Thesis (Ph. D.)--University of Washington, 1999. / Vita. Includes bibliographical references (leaves 98-115).

Techn. Hochsch., Diss., 2001--Aachen.

No description available.

No description available.

Les ribonucléases et les hélicases à ARN sont des acteurs clé du métabolisme des ARN et jouent donc des rôles cruciaux pour la régulation de l'expression des gènes. Peu de données sont connues concernant ce métabolisme chez les Archées, le troisième domaine du vivant. L'équipe dans laquelle j'ai effectué mes travaux de thèse s'intéresse au métabolisme de l'ARN chez les archées et plus particulièrement aux ribonucléases ß-CASP. Dans ce contexte, nous focalisons nos études sur la compréhension physiologique que pourrait jouer les ribonucléases ß-CASP aCPSF1 et aRNase J, orthologue respectivement du facteur de terminaison de la transcription eucaryotes CPSF-73 et RNase J bactérienne. Par analogie avec CPSF-73 et RNase J, qui font partie de complexes multi-protéiques, des indices sur les fonctions des homologues archéens de ces ribonucléases pourraient provenir de l'identification des complexes autour de aCPSF1 et aRNase J. Utilisant des extraits de Pyrococcus abyssi et les protéines recombinantes aCPSF1 et aRNase J comme appâts, nous avons identifié que aRNase J fait partie d'un réseau d'interaction incluant une hélicase de la famille des Ski2-like (ASH-Ski2). En parallèle, des fractionnements d'extrait de P. abyssi sur gradient de saccharose par ultracentrifugation indiquent que aRNase J et ASH-Ski2 sont présentes toutes deux dans les fractions de haut poids moléculaires avec les sous-unités du ribosome et ceux de l'exosome. Nous avons aussi démontré une interaction stable entre aRNase J et ASH-Ski2 ainsi que des motifs impliquées dans cette interaction par des expériences de co- purification par chromatographie d'affinité. De plus, les caractérisations biochimiques de ASH-Ski2 indiquent que cette protéine possède une activité d'hydrolyse de l'ATP dépendant de la présence d'acides nucléiques. ASH-Ski2 possède de plus la capacité d'hybridation et de déroulement de deux brins d'acides nucléiques en présence d'ATP. A notre connaissance, nos résultats sont les premiers à indiquer un complexe contenant une ribonucléase et d'une hélicase à ARN Ski2-like chez les archées. De manière intriguent, aRNase J est orthologue de la RNase J bactérienne et ASH-Ski2 des hélicases Ski2-like des eucaryotes. Cela démontre que les Archées pourraient posséder un système composite impliqué dans le métabolisme des ARN partageant des caractéristiques bactériens et eucaryotes. Ces résultats mettent en lumière l'avantage de l'étude des Archées pour la compréhension des mécanismes moléculaires et évolutives des processus fondamentaux des trois domaines du vivant. / Ribonucleases and RNA helicases are the main actors of RNA processing and have a critical role in gene expression regulation. Little is known about this process in Archaea. Our group focuses in RNA metabolism in Archaea involving ß-CASP ribonucleases. Recently, we published phylogenomic and experimental work demonstrating that archaeal ß-CASP proteins, aCFSF1 and aRNase J, are highly conserved ribonucleases in Archaea. Archaeal aCPSF1, an ortholog of the eukaryal transcription termination factor CPSF73, is ubiquitous in Archaea suggesting an essential conserved function. Archaeal aRNase J, an ortholog of the bacterial ribonuclease RNase J, is conserved through a major phylum of the Archaea, the Euryarchaeota. These findings suggest that the role of these enzymes in RNA processing can be reminiscent of ancient functions that had arisen early in evolution. We now want to focus on understanding the physiological role of aCPSF1 and aRNase J with the hyperthermophilic euryarchaeal Pyrococcus abyssi as model. By analogy to eukaryal CPSF73 and bacterial RNase J, which are part of multiprotein complexes, clues to the function of the archaeal ß-CASP homologs might come from the identification of archaeal multiprotein complex(es) containing aCPSF1 and aRNase J orthologs. Using P. abyssi cell extracts and recombinant aCPSF1 or aRNase J as bait, we have found that aRNase J is a part of protein interaction networks that include Ski2-like RNA helicase (ASH-Ski2). In parallel, fractionation of P. abyssi whole cell extracts in sucrose gradient by ultracentrifugation shows that aRNase J and ASH-Ski2 are present in high sedimentation fractions with ribosomal and exosome sub-units. We also demonstrate a direct interaction of aRNase J with ASH-Ski2 by co-purification affinity chromatography experiments and identify motifs that potentially involve in this interaction. Biochemical characterization of ASH-Ski2 demonstrates a nucleic dependant ATPase activity. ASH-Ski2 also possesses annealing and unwinding activities in presence of ATP. To our knowledge, our results are the first experimental indications of interacting of a complex containing ribonuclease and RNA helicase-like proteins in Archaea. Remarkably, aRNase J is an orthologue of the bacterial RNase J and ASH-Ski2 is an orthologue of the eukaryotic Ski2-like family proteins. This shows that Archaea might possess a composite RNA processing system sharing both eukaryal and bacterial features. This highlights the advantage of an archaeal model to gain further mechanistic and evolutionary information of fundamental processes across the three domains of life.

3′ repair exonuclease 1 (TREX1) is a known DNA exonuclease involved in autoimmune disorders and the antiviral response. In this work, we show that TREX1 is also a RNA exonuclease. Purified TREX1 displays robust exoribonuclease activity that degrades single-stranded, but not double-stranded, RNA. TREX1-D200N, an Aicardi-Goutieres syndrome disease-causing mutant, is defective in degrading RNA. TREX1 activity is strongly inhibited by a stretch of pyrimidine residues as is a bacterial homolog, RNase T. Kinetic measurements indicate that the apparent Km of TREX1 for RNA is higher than that for DNA. Like RNase T, human TREX1 is active in degrading native tRNA substrates. Previously reported TREX1 crystal structures have revealed that the substrate binding sites are open enough to accommodate the extra hydroxyl group in RNA, further supporting our conclusion that TREX1 acts on RNA. These findings indicate that its RNase activity needs to be taken into account when evaluating the physiological role of TREX1.

No description available.

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第22493号 / 農博第2397号 / 新制||農||1076(附属図書館) / 学位論文||R2||N5273(農学部図書室) / 京都大学大学院農学研究科食品生物科学専攻 / (主査)教授 保川 清, 教授 佐々木 努, 教授 橋本 渉 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

<p>The food-borne pathogen, <em>Listeria monocytogenes</em>, is a global health concern as it has been responsible for multiple food contamination outbreaks over the past century. Current detection methods like the enzyme-linked immunoassays (ELISA), and polymerase chain reaction (PCR) take over 24 h to attain results, are costly, require specialized equipment and trained personnel. In this study we investigated the use of functional nucleic acid (FNA) to develop a rapid and cost-effective detection method for <em>L. monocytogenes</em>. We carried out in<em> vitro</em> selection in order to isolate a fluorescently labeled DNA-RNA hybrid strand that can be bound and cleaved by specific endoribonucleases (RNase) from <em>L. monocytogenes</em>. We termed these DNA-RNA hybrid strands RNase-cleaved fluorescent substrate (RFS). Since no past studies have isolated RNases from <em>L. monocytogenes</em>, we first identified the genes based on sequence similarities with well characterized RNases. We purified and characterized RNase HII, RNase III and RNase G. Since this study focused primarily on developing RFS for RNase HII, we performed an in depth <em>in vitro</em> biochemical analysis to characterize this enzyme. We found that RNase HII from <em>L. monocytogenes</em> plays an important role in DNA replication and repair. Furthermore, we obtained six sequence classes by <em>in vitro</em> selection which could interact with RNase HII. The key nucleotide regions involved with RNase HII interactions were identified. In the final study, we showed the sequences isolated by <em>in vitro</em> selection could also be used as a tool to study ribonuclease function and identify new interaction between enzyme and substrate.</p> / Master of Science (MSc)

The bacteriophage T7 protein kinase enhances T7 growth under suboptimal growth conditions, including elevated temperature or limiting carbon source. T7PK phosphorylates numerous E. coli proteins, and it has been proposed that phosphorylation of these proteins is responsible for supporting T7 replication under stressful growth conditions. How the phosphorylation of host proteins supports T7 growth is not understood. Escherichia coli (Ec) RNase III is phosphorylated on serine in bacteriophage T7-infected cells. Phosphorylation of Ec-RNase III induces a ~4-fold increase in catalytic activity in vitro. Ec-RNase III is involved in the maturation of several T7 mRNAs, and it has been shown that RNase III processing controls the translational activity and stability of the T7 mRNAs. Perhaps T7PK phosphorylation of Ec- RNase III ensures optimal processing of T7 mRNAs under suboptimal growth conditions. In this study a biochemical analysis was performed on the N-terminal portion of the 0.7 gene (T7PK), exhibiting only the protein kinase activity. In addition to phosphotransferase activity, T7PK also undergoes self-phosphorylation on serine, which down-regulates catalytic activity by an unknown mechanism. Mass spectral analysis revealed that Ser216 is the autophosphorylation site in T7PK. The serine residue is highly conserved, which in turn suggests that autophosphorylation is a conserved reaction with functional importance. Phosphorylated T7PK exhibits reduced phosphotransferase activity, compared to its dephosphorylated counterpart (dT7PK). The dT7PK exhibits enhanced ability to phosphorylate proteins, as well as undergo autophosphorylation. The mechanism by which autophosphorylation inhibits T7PK activity is unknown. An in vitro phosphorylation assay revealed that T7PK directly phosphorylates RNase III. Ec-RNase III processing activity is stimulated from two to ten-fold upon phosphorylation by the T7PK. The primary site of phosphorylation in RNase III is found to be Ser33, and Ser34 may act as the recognition determinant for T7PK. This was established by Ser →Ala mutations at the concerned site. The enhancement of catalytic activity is primarily due to a larger turnover number (kcat), with some additional contribution from a greater substrate binding affinity, as revealed by lower Km and K‟D values. Substrate cleavage assays under single turn over conditions established that the product release is the rate limiting step. Since there is no significant increase in the kcat as measured under single-turnover (enzyme excess) conditions, the increase in the kcat in the steady-state is due to enhancement of the product release step, and not due to an enhancement of the hydrolysis (chemical) step. / Chemistry