No description available.

Phosphoinositide-dependent protein kinase-1 (PDK1) plays an integral role in signaling cellular growth and proliferation, one that's dependent on its ability to autophosphorylate Ser-241 in its T-loop. This process appears to have a strict requirement for its C-terminal pleckstrin homology (PH) domain. Thus, the overall objective of this work was to determine the mechanism by which the PH domain induces an active kinase conformation in unphosphorylated PDK1, capable of Ser-241 autophosphorylation. First, computational modeling and protein cross linking studies were combined with site-directed mutagenesis and kinetic assays in order to provide initial assessment of how the PH domain scaffolds Ser-241 autophosphorylation. A significant number of contacts were identified between the enigmatic "N-bud" region of the PH domain and the kinase domain. Specifically, these studies implicated Glu-432 and Glu-453 of the N-bud region of the PH domain that bind and serve as mimics of the phosphorylated Ser-241 in the T-loop and the phosphorylated C-terminal tail of PDK1 substrates, respectively. Next, a novel method for protein trans-splicing of the regulatory and catalytic kinase domains of PDK1 was developed. The method utilizes the N- and C-terminal split inteins of the gene dnaE from Nostoc punctiforme [(N)NpuDnaE] and Synechocystis sp. strain PCC6803 [(C)SspDnaE], respectively. The cross-reacting KINASE(AEY)-(N)NpuDnaE-His6 and GST-His6-(C)SspDnaE-(CMN)PH fusion constructs generated full length spliced-PDK1 with kobs = (2.8 +- 0.3) x 10-5 s-1. Finally, NMR was used to further characterize the structural and dynamical properties of the PH domain in both its isolated form and in full length PDK1. Whereas, it was not possible to obtain chemical shift assignments of any backbone or side chain nuclear resonances, methods were optimized for 2H,13C,15N-isotopic labeling of the recombinant PH domain. Furthermore, the protein trans-splicing method was significantly improved and utilized for segmental isotopic labeling of the PH domain in full length PDK1. These new findings and developments may provide specific insight and technological improvements towards future studies aimed to better understand and target autoinhibited conformations of PDK1 for translational purposes.

I investigated SL trans-splicing in the troponin I gene of Ciona intestinalis. Experimental mutation of the AG dinucleotide adjacent to the natural trans-splice acceptor site (-64) in CiTnI/nuclacZ constructs eliminated trans-splicing to that site in Ciona embryos but activated trans-splicing at cryptic acceptor sites at -76 and -39, adjacent to the nearest AG dinucleotides. However, not all AG dinucleotides specify cryptic acceptor sites because outron internal deletions or 3'truncation mutants were trans-spliced at a far-upstream AG-adjacent cryptic site (-346), leaving many AGs in the retained outron segments. Thus, additional sequence elements that are present only in the -346 and -76/-64/-39 regions are required for cryptic acceptor activity. All mutant constructs generated detectable beta-gal enzyme expression, although the mutant with the longest retained-outron segment appeared less active. Therefore, mRNA accumulation and translation do not require trans-splicing to the natural acceptor site, although they may be facilitated by the normal removal of the outron during trans-splicing.

Orientador: Regina Maria Barretto Cicarelli / Banca: Maria Teresa Marques Novo / Banca: Cleslei Fernando Zanelli / Banca: Marcia Aparecida Silva Graminha / Banca: Otávio Henrique Thiemann / Resumo: A família Trypanosomatidae inclui diversos parasitas protozoários responsáveis por diferentes doenças humanas. Várias evidências sugerem importantes diferenças entre a maquinária de tradução e processamento de mRNA (trans-splicing) em Tripanosomatídeos quando comparados com eucariótos superiores. Neste contexto, alguns fatores importantes para o funcionamento da célula eucarióticas são os pequenos complexos constituídos de proteínas e RNA, chamados de ribonucleoproteínas (U snRNPs). Esta partículas possuem papel essencial no processamento de RNA mensageiros e durante a reação de splicing apresenta um core comum composto por proteínas (proteínas Sm) and RNAs estruturais (U snRNAs) e um conjunto de proteínas específicas de cada complexo. Embora bem definidas em mamíferos, snRNPs permanecem pouco caracterizadas em Tripanosomatídeos. Ferramentos de bioinformática identificaram quatro possíveis proteínas específicas do complexo U5 snRNP (U5-15K, U5-40K, U5-102K e U5-116K), e importantes parâmetros foram determinados, como peso molecular estimado, domínios e motivos conservados. Este trabalho demonstrou que U5-15K e 45-102K são altamente conservadas entre o Tripanosomatídeos e os domínios Dim1 and Prp1 foram identificados, respectivamente. Técnicas de purificação de complexos (PTP-tag) revelaram que estas proteínas interagem com o U5 snRNA, sugerindo que participem do complexo U5 snRNP. Análises funcionais demonstraram que U5-15K é essencial para viabilidade celular e que de alguma forma esta asssociada tanta a reação de cis quanto de tras-splcing. Experimentos de imunolocalização de U5-15K and U5-102K corroboram este dados, uma vez que as protínas em questão possuem localização nuclear. / Abstract:There are several protozoan parasites in Trypanosomatidae family, including different agents responsible for human diseases. Several evidences suggest important differences in the translational system and mRNA processing (trans-splicing) in Trypanosomatids when compared to higher eukaryotes. In this context, some important factors for the functioning of eukaryotic cells are the small complexes of RNA and proteins; these particles of ribonucleoproteins (UsnRNPs) have an essential role in the pre-mRNA processing, mainly during splicing. UsnRNP presents a common protein core associated between itself and with the snRNA, named Sm proteins and specific proteins of each snRNP. Even though they are well defined in mammals, snRNPs are still not well characterized in certain Trypanosomatids. Bioinformatics analysis identified four possible U5 snRNP specific proteins (U5-15K, U5-40K, U5-102K and U5-116K), and important parameters were determinated, as estimated molecular weight, motifs and conserved domains. This work shows that the U5-15K and U5-102K proteins are highly conserved among different Tryponosomatids species and Dim1 and Prp1 domains were identified, respectively. Tandem affinity pull-down assay revealed that these proteins interact with U5snRNA, suggesting its participation in U5snRNP particle, and functional analysis showed that U5-15K is essential for cell viability and it is associated in some way to trans and cis-splicing machinery. Immunolocalization experiments corroborated those data, showed U5-15K and U5-102K in the nucleus of the cell. / Doutor

Orientador: Regina Maria Barretto Cicarelli / Banca: Marcia Aparecida Silva Graminha / Banca: Lucile Maria Floeter-Winter / Resumo: Alguns fatores importantes no funcionamento das células eucarióticas correspondem à pequenos complexos de RNA e proteínas; essas partículas de ribonucleoproteínas (UsnRNPs) têm um papel essencial no processamento do pré-mRNA, principalmente durante o splicing (corte de íntrons e união de éxons). Embora as snRNPs estejam definidas em mamíferos, ainda não estão bem caracterizadas em certos tripanosomatídeos como o Trypanosoma cruzi. Assim, este trabalho propôs a caracterização molecular dos snRNAs (U2, U4, U5 e U6), por PCR e RT-PCR de formas epimastigotas de T. cruzi (cepa Y). Essas seqüências amplificadas foram clonadas, seqüenciadas e comparadas entre os tripanosomatídeos e o alinhamento múltiplo apresentou mais de 70% de identidade, exceto da U5 snRNA, que se mostrou menos conservada. Árvores filogenéticas mostraram a proximidade evolutiva dos snRNAs analisados em Trypanosoma brucei e Trypanosoma cruzi. As respectivas estruturas secundárias foram preditas, confirmando-se também as semelhanças com aquelas de T. brucei. O alinhamento das snRNAs de T. cruzi com as seqüências de Homo sapiens mostrou regiões únicas em U2, U4 e U5 snRNAs, nessa espécie, enquanto U6 mostrou-se fortemente conservada. Até o momento, ainda não foi possível a obtenção da seqüência completa de U1 snRNA de T. cruzi. / Abstract: Some important factors in functioning of the eucariotic cells are the small complexes of RNA and proteins; these particles of ribonucleoproteins (UsnRNPs) have an essential role in the pre-mRNA processing, mainly during splicing (cut of introns and union of exons). Even though they are well defined in mammals, snRNPs are still not characterized in certain Trypanosomatids, as well, Trypanosoma cruzi. So, this work proposed the molecular characterization of the snRNAs (U2, U4, U5 and U6), by PCR and RT-PCR with T. cruzi epimastigote forms (Y strain). These amplified sequences were cloned, sequenced and compared among the Trypanosomatids and the multiple alignment presented more than 70% of identity, except for U5 snRNA, which showed less conserved. Phylogenetic trees showed the evolutionary proximity between the Trypanosoma brucei and Trypanosoma cruzi snRNAs analysed. The respective secondary structures were predicted and also confirmed similarity with T. brucei. The alignment of T. cruzi snRNAs with Homo sapiens sequences showed unique regions in U2, U4 and U5 snRNAs in this species, while U6 was strongly conserved. Until this moment, it was not still possible to obtain U1 snRNA of T. cruzi complete sequence. / Mestre

La maladie de Huntington (MH) est une maladie autosomale dominante causée par une expansion de la répétition CAG codant pour une expansion de la polyglutamine dans le premier exon du gène Huntingtine (HTT). Ce gène code pour une protéine ubiquitaire dont la mutation entraine de graves symptômes moteurs, psychiatriques et cognitifs, dus à la dégénérescence spécifique des neurones GABAergique épineux moyens du striatum. Nous proposons d'utiliser le trans-épissage pour développer un vecteur de thérapie génique qui réduira significativement voir éliminera l'expression de la protéine mutée tout en restaurant un niveau physiologique de HTT normale dans les cellules affectées par la mutation du gène Huntingtine. Cette technologie est basée sur le remplacement de l'exon muté par un exon sans mutation pendant l'étape de maturation de l'ARNm. Du fait du caractère dominant de la mutation,l'efficacité thérapeutique nécessitera une réaction de trans-épissage très efficace capable de convertir une portion significative de pre-ARNm HTT mutés en en ARNm HTT normaux. Nous avons donc développé un système rapporteur fluorescent permettant la détection des évènements de trans-épissage afin d’identifier les séquences les plus performantes parmi une centaine de molécules candidates. Nous avons validé notre stratégie de criblage basée sur la fluorescence et réalisé le criblage sur plusieurs introns HTT (3, 9 et 20) qui ont démontré des zones favorables au trans-épissage. Une méthode de quantification directe et absolue du taux de trans-épissage a également été validée pour déterminer très précisément le taux de correction. L’ensemble de ce travail a permis de contribuer à la mise en évidence de la faisabilité du trans-épissage dans le contexte de la MH. / Huntington’s disease (HD) is an autosomal dominant genetic disorder caused by the expansion of a CAG repeat encoding a polyglutamine tract in the first exon of the Huntingtin gene (HTT). This gene encode a ubiquitous protein in which mutation lead to severe motor, psychiatric and cognitive deficits and causes degeneration of specific neuronal populations, in particular the GABAergic medium spiny neurons of the striatum. We propose to use trans-splicing to develop a gene therapy vector that will significantly reduce or eliminate the expression of the mutant protein while restoring a physiological level of normal HTT in cells affected by the HD mutation. This technology is based on replacement of the mutated exon by a normal version during the mRNA maturation process. HTT mutation being dominant, therapeutic benefits necessitates a highly efficient trans-splicing reaction that would convert a significant proportion of mutant-HTT pre-mRNA into normal HTT mRNA. For this purpose, we developed a fluorescent reporter system enabling the detection of trans-splicing events in high content screening in order to identify the most potent trans-splicing sequences among hundreds of molecules. We validated our fluorescent screening strategy and implement trans-splicing screening on 3 HTT introns (3, 9 and 20), in which we demonstrated the presence of hotspot promoting trans-splicing reactions. A direct and absolute quantification method was also validated to accurately assess the correction rate. Overall, this work generated additional evidences of trans-splicing feasibility in HD.

Anopheles stephensi is a potent vector of malaria throughout the Indian subcontinent and Middle East. An. stephensi is emerging as a model for molecular and genetic studies of mosquito-parasite interactions. Here we conducted a series of genomic and transcriptomic studies to improve the understanding of the biology of Anopheles stephensi and mosquito in general. First we reported the genome sequence and annotation of the Indian strain of the type form of An. stephensi. The 221 Mb genome assembly was produced using a combination of 454, Illumina, and PacBio sequencing. This hybrid assembly method was significantly better than assemblies generated from a single data source. A total of 11,789 protein-encoding genes were annotated using a combination of homology and de novo prediction. Secondly, we demonstrated the presence of complete dosage compensation in An. stephensi by determining that autosomal and X-linked genes have very similar levels of expression in both males and females. The uniformity of average expression levels of autosomal and X-linked genes remained when An. stephensi gene expression was normalized by that of their Ae. aegypti orthologs, strengthening the conclusion of complete dosage compensation in Anopheles. Lastly, we investigated trans-splicing events in Anopheles stephensi. We identified six trans-splicing events and all the trans-splicing sites are conserved and present in Ae. aegypti. The proteins encoded by the trans-spliced mRNAs are also highly conserved and their orthologs are co-linearly transcribed in out-groups of family Culicidae. This finding indicates the need to preserve the intact mRNA and protein function of the broken-up genes by trans-splicing during evolution. In summary, we presented the first genome assembly of Anopheles stephensi and studied two interesting evolution events" dosage compensation and trans-splicing - via transcriptomic analysis. / Ph. D.

No description available.

Pour certaines espèces, les nouvelles technologies de séquençage à haut débit et les pipelines automatiques d'annotation permettent actuellement de passer du tube Eppendorf au fichier genbank en un clic de souris, ou presque. D'autres organismes, en revanche, résistent farouchement au bio-informaticien le plus acharné en leur opposant une complexité génomique confondante. Les diplonémides en font partie. Ma thèse est centrée sur la découverte de nouvelles stratégies d'encryptage de l'information génétique chez ces eucaryotes, et l'identification des processus moléculaires de décodage. Les diplonémides sont des protistes marins qui prospèrent à travers tous les océans de la planète. Ils se distinguent par une diversité d'espèces riche et inattendue. Mais la caractéristique la plus fascinante de ce groupe est leur génome mitochondrial en morceaux dont les gènes sont encryptés. Ils sont décodés au niveau ARN par trois processus: (i) l'épissage en trans, (ii) l'édition par polyuridylation à la jonction des fragments de gènes, et (iii) l'édition par substitution de A-vers-I et C-vers-T; une diversité de processus posttranscriptionnels exceptionnelle dans les mitochondries. Par des méthodes bio-informatiques, j'ai reconstitué complètement le transcriptome mitochondrial à partir de données de séquences ARN à haut débit. Nous avons ainsi découvert six nouveaux gènes dont l'un présente des isoformes par épissage alternatif en trans, 216 positions éditées par polyuridylation sur 14 gènes (jusqu'à 29 uridines par position) et 114 positions éditées par déamination de A-vers-I et C-vers-T sur sept gènes (nad4, nad7, rns, y1, y2, y3, y5). Afin d'identifier les composants de la machinerie réalisant la maturation des ARNs mitochondriaux, le génome nucléaire a été séquencé, puis je l'ai assemblé et annoté. Cette machinerie est probablement singulière et complexe car aucun signal en cis ni acteur en trans caractéristiques des machineries d'épissage connues n'a été trouvé. J'ai identifié plusieurs candidats prometteurs qui devront être validés expérimentalement: des ARN ligases, un nombre important de protéines de la famille des PPR impliquées dans l'édition des ARNs dans les organites de plantes, ainsi que plusieurs déaminases. Durant ma thèse, nous avons mis en évidence de nouveaux types de maturation posttranscriptionnelle des ARNs dans la mitochondrie des diplonémides et identifié des candidats prometteurs de la machinerie. Ces composants, capables de lier précisément des fragments d'ARN et de les éditer pourraient trouver des applications biotechnologique. Au niveau évolutif, la caractérisation de nouvelles excentricités moléculaires de ce type nous donne une idée des processus de recrutement de gènes, de leur adaptation à de nouvelles fonctions, et de la mise en place de machineries moléculaires complexes. / Thanks to new high throughput sequencing technologies and automatic annotation pipelines, proceeding from an eppendorf tube to a genbank file can be achieved in a single mouse click or so, for some species. Others, however, fiercely resist bioinformaticians with their confounding genomic complexity. Diplonemids are one of them. My thesis is centered on the discovery of new strategies for encrypting genetic information in eukaryotes, and the identification of molecular decoding processes. Diplonemids are a group of poorly studied marine protists. Unexpectedly, metagenomic studies have recently ranked this group as one of the most diverse in the oceans. Yet, their most distinctive feature is their multipartite mitochondrial genome with genes in pieces, and encryption by nucleotide deletions and substitutions. Genes are decrypted at the RNA level through three processes: (i) trans-splicing, (ii) polyuridylation at the junction of gene pieces and (iii) substitutions of A-to-I and C-to-T. Such a diverse arsenal of mitochondrial post-transcriptional processes is highly exceptional. Using a bioinformatics approach, I have reconstructed the mitochondrial transcriptome from RNA-seq libraries. We have identified six new genes including one that presents alternative trans-splicing isoforms. In total, there are 216 uridines added in 14 genes with up to 29 U insertions, and 114 positions edited by deamination (A-to-I or C-to-T) among seven genes (nad4, nad7, rns, y1, y2, y3, y5). In order to identify the machinery that processes mitochondrial RNAs, the nuclear genome has been sequenced. I have then assembled and annotated the genome. This machinery is probably unique and complex because no cis signal or trans actor typical for known splicing machineries have been found. I have identified promising protein candidates that are worth to be tested experimentally, notably RNA ligases, numerous members of the PPR family involved in plants RNA editing and deaminases. During my thesis, we have identified new types of post-transcriptional RNA processing in diplonemid mitochondria and identified new promising candidates for the machinery. A system capable of joining precisely or editing RNAs could find biotechnological applications. From an evolutionary perspective, the discovery of new molecular systems gives insight into the process of gene recruitment, adaptation to new functions and establishment of complex molecular machineries.

Diplonema papillatum est un organisme unicellulaire qui vit dans l’océan. Son génome mitochondrial possède une caractéristique spéciale: tous les gènes sont brisés en de multiples fragments qui s’appellent modules. Chaque module est codé par un chromosome différent. L’expression d’un gène exige des épissages-en-trans qui assemblent un ARN messager complet à partir de tous les modules du gène. Nous avons précédemment montré que le gène cox1 est encodé dans neuf modules avec six Us non encodés entre le module 4 et le module 5 de l’ARN messager mature [1]. Nous n’avons identifié aucune séquence consensus connue de site d’épissage près des modules. Nous spéculons qu’un ARN guide (gRNA) a dirigé l’épissage-en-trans du gène cox1 par un mécanisme qui est semblable à l’édition d’ARN par l’insertion/la suppression des Us chez les kinétoplastides, le groupe sœur des diplonémides. Nous avons trouvé que les six Us sont ajoutés au bout 3’ de l’ARN d’une façon semblable à ceux ajoutés par le TUTase lors de l’édition de l’insertion des Us chez les kinétoplastides. Nous avons construit des profils de gRNA de l’épissage-en-trans avec les expressions régulières basé sur notre connaissance des gRNAs dans l’édition d’ARN chez les kinétoplastides. Selon la complémentarité partielle entre le gRNA et les deux modules adjacents, nous avons généré des amorces pour RT-PCR visant à détecter des séquences qui sont assorties à un des profils de gRNA. Une expérience pilote in vitro n’a pas permis de reconstituer l’épissage-en-trans des modules 3, 4, et 5, suggérant que nous devons améliorer nos techniques. / Diplonema papillatum is a single cellular organism that lives in the ocean. Its mitochondrial genome possesses a special feature: all genes are fragmented in multiple pieces that are called modules and each module is encoded by a different chromosome. Expression of a gene requires trans-splicing that successfully assemble a full-length mRNA from all modules of the gene. It was previously shown that the cox1 gene is encoded in nine modules that are all located on different chromosomes; moreover, a stretch of six non-encoded Us exist between Module 4 and 5 in the mature mRNA [1]. No consensus sequence of known splicing sites was identified near the modules. We speculate that trans-splicing of the cox1 gene is directed by guide RNAs (gRNAs) via a mechanism that is similar to U-insertion/deletion editing in kinetoplastids, the sister group of diplonemids. We have detected populations of small RNA molecules that could come from mitochondrial. We found that the six Us were added to the 3’ end of Module 4 in a similar way to the Us added by the TUTase in kinetoplastid U-insertional editing. Sequence profiles of possible trans-splicing gRNAs were constructed in regular expressions based on our knowledge of known gRNAs in kinetoplastid RNA editing. According to the complementarity between the gRNA and the two adjacent modules, primers were designed for RT-PCR that aims to detect gRNA sequences. Among the results, we identified sequences that match or partially match the gRNA profiles. A pilot in vitro assay did not reconstitute trans-splicing of module 3, 4 and 5, suggesting that further technical improvements are needed.