Thesis (M.Sc.). / Written for the Dept. of Biochemistry. Title from title page of PDF (viewed 2008/12/10). Includes bibliographical references.

Thesis (Ph. D.)--Cornell University, August, 2007. / Vita. Includes bibliographical references (leaves 165-176).

Thesis (Ph. D.)--University of Washington, 2004. / Vita. Includes bibliographical references (leaves 70-79).

Thesis (Ph. D.)--University of Washington, 1999. / Vita. Includes bibliographical references (leaves 111-124).

Made available in DSpace on 2014-06-11T19:32:54Z (GMT). No. of bitstreams: 0 Previous issue date: 2006-08-22Bitstream added on 2014-06-13T19:03:37Z : No. of bitstreams: 1 souza_jam_dr_jabo.pdf: 4083420 bytes, checksum: cb86ca179e1196f514509e27854de1c3 (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / O nitrogênio é o nutriente requerido em maior quantidade para a cultura da soja. Avanços nas pesquisas de melhoramento genético vegetal e microbiologia do solo permitiram expandir o uso de inoculantes comerciais contendo estirpes de Bradyrhizobium japonicum e Bradyrhizobium elkanii. Estas bactérias infectam as raízes da planta e induzem a formação de nódulos, que abrigam a forma bacterióide, diferenciada da bactéria, responsável pela fixação simbiótica do nitrogênio. Informações sobre processos bioquímicos envolvidos no metabolismo da relação simbiótica podem ser adquiridas através de análises globais de expressão gênica. Para esta finalidade, destaca-se a tecnologia de microarranjo de DNA para detecção de genes diferencialmente expressos em larga escala. O objetivo geral deste trabalho foi identificar genes diferencialmente expressos, por meio de microarranjos de DNA, em Bradyrhizobium elkanii SEMIA 587 cultivada em diferentes meios de cultura, RDM (Rhizobia Defined Medium), TY (Triptone-Yeast Medium) e YMB (Yeast-Mannitol Medium), e em bacterióides isolados de nódulos de soja em diferentes períodos de desenvolvimento, 13, 28 e 48 dias após inoculação. Para esta finalidade, a partir do seqüenciamento de DNA genômico de B. elkanii, um microarranjo (Be587) foi gerado contendo 2654 genes. Em meio RDM, a bactéria confrontou-se com a necessidade de se adaptar e sintetizar suas subunidades formadoras de macromoléculas a partir de uma única fonte de carbono, refletindo em um metabolismo mais ativo nas fases lag e log. Por outro lado, em meio TY, as células cultivadas na presença de uma boa fonte de carbono e energia cresceram rapidamente esgotando os recursos disponíveis no meio, 8 o que pode ter causado uma situação de estresse que se refletiu na identificação... / Nitrogen is the most required nutrient by soybean culture. Advanced researches in genetic plant breeding and soil microbiology allowed the expansion in commercial inoculants applications containing strains of Bradyrhizobium japonicum and Bradyrhizobium elkanii. These bacteria infect plant roots and induce nodule formation which home the differentiated bacteria, named bacteroid. The bacteroid in turn is responsible for symbiotic nitrogen fixation. Biochemical knowledge about processes of symbiotic regulation can be acquired by global analysis of gene expression. To achieve such information, the DNA microarray technology, used for detection of differentially expressed genes in large scale, was used. The purpose of this work was identificate differentially expressed genes of Bradyrhizobium elkanii SEMIA 587, grown under different media conditions, such as RDM (Rhizobia Defined Medium), TY (Triptone- Yeast Medium) and YMB (Yeast-Mannitol Medium), and in bacteroids from soybean nodules at different developmental stages, 13, 28 e 49 days after inoculation. For this purpose, the DNA microarray Be587 with 2654 genes was generated from B. elkanii genomic DNA. In RDM medium the bacterium was confronted with the need of adaptation and building of macromolecules subunits from a single carbon source, what was reflected in a more active metabolism in lag and log phases. In turn, in TY medium with good carbon and energy sources the cells grew fastly and exhaust the medium sources available. Such condition can submitted the bacterial cells to a stress condition that reflected in the identification of higher number differentially expressed genes. At different bacteroids stages, the analysis detected genes related to nodulation and 10 nitrogen fixation regulation more than structural genes. Inasmuch, an organic nitrogen recycle might be involved... (Complete abstract, click electronic access below)

G-protein pathway suppressor 2 (GPS2) is a 36kD protein involved in a number of regulatory functions in key metabolic organs. First discovered as a suppressor of the RAS- and MAPK- signaling pathways, GPS2 is subsequently identified as part of the NCoR/SMRT corepressor complex that play an important regulatory role in gene transcription, and GPS2 is also involved in meiotic recombination in the nucleus. Recently, we identified a non-transcriptional role of GPS2 as an inhibitor of the pro-inflammatory JNK pathway activation in response to tumor necrosis factor alpha (TNF-a;) in the cytosol. This suggests that GPS2 function may be dependent on its cellular localization. However, an understanding of how GPS2 differentially target cellular compartments is still lacking. In this study, we show that a tightly controlled balance between GPS2 protein stabilization and degradation regulates the function of nuclear GPS2. Our results reveal that methylation by arginine methyltransferase PRMT6 and interaction with exchange factor TBL1 cooperate to protect GPS2 from Siah2-dependent proteasomal degradation, thus promoting GPS2 nuclear localization. In addition, our results link GPS2 protein instability to decreased nuclear-encoded mitochondrial gene expression, suggesting that GPS2 may play an important role in regulating mitochondrial oxidative capacity, whose imbalance has been linked to chronic inflammation and insulin resistance. In conclusion, our findings illustrate post-transcriptional modification is important in the regulation of GPS2 cellular function. Understanding such molecular regulation of GPS2 is critical in furthering future efforts to investigate its roles in cellular homeostasis and inflammatory responses.

Ebola virus (EBOV) causes severe disease in humans characterized by high case fatality rates and significant immune dysfunction. A hallmark of EBOV infection is the formation of viral inclusions in the cytoplasm of infected cells. These inclusions contain the EBOV nucleocapsids and are sites of viral replication and nucleocapsid maturation. Although there is growing evidence that viral inclusions create a protected environment that fosters EBOV gene expression and genome replication, little is known about their role in the host response to infection. The cellular stress response is an antiviral strategy that leads to stress granule (SG) formation and translational arrest mediated by the phosphorylation of the alpha subunit of eukaryotic translation initiation factor 2 (eIF2α). Related to this response is the post-transcriptional regulation of RNA mediated by stability elements called AU-rich elements (AREs) and their associated binding proteins (ARE-BPs), many of which are found in SGs. Because these processes have antiviral implications, many viruses have evolved strategies to interfere with SG formation, or appropriate ARE-BPs to benefit viral replication. However, it is unknown if EBOV interacts with these cellular systems. Here, we show that SG proteins were sequestered within EBOV inclusions where they formed distinct granules that colocalized with viral RNA. The inclusion-bound aggregates were not canonical SGs, and did not lead to translational arrest in infected cells. EBOV did not induce cytoplasmic SGs at any time post infection, but was unable to overcome SG formation induced by additional stressors. Despite the sequestration of SG proteins, canonical SGs did not form within inclusions. At high levels of expression, viral protein 35 (VP35), the viral polymerase co-factor that also mediates various immune evasion functions, disrupted SGs formation independently of eIF2α phosphorylation. Finally, we found that the cellular ARE-BP tristetraprolin (TTP) specifically targeted the 3’untranslated region (UTR) of the viral nucleoprotein (NP) mRNA and promoted its degradation. Interestingly, TTP was not found within viral inclusions, leading us to speculate that inclusions might serve to prevent viral RNA from encountering TTP. These results indicate that EBOV interacts with the cellular stress response and associated RNA regulatory proteins in ways that promote viral replication.

Splicing mainly occurs co-transcriptionally, suggesting that transcription and premRNA splicing could be synchronized. The nature of this phenomenon suggests that transcription elongation rate may influence splicing outcomes and, indeed, there is evidence for effects on alternative splicing in mammals. To elucidate potential effects of transcription rate on splicing efficiency and fidelity, splicing of nascent transcripts was investigated in fast and slow elongating RNA polymerase II (RNAPII) mutants in Saccharomyces cerevisiae. High kinetic resolution 4-thio Uracil labelling of nascent RNA reveals that fast RNAPII accumulates unspliced pre-mRNA that represents reduced co-transcriptional splicing. Conversely, low levels of unspliced pre-mRNA were detected in the slow mutant due to increased co-transcriptional splicing. The highly stable association of nascent transcripts with elongating RNAPII permits co-transcriptional splicing to be measured by analysis of transcripts that co-purify with RNAPII. Measuring co-precipitation of the spliced mRNA and excised intron that are associated with RNAPII demonstrates that splicing is mostly co-transcriptional with the slow mutant, and the fast mutant reduces co-transcriptional splicing. How elongation rate affects splicing fidelity in budding yeast and whether faster and slower transcription have the opposite effect on splicing fidelity as might be predicted by the kinetic coupling model is an open question. Using deep RNA sequencing, splicing fidelity was determined in yeast transcription elongation mutants. Results show that both fast and slow transcription reduce splicing fidelity mainly in ribosomal protein coding transcripts. Analysis reveals that splicing fidelity depends largely on intron length, secondary structure and splice site score. These analyses also provide new insights regarding the effect of altering transcription rate on selection of transcription start sites. Together, these results indicate that optimal splicing efficiency and fidelity require finely-tuned transcription speed.

Le virus de la maladie de Marek (GaHV-2), est un α-herpèsvirus induisant des lymphomes T chez le poulet. L’étude de la protéine IE ICP22 a montré que cette protéine est principalement asssociée à la phase lytique du cycle viral avec une localisation majoritairement cytoplasmique. Nos résultats montrent que cette protéine réprime la transcription des promoteurs viraux. Par ailleurs, nous avons montré que la protéine était produite à la fois à partir de deux transcrit, un transcrit monocistronique et un transcrit bicistronique de façon majoritaire. La transcription d’ICP22 est pilotée par un promoteur unique dont nous avons localisé le « core » promoteur dans les 200 nt en amont du gène. Dans notre étude, nous avons montré que le promoteur du gène ICP22 était faiblement soumis au mécanisme de méthylation. Ce promoteur peut être régulé par la protéine virale ICP4 connue pour être un transactivateur majeur au sein des alphaherpèsvirus. Enfin, nous avons mis en évidence qu’ICP22 était la cible de 3 miR viraux parmi lesquels la cible prédite pour le mdv1-miR-M1 et mdv1-miR-M5-3p entraînaient une diminution du taux du transcrit. / Marek’s disease virus (GaHV-2) is an α-herpesvirus that induces T-cell lymphoma in chickens. The study of the IE ICP22 protein showed that this protein is mainly associated to the lytic phase of the viral cycle viral with a cytoplasmic localization. Our results showed that this protein represses the transcription of the viral promoters. ICP22 protein is produced from two transcript, a monocistronic and a bicistronic. The transcription of ICP22 is drived by a unique promoter whose "core" promoter was located in the 200 nt upstream to the gene. In our study, we showed that ICP22 promoter was weakly subjected to régulation by methylation. This promoter is regulated by the viral protein ICP4 known to be a major transactivateur within alphaherpèsvirus. Finally, we highlighted that ICP22 was the target of 3 miR viral among which the target predicted for mdv1-miR-M1 and mdv1-miR-M5-3p decreased the rate of the ICP22 transcripts.

This thesis focuses on the functional and structural characterization of FtsH proteases in Synechocystis PCC 6803. One of the aims was to determine localization and subunit organization of FtsH homologues in Synechocystis cells using GST and GFP tagged FtsH derivatives. The main result of the thesis is identification of two FtsH hetero-oligomeric complexes and one homo-oligomeric complex in Synechocystis cells. The large part of the thesis is aimed at establishing the role of the first hetero-oligomeric complex, FtsH2/FtsH3, in quality control of Photosystem II and at identification of a mechanism, how its substrate proteins D1 and D2 are recognized. Another part is dedicated to characterization of the second hetero-oligomeric complex, FtsH1/FtsH3, which consists of two essential FtsH homologues and which is here identified as an important regulatory element in maintaining iron homeostasis.