Novas informações assimiladas pelo sistema nervoso primeiramente ficam em um estado de labilidade para depois se estabilizarem através de um processo conhecido como consolidação, que envolve síntese de proteínas. Depois da reativação, uma memória previamente consolidada retorna ao seu estado de labilidade, e para que volte a ser estável, é necessário que haja novamente síntese de proteínas. Este segundo processo é chamado de reconsolidação. Recentemente os mecanismos moleculares e celulares envolvidos na regulação da síntese protéica relacionados à formação de memória de longa duração vêm sendo esclarecidos. A proteína alvo da rapamicina em mamíferos (mTOR) modula a plasticidade sináptica pela regulação da fosforilação de dois alvos: a proteína ribossomal S6K e a proteína de ligação 4E. A amígdala basolateral e o hipocampo dorsal são parte integrante do sistema neural envolvido na formação e expressão de diversos tipos de memórias. Estudos indicam que a via de sinalização da mTOR no hipocampo tem um papel importante na consolidação da memória de ratos submetidos a tarefa de esquiva inibitória e reconhecimento de objetos e na reconsolidação da memória de medo contextual condicionado. Contudo, estudos anteriores não avaliaram o efeito da inibição de mTOR amigdalar sobre a memória de esquiva inibitória e reconhecimento de objetos. O objetivo do presente trabalho é investigar o efeito da inibição de mTOR na amígdala basolateral por rapamicina na consolidação e reconsolidação da memória de esquiva inibitória e reconhecimento de objetos e comparar estes resultados com a inibição de mTOR no hipocampo. Ratos Wistar machos foram submetidos à cirurgia estereotáxica para implantação de cânulas na amígdala basolateral e hipocampo dorsal. Os animais foram submetidos à tarefa de esquiva inibitória, um modelo animal de memória de caráter aversivo, e a tarefa de reconhecimento de objetos, um modelo animal de memória de caráter pouco aversivo. Para investigar o efeito da inibição de mTOR na consolidação e reconsolidação da memória, os animais receberam microinfusões de rapamicina intra-amigdalar e intra-hipocampal em diferentes tempos em torno do treino e do teste. Nós demonstramos que a via de sinalização de mTOR na amígdala basolateral é necessária para consolidação da memória de esquiva inibitória e de reconhecimento de objetos. Nós também mostramos que a reativação torna a memória novamente suscetível e sensível à inibição de mTOR por rapamicina. / Memory formation requires protein synthesis, but only recently the cellular and molecular mechanisms involved in the regulation of protein synthesis related to the formation of long term memory has been elucidated. During memory formation, new information is acquired by the central nervous system as an initially fragile trace that over time becomes stable through a process known as consolidation. After reactivation, previously consolidated memories might return to a labile state, requiring a new round of protein synthesis to be restabilized. This second process is called reconsolidation. The basolateral amygdala and dorsal hippocampus are part of the neural systems involved in the formation and expression of several types of memory. One key regulator of protein synthesis is mTOR, a protein critical for different forms of synaptic plasticity by regulation of two targets: S6K and 4EBP. Evidence indicates that the mTOR signaling pathway in hippocampus has an important role in consolidation in rats of inhibitory avoidance and object recognition in rats, as well as in reconsolidation of contextual fear conditioning. However, previous studies have not examinated the effect of amygdalar mTOR inhibition on reconsolidation of inhibitory avoidance and object recognition. The aim of the present study was to evaluate the effect of amygdalar mTOR inhibition by rapamycin on consolidation and reconsolidation of inhibitory avoidance and object recognition, and compare the results with those obtained with hippocampal mTOR inhibition. Male rats Wistar underwent stereotaxic surgeries for cannulae implantation above the basolateral amygdala or dorsal hippocampus. After recovery, the animals were trained in inhibitory avoidance, an aversive memory task, or object recognition, a less aversive task. To investigate the effect of mTOR inhibition on memory consolidation and reconsolidation, we administered rapamycin, a specific mTOR inhibitor, into the basolateral amygdala or the dorsal hippocampus before or after training or reactivation. Our results provide evidence that mTOR in the basolateral amygdala and hippocampus might play a role in inhibitory avoidance and object recognition memory formation and reconsolidation.

The development of lean body mass (LBM) is closely linked to protein feeding. Along with resistance exercise protein feeding, or amino acid provision, stimulate muscle protein synthesis (MPS). Repeated stimulation of MPS above protein breakdown results in lean mass accretion. Many athletes aim to build or maintain LBM. The aim of this thesis was to better understand the relationship between LBM and protein feeding in trained individuals. This aim was studied in the applied setting and at whole body, muscle and molecular level. Chapter 2 revealed differences in total body mass and LBM between young rugby union players competing at different playing standards. Protein consumption was higher in players that played at a higher standard. The protein consumption of players at both playing standards was higher than current protein recommendations for athletes. The Under 20 (U20) rugby union players in Chapter 3 also consumed more protein than current recommendations state. Their dietary habits changed depending on their environment and they consumed more protein while in Six Nations (6N) camp compared with out of camp. Also, there were changes in dietary habits for individuals, however, those changes did not occur at the group level. Using the camp as an education tool for good nutrition habits could be advantageous. As a group, rugby union players’ body composition did not change from pre to post a 6N tournament. However, there was individual variation, which could be meaningful for the individual players. We provide evidence suggesting that in elite sport, athletes should be considered as individuals as well as part of a group if appropriate. The protein ribosomal protein S6 kinase 1 (p70S6K1) is part of the mammalian target of rapamycin complex 1 (mTORC1) pathway, which regulates MPS. The response of p70S6K1 activity was 62% greater following resistance exercise coupled with protein feeding compared with protein feeding alone in Chapter 3. P70S6K1 activity explained a small amount of the variation in previously published MPS data. The activity of the signalling protein p70S6K1 was unchanged in response to different doses of whey protein in Chapter 4 and 5. These data suggest that resistance exercise is a larger stimulus of p70S6K1 activity and when manipulating aspects of protein feeding p70S6K1 activation may be a limited measure. Consumption of 40 g of whey protein stimulated myofibrillar MPS to a greater extent than 20 g after a bout of whole body resistance exercise. The amount of LBM that the trained individual possessed did not influence this observed response. These data suggest that the amount of muscle mass exercised may influence the amount of protein required to increase MPS stimulation. For those engaging in whole body resistance exercise 20 g of protein is not sufficient to maximally stimulate MPS. The athletes in Chapters 2 and 3 of this thesis consumed more protein than current recommendations that do not take into account whole body exercise. Current post-exercise protein recommendations may no longer be optimal given this new information. Future work should directly investigate the MPS response to protein ingestion following resistance exercise engaging different amounts of muscle mass in well trained and elite populations. Identifying the protein dose required for maximal stimulation of MPS following whole body exercise would be an informative area of future research.

abstract: In vitro selection technologies allow for the identification of novel biomolecules endowed with desired functions. Successful selection methodologies share the same fundamental requirements. First, they must establish a strong link between the enzymatic function being selected (phenotype) and the genetic information responsible for the function (genotype). Second, they must enable partitioning of active from inactive variants, often capturing only a small number of positive hits from a large population of variants. These principles have been applied to the selection of natural, modified, and even unnatural nucleic acids, peptides, and proteins. The ability to select for and characterize new functional molecules has significant implications for all aspects of research spanning the basic understanding of biomolecules to the development of new therapeutics. Presented here are four projects that highlight the ability to select for and characterize functional biomolecules through in vitro selection. Chapter one outlines the development of a new characterization tool for in vitro selected binding peptides. The approach enables rapid screening of peptide candidates in small sample volumes using cell-free translated peptides. This strategy has the potential to accelerate the pace of peptide characterization and help advance the development of peptide-based affinity reagents. Chapter two details an in vitro selection strategy for searching entire genomes for RNA sequences that enhance cap-independent initiation of translation. A pool of sequences derived from the human genome was enriched for members that function to enhance the translation of a downstream coding region. Thousands of translation enhancing elements from the human genome are identified and the function of a subset is validated in vitro and in cells. Chapter three discusses the characterization of a translation enhancing element that promotes rapid and high transgene expression in mammalian cells. Using this ribonucleic acid sequence, a series of full length human proteins is expressed in a matter of only hours. This advance provides a versatile platform for protein synthesis and is espcially useful in situations where prokaryotic and cell-free systems fail to produce protein or when post-translationally modified protein is essential for biological analysis. Chapter four outlines a new selection strategy for the identification of novel polymerases using emulsion droplet microfluidics technology. With the aid of a fluorescence-based activity assay, libraries of polymerase variants are assayed in picoliter sized droplets to select for variants with improved function. Using this strategy a variant of the 9°N DNA polymerase is identified that displays an enhanced ability to synthesize threose nucleic acid polymers. / Dissertation/Thesis / Doctoral Dissertation Biological Design 2015

Novas informações assimiladas pelo sistema nervoso primeiramente ficam em um estado de labilidade para depois se estabilizarem através de um processo conhecido como consolidação, que envolve síntese de proteínas. Depois da reativação, uma memória previamente consolidada retorna ao seu estado de labilidade, e para que volte a ser estável, é necessário que haja novamente síntese de proteínas. Este segundo processo é chamado de reconsolidação. Recentemente os mecanismos moleculares e celulares envolvidos na regulação da síntese protéica relacionados à formação de memória de longa duração vêm sendo esclarecidos. A proteína alvo da rapamicina em mamíferos (mTOR) modula a plasticidade sináptica pela regulação da fosforilação de dois alvos: a proteína ribossomal S6K e a proteína de ligação 4E. A amígdala basolateral e o hipocampo dorsal são parte integrante do sistema neural envolvido na formação e expressão de diversos tipos de memórias. Estudos indicam que a via de sinalização da mTOR no hipocampo tem um papel importante na consolidação da memória de ratos submetidos a tarefa de esquiva inibitória e reconhecimento de objetos e na reconsolidação da memória de medo contextual condicionado. Contudo, estudos anteriores não avaliaram o efeito da inibição de mTOR amigdalar sobre a memória de esquiva inibitória e reconhecimento de objetos. O objetivo do presente trabalho é investigar o efeito da inibição de mTOR na amígdala basolateral por rapamicina na consolidação e reconsolidação da memória de esquiva inibitória e reconhecimento de objetos e comparar estes resultados com a inibição de mTOR no hipocampo. Ratos Wistar machos foram submetidos à cirurgia estereotáxica para implantação de cânulas na amígdala basolateral e hipocampo dorsal. Os animais foram submetidos à tarefa de esquiva inibitória, um modelo animal de memória de caráter aversivo, e a tarefa de reconhecimento de objetos, um modelo animal de memória de caráter pouco aversivo. Para investigar o efeito da inibição de mTOR na consolidação e reconsolidação da memória, os animais receberam microinfusões de rapamicina intra-amigdalar e intra-hipocampal em diferentes tempos em torno do treino e do teste. Nós demonstramos que a via de sinalização de mTOR na amígdala basolateral é necessária para consolidação da memória de esquiva inibitória e de reconhecimento de objetos. Nós também mostramos que a reativação torna a memória novamente suscetível e sensível à inibição de mTOR por rapamicina. / Memory formation requires protein synthesis, but only recently the cellular and molecular mechanisms involved in the regulation of protein synthesis related to the formation of long term memory has been elucidated. During memory formation, new information is acquired by the central nervous system as an initially fragile trace that over time becomes stable through a process known as consolidation. After reactivation, previously consolidated memories might return to a labile state, requiring a new round of protein synthesis to be restabilized. This second process is called reconsolidation. The basolateral amygdala and dorsal hippocampus are part of the neural systems involved in the formation and expression of several types of memory. One key regulator of protein synthesis is mTOR, a protein critical for different forms of synaptic plasticity by regulation of two targets: S6K and 4EBP. Evidence indicates that the mTOR signaling pathway in hippocampus has an important role in consolidation in rats of inhibitory avoidance and object recognition in rats, as well as in reconsolidation of contextual fear conditioning. However, previous studies have not examinated the effect of amygdalar mTOR inhibition on reconsolidation of inhibitory avoidance and object recognition. The aim of the present study was to evaluate the effect of amygdalar mTOR inhibition by rapamycin on consolidation and reconsolidation of inhibitory avoidance and object recognition, and compare the results with those obtained with hippocampal mTOR inhibition. Male rats Wistar underwent stereotaxic surgeries for cannulae implantation above the basolateral amygdala or dorsal hippocampus. After recovery, the animals were trained in inhibitory avoidance, an aversive memory task, or object recognition, a less aversive task. To investigate the effect of mTOR inhibition on memory consolidation and reconsolidation, we administered rapamycin, a specific mTOR inhibitor, into the basolateral amygdala or the dorsal hippocampus before or after training or reactivation. Our results provide evidence that mTOR in the basolateral amygdala and hippocampus might play a role in inhibitory avoidance and object recognition memory formation and reconsolidation.

Novas informações assimiladas pelo sistema nervoso primeiramente ficam em um estado de labilidade para depois se estabilizarem através de um processo conhecido como consolidação, que envolve síntese de proteínas. Depois da reativação, uma memória previamente consolidada retorna ao seu estado de labilidade, e para que volte a ser estável, é necessário que haja novamente síntese de proteínas. Este segundo processo é chamado de reconsolidação. Recentemente os mecanismos moleculares e celulares envolvidos na regulação da síntese protéica relacionados à formação de memória de longa duração vêm sendo esclarecidos. A proteína alvo da rapamicina em mamíferos (mTOR) modula a plasticidade sináptica pela regulação da fosforilação de dois alvos: a proteína ribossomal S6K e a proteína de ligação 4E. A amígdala basolateral e o hipocampo dorsal são parte integrante do sistema neural envolvido na formação e expressão de diversos tipos de memórias. Estudos indicam que a via de sinalização da mTOR no hipocampo tem um papel importante na consolidação da memória de ratos submetidos a tarefa de esquiva inibitória e reconhecimento de objetos e na reconsolidação da memória de medo contextual condicionado. Contudo, estudos anteriores não avaliaram o efeito da inibição de mTOR amigdalar sobre a memória de esquiva inibitória e reconhecimento de objetos. O objetivo do presente trabalho é investigar o efeito da inibição de mTOR na amígdala basolateral por rapamicina na consolidação e reconsolidação da memória de esquiva inibitória e reconhecimento de objetos e comparar estes resultados com a inibição de mTOR no hipocampo. Ratos Wistar machos foram submetidos à cirurgia estereotáxica para implantação de cânulas na amígdala basolateral e hipocampo dorsal. Os animais foram submetidos à tarefa de esquiva inibitória, um modelo animal de memória de caráter aversivo, e a tarefa de reconhecimento de objetos, um modelo animal de memória de caráter pouco aversivo. Para investigar o efeito da inibição de mTOR na consolidação e reconsolidação da memória, os animais receberam microinfusões de rapamicina intra-amigdalar e intra-hipocampal em diferentes tempos em torno do treino e do teste. Nós demonstramos que a via de sinalização de mTOR na amígdala basolateral é necessária para consolidação da memória de esquiva inibitória e de reconhecimento de objetos. Nós também mostramos que a reativação torna a memória novamente suscetível e sensível à inibição de mTOR por rapamicina. / Memory formation requires protein synthesis, but only recently the cellular and molecular mechanisms involved in the regulation of protein synthesis related to the formation of long term memory has been elucidated. During memory formation, new information is acquired by the central nervous system as an initially fragile trace that over time becomes stable through a process known as consolidation. After reactivation, previously consolidated memories might return to a labile state, requiring a new round of protein synthesis to be restabilized. This second process is called reconsolidation. The basolateral amygdala and dorsal hippocampus are part of the neural systems involved in the formation and expression of several types of memory. One key regulator of protein synthesis is mTOR, a protein critical for different forms of synaptic plasticity by regulation of two targets: S6K and 4EBP. Evidence indicates that the mTOR signaling pathway in hippocampus has an important role in consolidation in rats of inhibitory avoidance and object recognition in rats, as well as in reconsolidation of contextual fear conditioning. However, previous studies have not examinated the effect of amygdalar mTOR inhibition on reconsolidation of inhibitory avoidance and object recognition. The aim of the present study was to evaluate the effect of amygdalar mTOR inhibition by rapamycin on consolidation and reconsolidation of inhibitory avoidance and object recognition, and compare the results with those obtained with hippocampal mTOR inhibition. Male rats Wistar underwent stereotaxic surgeries for cannulae implantation above the basolateral amygdala or dorsal hippocampus. After recovery, the animals were trained in inhibitory avoidance, an aversive memory task, or object recognition, a less aversive task. To investigate the effect of mTOR inhibition on memory consolidation and reconsolidation, we administered rapamycin, a specific mTOR inhibitor, into the basolateral amygdala or the dorsal hippocampus before or after training or reactivation. Our results provide evidence that mTOR in the basolateral amygdala and hippocampus might play a role in inhibitory avoidance and object recognition memory formation and reconsolidation.

Submitted by Fabio Sobreira Campos da Costa (fabio.sobreira@ufpe.br) on 2016-08-12T13:39:46Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) tese amaranta.pdf: 1596892 bytes, checksum: 5d4ba09b331b3e559fa3f104e519a054 (MD5) / Made available in DSpace on 2016-08-12T13:39:46Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) tese amaranta.pdf: 1596892 bytes, checksum: 5d4ba09b331b3e559fa3f104e519a054 (MD5) Previous issue date: 2015-03-09 / CNPq / A iniciação da tradução é a etapa mais complexa de um processo crítico para a sobrevivência dos seres vivos, onde se destaca a atuação do complexo eIF4F, formado pelas subunidades eIF4E, eIF4A, e eIF4G. Seis homólogos de eIF4E (EIF4E1 a 6) e cinco de eIF4G (EIF4G1 a 5) foram identificados no protozoário Trypanosoma brucei. Este trabalho buscou contribuir no estudo de complexos do tipo eIF4F neste patógeno, inicialmente analisando a expressão de subunidades de complexos já definidos, formado pelos EIF4E4/EIF4G3 e EIF4E3/EIF4G4. Observou-se que, à exceção do EIF4G3, essas subunidades são representadas por isoformas originárias de eventos de fosforilação. No caso do EIF4E4, esses eventos estão associados às fases de crescimento do microorganismo e as fosforilações dos EIF4E3 e EIF4E4 são direcionadas às suas extremidades N-terminais. A etapa seguinte compreendeu o estudo de duas proteínas hipotéticas, encontradas com novos complexos baseados nos EIF4E5/EIF4G1 e EIF4E6/EIF4G5 (Tb117.5 e TbG5-IP). Essas são homólogas de enzimas associadas a formação da extremidade 5’ dos mRNAs, porém apresentaram localização citoplasmática. Sua associação aos referidos complexos foi investigada e enquanto a Tb117.5 se associa com uma subpopulação do complexo EIF4E5/EIF4G1, a TbG5-IP se mostrou parte integrante do complexo EIF4E6/EIF5G5. A depleção por RNA interferência dessas proteínas não alterou a viabilidade celular apesar do insucesso na obtenção de deleção dupla dos seus genes. Os dados obtidos sugerem uma divergência funcional nesses complexos ainda não encontrada em outros eucariotos. / The initiation of translation is the most complex stage of a critical process required for the survival of all living beings and which requires the activity of the eIF4F complex, formed by the eIF4E, eIF4A, and eIF4G subunits. Six homologues of eIF4E (EIF4E1 to 6) and five of eIF4G (EIF4G1 to 5) were identified in the protozoan Trypanosoma brucei. This study aimed to contribute to the study of eIF4F-like complexes within this pathogen, initially analyzing the expression of subunits found in already defined complexes, formed by EIF4E4/EIF4G3 and EIF4E3/EIF4G4. Except for EIF4G3, all these subunits are represented by multiple isoforms originating from phosphorylation events. For EIF4E4, these events are associated with the microorganism’s growth phase and the phosphorylations of both EIF4E3 and EIF4E4 are directed to their N- terminal ends. The next step included the study of two hypothetical proteins found within new complexes based on EIF4E5/EIF4G1 and EIF4E6/EIF4G5 (Tb117.5 and TbG5-IP). These are homologous to enzymes associated with the formation of the mRNAs’ 5’ end but showed cytoplasmic localization. Their association with the new complexes was investigated and while Tb117.5 is associated with a subset of the EIF4E5/EIF4G1 complex, TbG5-IP proved to be an integral part of the EIF4E6/EIF5G5 complex. The depletion by RNA interference of these proteins did not affect cell viability despite the failure to achieve a double deletion of their genes. The data suggest a functional divergence in these complexes that is not found in other eukaryotes.

Submitted by Fabio Sobreira Campos da Costa (fabio.sobreira@ufpe.br) on 2016-08-12T13:48:49Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) tese amaranta.pdf: 1596892 bytes, checksum: 5d4ba09b331b3e559fa3f104e519a054 (MD5) / Made available in DSpace on 2016-08-12T13:48:49Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) tese amaranta.pdf: 1596892 bytes, checksum: 5d4ba09b331b3e559fa3f104e519a054 (MD5) Previous issue date: 2015-03-09 / CNPq / A iniciação da tradução é a etapa mais complexa de um processo crítico para a sobrevivência dos seres vivos, onde se destaca a atuação do complexo eIF4F, formado pelas subunidades eIF4E, eIF4A, e eIF4G. Seis homólogos de eIF4E (EIF4E1 a 6) e cinco de eIF4G (EIF4G1 a 5) foram identificados no protozoário Trypanosoma brucei. Este trabalho buscou contribuir no estudo de complexos do tipo eIF4F neste patógeno, inicialmente analisando a expressão de subunidades de complexos já definidos, formado pelos EIF4E4/EIF4G3 e EIF4E3/EIF4G4. Observou-se que, à exceção do EIF4G3, essas subunidades são representadas por isoformas originárias de eventos de fosforilação. No caso do EIF4E4, esses eventos estão associados às fases de crescimento do microorganismo e as fosforilações dos EIF4E3 e EIF4E4 são direcionadas às suas extremidades N-terminais. A etapa seguinte compreendeu o estudo de duas proteínas hipotéticas, encontradas com novos complexos baseados nos EIF4E5/EIF4G1 e EIF4E6/EIF4G5 (Tb117.5 e TbG5-IP). Essas são homólogas de enzimas associadas a formação da extremidade 5’ dos mRNAs, porém apresentaram localização citoplasmática. Sua associação aos referidos complexos foi investigada e enquanto a Tb117.5 se associa com uma subpopulação do complexo EIF4E5/EIF4G1, a TbG5-IP se mostrou parte integrante do complexo EIF4E6/EIF5G5. A depleção por RNA interferência dessas proteínas não alterou a viabilidade celular apesar do insucesso na obtenção de deleção dupla dos seus genes. Os dados obtidos sugerem uma divergência funcional nesses complexos ainda não encontrada em outros eucariotos. / The initiation of translation is the most complex stage of a critical process required for the survival of all living beings and which requires the activity of the eIF4F complex, formed by the eIF4E, eIF4A, and eIF4G subunits. Six homologues of eIF4E (EIF4E1 to 6) and five of eIF4G (EIF4G1 to 5) were identified in the protozoan Trypanosoma brucei. This study aimed to contribute to the study of eIF4F-like complexes within this pathogen, initially analyzing the expression of subunits found in already defined complexes, formed by EIF4E4/EIF4G3 and EIF4E3/EIF4G4. Except for EIF4G3, all these subunits are represented by multiple isoforms originating from phosphorylation events. For EIF4E4, these events are associated with the microorganism’s growth phase and the phosphorylations of both EIF4E3 and EIF4E4 are directed to their N- terminal ends. The next step included the study of two hypothetical proteins found within new complexes based on EIF4E5/EIF4G1 and EIF4E6/EIF4G5 (Tb117.5 and TbG5-IP). These are homologous to enzymes associated with the formation of the mRNAs’ 5’ end but showed cytoplasmic localization. Their association with the new complexes was investigated and while Tb117.5 is associated with a subset of the EIF4E5/EIF4G1 complex, TbG5-IP proved to be an integral part of the EIF4E6/EIF5G5 complex. The depletion by RNA interference of these proteins did not affect cell viability despite the failure to achieve a double deletion of their genes. The data suggest a functional divergence in these complexes that is not found in other eukaryotes.

La protéine tRip de Plasmodium, l’agent du paludisme, fait l’objet de mon travail de thèse. Identifiée au laboratoire, elle est localisée à la membrane plasmique de P. berghei, le modèle murin étudié in vivo. Elle permet l’import d’ARNt exogènes à l’intérieur du parasite. La génération et l’étude d’une souche P. berghei tRip-KO m’ont permis d’explorer l’importance de ce mécanisme et l’implication de tRip dans un complexe multiprotéique. J’ai démontré que la multiplication de P. berghei est très réduite lors du stade sanguin chez la souche tRip-KO. Par protéomique, j’ai montré qu’en l’absence de tRip, de nombreuses protéines sont sous-exprimées, en particulier celles riches en asparagines. Enfin, j’ai identifié trois partenaires protéiques de tRip, dont le substrat est l’ARNt. Ces résultats suggèrent que les ARNt importés par Plasmodium via tRip pourraient être substrat de protéines plasmodiales et acteurs de la synthèse protéique du parasite. Le transport d’ARNt étrangers dans une cellule est un mécanisme inconnu en dehors de cette étude. Il révèle une interaction inédite entre un hôte et son parasite intracellulaire, propice au développement de ce dernier. / The organism studied in this work is Plasmodium, the malaria parasite. The laboratory identified a membrane protein, called tRip for tRNA import protein, displaying a tRNA binding domain exposed outside of the parasite. In vivo, in P. berghei which is the murine model used, tRip mediates the import of exogenous tRNAs into the parasite cytosol. My PhD work begun with the construction of a tRip-KO strain of P. berghei to investigate the role of tRNA import and the putative involvement of tRip within a proteic complex. The phenotype of the tRip-KO strain is significantly modified compared to the wild-type parasite during the blood stage: its rate of multiplication is much lower. By proteomic analyses, I showed that many proteins are under-regulated in the tRip-KO strain, especially those very rich in asparagines. Moreover, I dentified three protein partners for tRip, being tRNA aminoacylation or modification enzymes. These results suggest that host imported tRNAs could be taken in charge by parasitic enzymes and take part to Plasmodium protein synthesis. This work reveals a new host pathogen interaction and is the first example showing exogenous tRNA import into a cell.

Philosophiae Doctor - PhD / The estimated 5 × 10³⁰ prokaryotic cells inhabiting our planet sequester some 350–550 Petagrams (1 Pg = 1015 g) of carbon, 85–130 Pg of nitrogen, and 9–14 Pg of phosphorous, making them the largest reservoir of those nutrients on Earth (Whitman et al. 1998). However, reports suggest that only less than 1% of these microscopic organisms are cultivable (Torsvik et al. 1990; Sleator et al. 2008). Until recently with the development of metagenomic techniques, the knowledge of microbial diversity and their metabolic capabilities has been limited to this small fraction of cultivable organisms (Handelsman et al. 1998). While metagenomics has undoubtedly revolutionised the field of microbiology and biotechnology it has been generally acknowledged that the current approaches for metagenomic bio- rospecting / screening have limitations which hinder this approach to fully access the metabolic potentials and genetic variations contained in microbial genomes (Beloqui et al. 2008). In particular, the construction of metagenomic libraries and heterologous expression are amongst the major obstacles. The aim of this study was to develop an ultra-high throughput approach for screening enzyme activities using uncloned metagenomic DNA, thereby eliminating cloning steps, and employing in vitro heterologous expression. To achieve this, three widely used techniques: cell-free transcription-translation, in vitro compartmentalisation (IVC) and Fluorescence Activated Cell Sorting (FACS) were combined to develop this robust technique called metagenomic in vitro compartmentalisation (mIVC-FACS). Moreover, the E. coli commercial cell-free system was used in parallel to a novel, in-house Rhodococcus erythropolis based cell-free system. The versatility of this technique was tested by identifying novel beta-xylosidase encoding genes derived from a thermophilic compost metagenome. In addition, the efficiency of mIVC-FACS was compared to the traditional metagenomic approaches; function-based (clone library screening) and sequence-based (shotgun sequencing and PCR screening). The results obtained here show that the R. erythropolis cell-free system was over thirty-fold more effective than the E. coli based system based on the number of hits obtained per million double emulsions (dE) droplets screened. Six beta-xylosidase encoding genes were isolated and confirmed from twenty-eight positive dE droplets. Most of the droplets that were isolated from the same gate encoded the same enzyme, indicating that this technique is highly selective. A comparison of the hit rate of this screening approach with the traditional E. coli based fosmid library method shows that mIVC-FACS is at least 2.5 times more sensitive. Although only a few hits from the mIVC-FACS screening were selected for confirmation of beta-xylosidase activity, the proposed hit rate suggests that a significant number of positive hits are left un-accessed through the traditional clone library screening system. In addition, these results also suggest that E. coli expression system might be intrinsically sub-optimal for screening for hemicellulases from environmental genomes compared to R. erythropolis system. The workflow required for screening one million clones in a fosmid library was estimated to be about 320 hours compared to 144 hours required via the mIVC-FACS screening platform. Some of the gene products obtained in both screening platforms show multiple substrate activities, suggesting that the microbial consortia of composting material consist of microorganisms that produce enzymes with multiple lignocellulytic activities. While this platform still requires optimisation, we have demonstrated that this technique can be used to isolate genes encoding enzymes from mixed microbial genomes. mIVC-FACS is a promising technology with the potential to take metagenomic studies to the second generation of novel natural products bio-prospecting. The astonishing sensitivity and ultra-high throughput capacity of this technology offer numerous advantages in metagenomic bio-prospecting. / National Research Foundation (NRF)

The studies reported in this thesis describe the work done in the area of translation initiation where a previously unknown role of multiple copies of initiator tRNA in E. coli has been reported. Also the role of SsrA resume codon in resumption of translation, until not clearly known has been reported here. Chapter -1 discusses the relevant literature in understanding translation and initiator tRNA selection on the ribosome during initiation. It also discusses the literature pertaining to the aspect of release of stalled ribosomal complexes by SsrA. This is followed by the next chapter (chapter- 2) which discusses the materials and methods used throughout the study. Chapter- 3 describes the studies leading to the role of multiple copies of initiator tRNA in E. coli in governing the fidelity of initiator tRNA selection on the P site of the ribosome. This is followed by Chapter-4 which describes the role of the resume codon of the SsrA in governing the efficiency of trans-translation in releasing the stalled ribosomal complexes. The summaries of the chapters 3 and chapter 4 are briefly described below. i) Role of conserved 3GC base pairs of initiator tRNA in the initiator-elongator tRNA discrimination. Translation initiation is the first step in the very important and highly conserved biological process of protein biosynthesis. The process involves many steps, a wide array of protein factors at each specialized step and a large ribonucleoprotein particle; the ribosome to decode the information of the mRNA template into biologically active proteins. The process of initiation is still unclear largely due to fewer reports of available structural data. One of the very interesting questions that people have been trying to address is how the initiator tRNA is selected on the P- site of the ribosome and what is the importance of the conserved three GC base pairs in the anticodon stem of the initiator tRNA. Here in this study, I have studied this question by using the classical genetic technique of generating and characterizing the mutant initiator tRNA defective at the step of initiation. I have identified and analyzed the suppressors which are capable of rescuing this defect in initiation. The study involves two such E. coli suppressor strains (named D4 and D27). These suppressors can initiate translation from a reporter CAT mRNA with amber codon, independent of the presence of the three consecutive GC base pairs in the anticodon stem of initiator tRNAs. Mapping of the mutations revealed that the mutants are defective in expression of the tRNA1fMet (metZVW) gene locus which encodes the initiator tRNA. Both the suppressors (D4 and D27) also allow initiation with elongator tRNA species in E. coli. Taken together, the results show that E. coli when deficient in the initiator tRNA concentration can lead to initiation with elongator tRNA species. ii) The Role of SsrA/tmRNA in ribosome recycling and rescue. Occasionally during the process of translation, the ribosomes stall on the mRNA before the polypeptide synthesis is complete. This situation is detrimental to the organism because of the sequestration of the tRNAs as ‘peptidyl tRNAs’ and the ribosomes. In E. coli one of the pathways to rescue stalled ribosomes involves disassembly of these stalled complexes to release peptidyl tRNAs which are then recycled by peptidyl tRNA hydrolase (Pth), an essiential enzyme in E. coli. The other pathway which is not essential in E. coli but is conserved in all prokaryotes involves SsrA or tmRNA (transfer messenger RNA). The tmRNA is charged with alanine and recognizes the stalled ribosomal complexes and acts as tRNA to bind the A-site. It also functions as mRNA by adding a undecapeptide (which is actually a tag for degradation by cellular proteases) to the existing polypeptide and there is normal resumption of the translation. In most sequences of SsrA ORF, the first codon of the ORF, called as resume codon, is conserved. I wanted to understand the importance of the conservation of the resume codon. Towards this end I randomly mutated the resume codon and studied the effect of the altered resume codon in the rescue of stalled ribosomal complexes. The effect of over-expression of these mutants was investigated in the rescue of the Pthts defect since it is known that the overexpression of SsrA rescues the temperature sensitive phenotype of the Pthts strain and so causes less accumulation of peptidyl–tRNA in E. coli .The effect for these mutants has also been studied by the growth of hybrid λimmP22 phages. I also used AGA minigene system to study the effect of various mutants which has been shown to sequester tRNAArg (UCU) in the ribosomal P-site, translation of this minigene causes toxicity to E. coli. I have tried to study the effect of the SsrA mutants in rescue of toxicity caused by the minigene. Overall, the observations indicate that the conservation of the resume codon is important in E. coli and having mutated resume codon probably leads to deficient trans-translation during one or the other growth conditions.