques are seeking to identify these microorganisms with more accuracy, speed and at a lower cost. Nowadays, a technique that is increasingly studied and used is the identification of microorganisms through mass spectra, generated by mass spectrometry. The mass spectra are able to generate a recognition profile from a microorganism, using the referring peaks to the most abundant molecular masses recorded in the spectrum. By analyzing the peaks, it is possible to designate a pattern, such as a fingerprint, to recognize a microorganism; this technique is known as the Peptide Mass Fingerprint (PMF). Another way to identify a mass spectrum is through the peaks that are expected to appear in the spectrum, which model this work used. To predict the expected peaks in the spectrum, the estimated molecular weights of ribosomal proteins were calculated. These proteins are responsible for the cellular functioning itself, so-called housekeeping. Besides they being abundant in the prokaryotic content, they are highly conserved, not altering their physiology to different environments or cell stage. The estimated weights formed a presumed database, containing all the information obtained from the NCBI’s repository. This presumed database was generalized at the specie level and later submitted to a machine learning algorithm. With this, it was possible to obtain a microorganism’s classificatory model based on ribosomal proteins values. Using the generated model by the machine learning, a software called Ribopeaks was developed to classify the microorganisms at the specie level with an accuracy of 94.83%, considering the related species. It was also observed the results at genus level, which obtained 98.69% of assertiveness. Values of biological ribosomal molecular masses from the literature were also tested in the acquihired model, obtaining a total assertiveness of 84.48% at the specie level, and 90.51% at the genus level.

Dissertation (Ph.D.)--University of South Florida, 2008. / Title from PDF of title page. Document formatted into pages; contains 197 pages. Includes vita. Includes bibliographical references.

Submitted by Ana Maria Fiscina Sampaio (fiscina@bahia.fiocruz.br) on 2014-08-11T13:24:14Z No. of bitstreams: 1 Diego Moura Santos. Avaliação... 2014.pdf: 3934510 bytes, checksum: 06fa6fa5250655c119370a03b641e2d0 (MD5) / Made available in DSpace on 2014-08-11T13:24:14Z (GMT). No. of bitstreams: 1 Diego Moura Santos. Avaliação... 2014.pdf: 3934510 bytes, checksum: 06fa6fa5250655c119370a03b641e2d0 (MD5) Previous issue date: 2014 / Fundação Oswaldo Cruz. Centro de Pesquisa Gonçalo Moniz. Salvador, BA, Brasil / A leishmaniose é uma doença de escala global, que afeta 12 milhões de pessoas e pode causar um espectro de doenças que vai desde a forma cutânea localizada, que tende para a cura espontânea, até a forma visceral que é fatal. Apesar da gravidade da doença, até o momento não existe uma vacina efetiva para prevenir a leishmaniose. Dentre os antígenos promissores para o desenvolvimento de uma vacina, destacam-se as proteínas ribossomais (S4, S6, L3 e L5) e a KMP-11, uma proteína de superfície presente nos membros da família tripanosomatidae. Nosso estudo consistiu em avaliar os efeitos da imunização com estes antígenos frente ao desafio com L. major e com L. braziliensis, empregando modelos experimentais de infecção. Primeiramente, avaliamos a capacidade protetora dos antígenos ribossomais frente à infecção por L. major. Dos quatro antígenos avaliados, apenas L3 ou L5 foram capazes de prevenir o desenvolvimento da lesão e de diminuir a carga parasitária. A vacinação de camundongos com estes antígenos, na presença de CpG, induziu um perfil de resposta Th1, com elevada produção de IFN-γ, baixa produção de IL-10 e presença de anticorpos IgG2a. Em seguida, avaliamos a capacidade protetora dos antígenos L3 e L5 contra o desafio por L. braziliensis, na presença da saliva do vetor. A imunização com os antígenos L3 e/ou L5 também induziu uma elevada produção de IFN-γ, resultando em significativa redução na espessura da lesão e menor carga parasitária. Com relação ao antígeno KMP-11, investigamos a sua capacidade protetora utilizando duas estratégias vacinais: a estratégia homóloga que consistiu na imunização de camundongos com um plasmídeo de DNA que codifica KMP11 (DNA KMP-11) e a estratégia heteróloga que consistiu na imunização com nanopartículas de PLGA contendo DNA KMP-11, seguido de um reforço com nanopartículas contendo a proteína KMP-11 sob forma recombinante, na presença de CpG. As nanopartículas protegem o antígeno da degradação enzimática e promovem a liberação controlada deste, além de atuar como um adjuvante. Ambas as estratégias não impediram o desenvolvimento da lesão, após o desafio com L. braziliensis e na presença de saliva do vetor. Entretanto, os animais imunizados com a estratégia heteróloga apresentaram uma maior redução da carga parasitária comparado com o grupo imunizado pela estratégia homóloga. Este efeito foi associado com uma maior produção de IFN-γ e de TNF-α no sítio da infecção. Por fim, avaliamos a indução da resposta imune inata em macrófagos estimulados com KMP-11 encapsulados em nanopartículas. Observamos que a estimulação de macrófagos murinos com KMP-11, encapsulada em nanopartículas de PLGA, reduziu a carga parasitária intracelular e aumentou a produção de oxido nítrico, superóxido, TNF-α, IFN-γ, IL-6, IL-1β, IL-18, CCL2/MCP-1, CXCL-1/KC sugerindo a indução de uma potente resposta imune inata. Assim, concluímos que os antígenos L3 e/ou L5 mostraram ser promissores para o desenvolvimento de uma vacina que proteja contra as principais espécies de Leishmania e que o encapsulamento de antígenos em nanopartículas é capaz de induzir uma forte resposta imune. Essa estratégia deve ser considerada quanto ao desenvolvimento de vacinas para a leishmaniose. / Leishmaniasis is a global disease affecting 12 million people and can cause diseases that range from self-healing localized cutaneous leishmaniasis to fatal visceral leishmaniasis. Despite the severity of the disease, there is no effective vaccine to prevent leishmaniasis. Among the promising antigens for the development of a vaccine, stand out the ribosomal proteins (S4, S6, L3, and L5) and KMP-11, a surface protein, widely found in the members of family Trypanosomatidae. Our study evaluated the effects of immunization with these antigens upon challenge with L. major and L. braziliensis, employing the experimental models of infection. First, we evaluated the protective ability of ribosomal antigens to infection by L. major. Among the four antigens examined only L3 or L5 were able to prevent lesion development and decrease the parasite load. Mice vaccinated with these antigens, plus CpG, developed a Th1-type response with high production of IFN-γ, low production of IL-10 and presence of IgG2a antibodies. Next, we evaluated the protective capacity of L3 and L5 antigens against challenge by L. braziliensis, in the presence of sand fly saliva. Vaccination with L3 or L5 also induced a high production of IFN-γ, resulting in significant inhibition of lesion development and lower parasite load. Regarding KMP-11, we investigated its protective capacity using two immunization strategies: the homologous strategy, which consisted in immunizing mice with a plasmid DNA encoding KMP-11(DNA KMP-11) while the heterologous immunization strategy consisted of inoculation of PLGA nanoparticles (NPs) containing DNA KMP-11 followed by a booster inoculation with nanoparticles containing recombinant KMP-11, in the presence of CpG. Nanoparticles protect the antigen from enzymatic degradation and promote controlled release, in addition to acting as an adjuvant. Lesion development was not inhibited following either immunization strategy, after challenge with L. braziliensis in the presence of sand fly saliva. However, animals immunized with the heterologous strategy showed a greater reduction in parasite load compared with the group immunized by the homologous strategy. This effect was associated with increased production of IFN-γ e TNF-α at the infection site. Finally, we evaluated the induction of the innate response in macrophages stimulated with KMP-11 encapsulated in NPs. We observed that stimulation of murine macrophages with KMP-11 encapsulated in NPs reduced the parasitic load and increased production of nitric oxide, superoxide, TNF-α, IFN-γ, IL-6, IL-1β, IL-18, CCL2/MCP-1, CXCL-1/KC suggesting the induction of a potent innate immune response. We conclude that the L3 and/or L5 are promising antigens for the development of a vaccine that protects against the main species of Leishmania and that encapsulation of antigens into nanoparticles induces strong immune response. This strategy should be considered for the development of vaccines against leishmaniasis.

CSIR / Translation initiation is a rate limiting step during protein biosynthesis. Initiation occurs by formation of an initiation complex comprising 30S subunit of ribosome, mRNA, initiator tRNA, and initiation factors. The initiator tRNA has a specialized function of binding to ribosomal P site whereas all the other tRNAs are selected in the ribosomal A site. The presence of a highly conserved 3 consecutive G-C base pairs in the anticodon stem of the initiator tRNA has been shown to be responsible for its P-site targeting. The exact molecular mechanism involved in the P-site targeting of the initiator tRNA is still unclear and focus of our study. Using genetic methods, we obtained mutant E. coli strains where initiator tRNA mutants lacking the characteristic 3-GC base pairs can also initiate translation. One such mutant strain, A30, was selected for this study. Using standard molecular genetic tools, the mutation was mapped and identified to be a mutation in a transcription remodeling factor, RapA (A511V). RapA is a transcription recycling factor and it displaces S1 when it performs its transcription recycling activity. We found this mutation to cause an increase in the S1-depleted ribosomes leading to decreased fidelity of translation initiation as the mutant RapA inefficiently displaces S1 from RNA polymerase complex. The mutation in the RapA was also found to cause changes in the transcriptome which leads to downregulation of major genes important for methionine and purine metabolism. Using mass spectrometric analysis, we identified deficiencies of methionine and adenine in the strain carrying mutant RapA. Our lab had previously reported that methionine and S-adenosyl methionine deficiency cause deficiency of methylations in ribosome which in turn decreases the fidelity of protein synthesis initiation. We used strains deleted for two newly identified methyltransferases, namely RlmH and RlmI, for our study and these strains also showed decreased fidelity of initiation. RlmH and RlmI methylate 1915 and 1962 positions of 23S rRNA respectively. We found that deletion of these methyltransferases also caused defects in ribosome biogenesis and compromised activity of ribosome recycling factor. We constructed phylogenetic trees of the initiator tRNA from 158 species which distinctly assembled into three domains of life. We also constructed trees using the minihelix or the whole sequence of species specific tRNAs, and iterated our analysis on 50 eubacterial species. We identified tRNAPro, tRNAGlu, or tRNAThr (but surprisingly not elongator tRNAMet) as probable ancestors of tRNAi. We then determined the factors imposing selection of methionine as the initiating amino acid. Overall frequency of occurrence of methionine, whose metabolic cost of synthesis is the highest among all amino acids, remains almost unchanged across the three domains of life. Our results indicate that methionine selection, as the initiating amino acid was possibly a consequence of the evolution of one-carbon metabolism, which plays an important role in regulating translation initiation. In conclusion, the current study reveals the importance of methylations in ribosome biogenesis and fidelity of translation initiation. It also strongly suggests a co-evolution of the metabolism and translation apparatus giving adaptive advantage to the cells where presence of methionine in the environment can be a signal to initiate translation with methionine initiator tRNA.

Indiana University-Purdue University Indianapolis (IUPUI) / The MDM2-p53 feedback loop is a well-characterized pathway. p53 is a transcription factor and regulates the transcriptional expression of genes that encode proteins responsible for cellular senescence, cell cycle arrest, apoptosis, and DNA repair. Various cellular stresses can result in p53 activation, including hypoxia, DNA damage by agents such as UV or IR, oncogenic signaling, nucleotide depletion and nucleolar stress from perturbation of ribosomal biogenesis. Under normal conditions, MDM2’s role in the pathway is to inhibit p53 function by directly binding to this protein and facilitating its ubiquitylation and 26S proteasome-mediated degradation. Under stressful cellular conditions, certain proteins interact with and rescue MDM2’s inhibition of p53. For example, upon exposure to small amounts of Actinomycin D, rRNA transcript synthesis is stalled resulting in the release of various ribosomal proteins including RPL5, RPL11 and RPL23; each of which has been shown to bind MDM2 within its central acidic domain and inhibit its ability to destabilize p53. Although the RPL5 binding region of MDM2 have been mapped in prior investigations, the MDM2-binding region(s) of RPL5 have yet to be characterized. By employing RPL5 deletion mutagenesis and in vitro GST-fusion protein-protein association assays with purified proteins, this dissertation attempts to elucidate those regions of RPL5 that may interact with MDM2. Normalizing RPL5-WT to 1.00, our study reveals that the basic N and C-terminals of RPL5 appear to bind with MDM2 while RPL5’s central region displays negligible binding to the central acidic domain of MDM2. Also, the possible meanings of these RPL5 MDM2 binding domains are discussed along with their utilization in potential future applications.

Les objectifs de cette thèse étaient d'apporter une percée conceptuelle pour une compréhension en profondeur des mécanismes moléculaires des protéines intrinsèquement désordonnées (IDPs) et de leurs rôles dans la physiologie cellulaire de Chlamydomonas reinhardtii. La combinaison d’approches expérimentale et bioinformatique m’a permis d’identifier 682 protéines thermorésistantes chez C. reinhardtii. Parmi celles-ci, 299 protéines sont systématiquement prédites comme potentielles IDP par quatre algorithmes de prédiction de désordre. Nos résultats indiquent que le pourcentage désordonné moyen de ces protéines prédites comme étant des IDPs est d'environ 20%, et la plupart d'entre elles (~70%) sont adressées à d'autres compartiments que la mitochondrie et le chloroplaste. Leur composition en acides aminés est biaisée par rapport à d'autres IDPs de la base de données de protéines désordonnées (DisProt). Ces IDPs potentielles jouent des fonctions moléculaires diverses, et 54% d'entre elles sont des cibles de phosphorylation.Notre travail a également augmenté l’état des connaissances sur l'adénylate kinase 3 (ADK3), une enzyme contenant une région intrinsèquement désordonnée (IDR). Cette enzyme a été isolée par notre approche globale pour caractériser les IDPs de l’algue verte. L’extension C-terminale désordonnée (CTE) de cette enzyme lui confère de nouvelles fonctions comme par exemple, la formation d’un complexe bi-enzymatique avec la glycéraldéhyde-3-phosphate déshydrogénase (GAPDH), la régulation (négative) de l'activité GAPDH avec le NADPH comme cofacteur, et le rôle de chaperon pour la GAPDH en la protégeant de la dénaturation par traitement thermique et de l’agrégation. / The objectives of this work were to bring a conceptual breakthrough for an in-depth understanding of the molecular mechanisms of intrinsically disordered proteins (IDPs) and their roles in the cellular physiology of Chlamydomonas reinhardtii. Using experimental approaches, 682 heat-resistant proteins were identified as putative IDPs. Among them, 299 proteins were consistently predicted as IDPs by all four disordered predictors. The mean percentage of disordered residues content of these IDPs is about 20%, and most of them (~70%) are addressed to other compartments than mitochondrion and chloroplast. These newly identified IDPs from C. reinhardtii have a biased amino acid composition as regard to other IDPs from the Database of protein disorder (DisProt). Furthermore, they play diverse molecular functions, and 54% of them are the targets for phosphorylation. Our work also revealed more knowledge of the IDR-containing protein adenylate kinase 3 (ADK3) that was extracted by heat-treatment. Its disordered C-terminal extension (CTE) brought new functions to this protein. For instance, via its CTE, ADK3 can form a bi-enzyme complex with glyceraldehyde-3-phosphate dehydrogenase (GAPDH), down-regulates the NADPH-dependent GAPDH activity, and behaves as a chaperone for GAPDH against its aggregation and inactivation under heat-treatment.