Дисертації з теми "Ribosomal RNA (rRNA)"
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Crandall, Jacob N. "Ribosomal RNA Mutations that Inhibit the Activity of Transfer-Messenger RNA of Stalled Ribosomes." Diss., CLICK HERE for online access, 2010. http://contentdm.lib.byu.edu/ETD/image/etd3535.pdf.
Повний текст джерелаKshetri, Man B. "N-TERMINAL DOMAIN OF rRNA METHYLTRANSFERASE ENZYME RsmC IS IMPORTANT FOR ITS BINDING TO RNA AND RNA CHAPERON ACTIVITY." Kent State University Honors College / OhioLINK, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=ksuhonors1621007414429417.
Повний текст джерелаBendele, Kylie Gayle. "Molecular characterization of Theileria spp. using ribosomal RNA." Texas A&M University, 2004. http://hdl.handle.net/1969.1/2649.
Повний текст джерелаPark, Tae Jin, and 朴台鎮. "Microbial community ecology in bioelectrochemical systems (BESs) using 16S ribosomal RNA (rRNA) pyrosequencing." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2014. http://hdl.handle.net/10722/212634.
Повний текст джерелаBelotserkovsky, Jaroslav. "Studies on the functional interaction of translation initiation factor IF1 with ribosomal RNA." Doctoral thesis, Stockholms universitet, Institutionen för genetik, mikrobiologi och toxikologi, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-75363.
Повний текст джерелаAt the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 3: Manuscript.
Ciriello, Giovanni. "Structural studies of the ribosome: rRNA building blocks characterization and interactions analysis." Doctoral thesis, Università degli studi di Padova, 2009. http://hdl.handle.net/11577/3426117.
Повний текст джерелаLe prime strutture cristallizate ad alta risoluzione diedero inizio ad una nuova era negli studi sui ribosomi, era nella quale la ricerca beneficia delle coordinate spaziali di ogni singolo atomo. Gli studi che ho condotto sulla struttura tridimensionale del ribosoma puntano a compredere l’organizzazione modulare della molecola, ed allo stesso tempo ad investigare i meccanismi di interazione proteine-RNA. Tutti i risultati presentati in questa tesi riferiscono alla subunità principale 50S di Haloarcula marismortui, omettendo il filamento di RNA 5S. Motivi tridimensionali ricorrenti sono i mattoni basilari dell’architettura dello RNA ribosomiale: essi sono caratterizzati da una struttura 3D conservata, e ricorrono frequentemente all’interno della molecola. Un nuovo metodo per ricercare queste sotto strutture, basato su shape histogram, è presentato al Capitolo 2. Lo shape histogram è una rappresentazione vettoriale della distribuzione delle distanze di un insieme di punti da uno fissato. Gli shape histogram non sono solo strumenti efficienti per confrontare frammenti diversi di RNA, sono inoltre in grado di catturare le similarità strutturali nascoste dalla struttura flessibile ed altamente variabile dello RNA ribosomiale. Il metodo infatti si dimostra più efficiente di quelli noti in letteratura, ed ugualmente efficace in termini di correttezza dei risultati. Tra i loop studiati, le giunzioni di tre o più eliche sono il tipo più variabile e complesso, ed il meno caratterizzato. Gli shape histogram insieme alle sequenze di angoli formati dai frammenti congiungenti più eliche sono in grado di dare molte informazioni sulla conformazione tridimensionale di queste giunzioni: gli angoli forniscono indicazioni sull’eccentricità di una giunzione, mentre range e distribuzione dei valori degli shape histogram rivelano il folding. Basandosi su queste caratteristiche, propongo una classificazione per questi motivi rispetto alla loro conformazione nello spazio. Infine il Capitolo 4 esamina le interazioni proteine-RNA all’interno del ribosoma. Osservazioni di tipo statistico rivelano caratteristiche distintive del ribosoma rispetto alle interazioni proteiche con altri tipi di RNA, come ad esempio il ruolo dominante del gruppo ribosio. Inoltre vengono studiati i meccanismi di interazione delle proteine con i motivi strutturali, in particolare standard tetraloop, kink-turn e basi esposte. Un pattern comune di interazioni è rintracciato per le superfici di contatto formate dalle proteine con i tetraloop, caratterizzato da zone dense di interazioni fatte da aminoacidi a carica positiva (principalmente arginine). Le proteine ribosomiali rivelano inoltre un sito di contatto caratteristico nelle interazioni con i kink-turn, in corrispondenza della base esposta. Per la sua forma questo sito è stato chiamato tripod, ovvero tripode. I tripodi si sono dimostrati essere in realtà comuni a molti nucleotidi non accoppiati la cui base è esposta. Oltre ad una conformazione tridimensionale conservata, i tripodi dimostrano una preferenza verso le purine, soprattutto adenina, e tipicamente formano legami idrogeno.
Zarubica, Tamara. "SPECIFICITY DETERMINANTS OF ArmA, A RIBOSOMAL RNA METHYLTRANSFERASE THAT CONFERS ANTIBIOTIC RESISTANCE." VCU Scholars Compass, 2010. http://scholarscompass.vcu.edu/etd/2273.
Повний текст джерелаTrinquier, Aude. "Coupling between transfer RNA maturation and ribosomal RNA processing in Bacillus subtilis." Thesis, Université de Paris (2019-....), 2019. http://www.theses.fr/2019UNIP7066.
Повний текст джерелаCellular protein synthesis both requires functional ribosomes and mature transfer RNAs (tRNAs) as adapter molecules. The ribosomes are large essential ribonucleoprotein complexes whose biogenesis accounts for most of cellular transcription and consumes a major portion of the cell’s energy. Ribosome biogenesis is therefore tightly adjusted to the cellular needs and actively surveilled to rapidly degrade defective particles that could interfere with translation. Interestingly, tRNAs and ribosomal RNAs (rRNAs) are both transcribed from longer primary transcripts and universally require processing to become functional for translation. In this thesis, I have characterized a coupling mechanism between tRNA processing and ribosome biogenesis in the Gram-positive model organism Bacillus subtilis. Accumulation of immature tRNAs during tRNA maturase depletion, specifically abolishes 16S rRNA 3’ processing by the endonuclease YqfG/YbeY, the last step in small ribosomal subunit formation. We showed that this maturation deficiency resulted from a late small subunit (30S) assembly defect coinciding with changes in expression of several key 30S assembly cofactors, mediated by both transcriptional and post-transcriptional effects. Interestingly, our results indicate that accumulation of immature tRNAs is sensed by the stringent factor RelA and triggers (p)ppGpp production. We showed that (p)ppGpp synthesis and the accompanying decrease in GTP levels inhibits 16S rRNA 3’ processing, most likely by affecting GTPases involved in ribosome assembly. The inhibition of 16S rRNA 3’ processing is thought to further lead to degradation of partially assembled particles by RNase R. Thus, we propose a model where RelA senses temporary slow-downs in tRNA maturation and this leads to an appropriate readjustment of ribosome biogenesis. This coupling mechanism would maintain the physiological balance between tRNAs and rRNAs, the two major components of the translation machinery
Punekar, Avinash S. "Ribosomal RNA Modification Enzymes : Structural and functional studies of two methyltransferases for 23S rRNA modification in Escherichia coli." Doctoral thesis, Uppsala universitet, Struktur- och molekylärbiologi, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-212394.
Повний текст джерелаBond, Andrew Thomas. "The Role of Dbp2p in Both Nonsense-Mediated mRNA Decay and rRNA Processing: A Dissertation." eScholarship@UMMS, 2002. http://escholarship.umassmed.edu/gsbs_diss/150.
Повний текст джерелаWhite, Delonna M. "A Molecular Phylogeny of the Genus Bonamia Based on Sequence Data of the Ribosomal RNA (rRNA) Gene Complex." W&M ScholarWorks, 2008. https://scholarworks.wm.edu/etd/1539617875.
Повний текст джерелаWakeman, Jane A. "Human ribosomal RNA : primary structure analysis of the 28S rRNA gene and preliminary studies on the distribution of pseudouridine residues in the 18S and 28S rRNA molecules." Thesis, University of Liverpool, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.317264.
Повний текст джерелаZentner, Gabriel Etienne. "Genomic analysis of ribosomal DNA and its application to the investigation of disease pathogenesis." Case Western Reserve University School of Graduate Studies / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=case1321478238.
Повний текст джерелаJakobsson, Tell. "Lactobacillus iners and the normal vaginal flora." Doctoral thesis, Linköping : Department of Clinical and Experimental Medicine, Linköping University, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-11334.
Повний текст джерелаDebeila, Thipe Jan. "Characterisation of selected Culicoides (Diptera : Ceratopogonidae) populations in South Africa using genetic markers." Diss., University of Pretoria, 2010. http://hdl.handle.net/2263/25696.
Повний текст джерелаVeterinary Tropical Diseases
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Herdman, Chelsea. "Relative roles of UBF and RRN3 in the transcription of the ribosomal RNA genes and ribosome biogenesis determined using in vivo mouse models." Doctoral thesis, Université Laval, 2017. http://hdl.handle.net/20.500.11794/28387.
Повний текст джерелаRibosome biogenesis, or the synthesis of ribosomes, is an important cell process occurring in the nucleolus that utilizes transcription by all three nuclear RNA polymerases. The initial and rate-limiting step is the transcription of the catalytic ribosomal RNAs 28S, 18S and 5.8S in the form of a precursor ribosomal RNA (pre-rRNA/47S) by RNA polymerase I (RPI, also known as Pol1 and POLR1). RPI has a dedicated set of basal factors responsible for its activation. These are the architectural factor UBF, the TBP containing factor SL1, the initiation factor RRN3, and the termination factor TTF1. Ribosomal RNA synthesis is tightly regulated and accounts for 30-50% of total gene transcription. As such, this process is linked to cell growth, transformation, proliferation and the actions of tumour suppressors and oncogenes. Notably, UBF and RRN3 are activated by many of the same growth signaling pathways. The human and mouse haploid genome contain ~200 copies of the ribosomal RNA genes, the ribosomal DNA (rDNA). These ribosomal DNA copies are arranged in tandem repeats on the short arms of acrocentric chromosomes. Interestingly, only a fraction of the rDNA copies are active, and a significant number are epigenetically silenced and heterochromatic. The reason for having so many copies and their regulation in vivo by silencing is not yet understood, though it has been connected with genome stability. This thesis presents the analysis of the in vivo requirements for UBF and RRN3 in rRNA transcription and rDNA chromatin structure. We had previously analyzed the loss of UBF in mouse embryonic fibroblasts using tamoxifen-dependent conditional knockout. As we wanted to compare the loss of RRN3 in a similar model, we re-analyzed the RRN3 knockout mice and created cell lines as was performed for the UBF knockout. Importantly, we find that RRN3 is essential for preimplantation and its loss arrests development at E3.5, contrary to previous work that showed a late E9.5 developmental arrest. Using mouse embryonic fibroblast (MEF) cell lines conditional for UBF or RRN3, we found that the loss of either factor prevented RPI transcription. However, we found that UBF was essential for the recruitment of the other RPI transcription factors and the formation of the preinitiation complex, as well as to maintain an open rDNA chromatin structure, while RRN3 was required only for RPI recruitment. These studies allowed us to identify an upstream boundary element on the rDNA formed of H2A.Z, TTF1, CTCF and activating histone marks, which is independent of RPI activity. We also found that UBF loss, but not RRN3 loss, led to a synchronous and massive p53-independent apoptosis, specifically in oncogenically transformed cells. This strongly suggests that drug targeting UBF could be a viable cancer treatment. Finally, we have observed that the rDNA activity status in pluripotent cells differs from that of differentiated cells. Embryonic stem cells (ESCs) were also generated from the mice conditional for UBF and RRN3. Preliminary results indicate that, unlike somatic cells, all the rRNA genes in these and other pluripotent cell lines are potentially active. This makes ESCs and their differentiation an ideal model in which to study the establishment of rDNA silencing and the role of UBF and/or RRN3 in this process. Together these data define the in vivo roles of UBF and RRN3 in ribosomal RNA transcription and suggest mechanisms by which they maintain rDNA integrity and may drive cell differentiation.
Granato, Daniela Campos. "Caracterização da função da proteína Nop53p de Saccharomyces cerevisiae." Universidade de São Paulo, 2007. http://www.teses.usp.br/teses/disponiveis/46/46131/tde-31012008-081416/.
Повний текст джерелаIn eukaryotes, the rRNA processing depends on several factors, such as, endonucleases, exonucleases, RNA helicases, rRNA modifying enzymes and components of the snoRNPs. With the purpose of characterizing new proteins involved in pre-rRNA processing, Nop53p was identified interacting with the nucleolar protein Nop17p in a two hybrid assay. The conditional yeast strain containing the sequence of the ORF NOP53 under the control of the galactose promoter cannot grow in medium containing glucose, indicating that the protein is essential for cell viability. The results of this work demonstrate that Nop53p is involved in the initial steps of pre-rRNA processing and in the cleavages responsible for the formation of the mature rRNAs 5.8S and 25S. A more detailed analysis of the pre-rRNA processing, by Northern blot and pulse-chase labeling, revealed that Nop53p affects the processing of the 27S precursor, that originates the rRNAs 5.8S and 25S. Nop53p participates in the processing of these RNAs by affecting the polyadenylation of the precursors of the rRNAs 5.8S and 25S. RNA co-imunoprecipitation assays with the fusion protein A-Nop53p confirmed the involvement of Nop53p in the processing of the 27S pre-rRNA, indicating that the protein may interact directly with the RNA. The capacity of Nop53p to bind RNA was confirmed by in vitro assays, while chromatin imunoprecipitation assays demonstrated that Nop53p binds the 5.8S rRNA co- transcriptionally. Nop53p regulates the function of the exosome by interacting directly with the exclusively nuclear subunit of the complex, Rrp6p.
Kuo, Tai-chih. "The group I ribozyme from the chloroplast rRNA gene of Chlamydomonas reinhardtii : kinetic and structural analysis of the divalent metal requirement and specific interactions with manganese (II) /." Digital version accessible at:, 1998. http://wwwlib.umi.com/cr/utexas/main.
Повний текст джерелаPulicherla, Nagesh. "Characterization of Yeast 18S rRNA Dimethyl Transferase, Dim1p." VCU Scholars Compass, 2008. http://hdl.handle.net/10156/1636.
Повний текст джерелаSchillewaert, Stéphanie. "Etude de la maturation et de l'assemblage du ribosome eucaryote: caractérisation fonctionnelle de nouveaux facteurs trans-." Doctoral thesis, Universite Libre de Bruxelles, 2011. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/209826.
Повний текст джерелаParmi ces facteurs de synthèse, nous avons caractérisé en détail, chez la levure et chez l’homme, la protéine Las1 impliquée dans la maturation des deux extrémités de l’ITS2, séquence qui sépare les ARNr 5.8S et 25S/28S. Chez la levure, en absence de la protéine Las1, les analyses de profils de polysomes révèlent un déficit de sous-unité 60S et l’apparition d’« halfmères ». Les techniques de purification d’affinité et de gradient de sédimentation nous indiquent que Las1 est associée aux pré-ribosomes 60S et qu’elle interagit avec de nombreux facteurs de synthèse de la petite, de la grande sous-unité ou des deux. De plus, Las1 copurifie avec des pré-ribosomes qui contiennent aussi les exoribonucléases 5’-3’ Rat1/Rai1 et Xrn1. Rai1 coordonne la maturation aux deux extrémités de l’ARNr 5.8S. Nous suggérons que Las1 appartient à un macrocomplexe connectant spatialement des sites de clivages éloignés sur la séquence primaire du pré-ARNr qui seraient rapprochés suite au reploiement de l’ITS2.
Un autre aspect de ce travail de thèse consiste en l’étude de l’assemblage des particules ribonucléoprotéiques et plus spécifiquement du pré-ribosome et des sous-unités ribosomiques eucaryotes. Nous avons utilisé la technique d’immunoprécipitation de chromatine (Ch-IP) pour caractériser l’assemblage d’une structure appelée le « SSU processome ». Celui-ci correspond à un pré-ribosome en formation ainsi que l’assemblage des protéines ribosomiques sur l’ARNr naissant.
Enfin, nous avons étudié le rôle d’une plateforme d’activation de méthyltransférases d’ARN et de protéines, la protéine Trm112 dans la ribogenèse. Nous avons montré que chez la levure, Trm112 est impliquée dans la synthèse du ribosome et dans la progression de la mitose. En absence de cette protéine, les pré-ARNr sont dégradés par un mécanisme de surveillance. Trm112 copurifie avec plusieurs facteurs de synthèse du ribosome dont la méthyltransférase Bud23, impliquée dans la modification post-transcriptionnelle de l’ARNr18S. Trm112 est requise pour cette méthylation et nous postulons que la protéine Bud23 est incapable de se lier aux pré-ribosomes en l’absence de Trm112.
Doctorat en Sciences
info:eu-repo/semantics/nonPublished
Fleming, Ian Murray Cameron. "Studies on RNA Modification and Editing in Trypanosoma brucei." The Ohio State University, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=osu1452245560.
Повний текст джерелаZorbas, Christiane. "Etudes de la biogenèse du ribosome chez l'Homme." Doctoral thesis, Universite Libre de Bruxelles, 2015. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/209010.
Повний текст джерелаAu cours de ma thèse de doctorat, j’ai contribué à un projet systématique d’identification de facteurs d’assemblage (FA) du ribosome chez l’homme. Pratiquement, nous avons identifié 286 FA humains, dont beaucoup sont homologues aux facteurs levuriens connus, et 74 sont sans équivalent chez la levure. Par ailleurs, j’ai caractérisé en détail certains facteurs. En particulier, Trm112 pour lequel j’ai montré qu’il agit comme un stabilisateur de la méthyltransférase (MTase) Bud23, spécifique à l’ARNr 18S de la sous-unité levurienne 40S. J’ai également participé à la caractérisation de mutations à l’interface du complexe Bud23-Trm112. Enfin, j’ai contribué à l’étude de trois FA que nous avons identifiés chez l’homme, DIMT1L et WBSCR22-TRMT112. J’ai montré que ces protéines sont les orthologues des MTases levuriennes Dim1 et Bud23-Trm112, qu’elles sont requises pour la synthèse et la modification de l’ARNr mature de la petite sous-unité ribosomique, et qu’elles seraient impliquées dans un mécanisme conservé contrôlant la qualité de la voie de biosynthèse du ribosome.
La totalité des FA que nous avons identifiés en cellule humaine sont à la disposition de la communauté scientifique dans une base de données en ligne accessible sur la page www.RibosomeSynthesis.com. Nous espérons que cette ressource contribuera à une meilleure compréhension des mécanismes moléculaires sous-jacents au développement des ribosomopathies et à l’élaboration d’agents thérapeutiques efficaces.
Doctorat en sciences, Spécialisation biologie moléculaire
info:eu-repo/semantics/nonPublished
Gonzalez-Rico, Susana. "The role of RNA-binding proteins in the synthesis of ribosomal RNA in Mycobacterium tuberculosis : a study of the interactions of ribosomal protein S10 and NusB with the leader region of the single rrn operon." Thesis, University College London (University of London), 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.286690.
Повний текст джерелаVan, Den Elzen Antonia. "Etude du complexe Dom34-Hbs1 ressemblant aux facteurs de terminaison : analyse fonctionnelle de ses rôles dans le contrôle qualité des ARN et dans la stimulation de la traduction par dissociation des ribosomes inactifs." Thesis, Strasbourg, 2013. http://www.theses.fr/2013STRAJ110/document.
Повний текст джерелаProtein production is a cyclic process that consists of four stages: initiation, elongation, termination and recycling. During recycling the subunits of terminated ribosomes are dissociated, to make them available for new rounds of translation. If ribosomes stall during translation, ribosomes cannot terminate properly and canonical recycling cannot occur. Cells have mechanisms to rescue these stalled ribosomes. A complex formed by the factors Dom34 and Hbs1 induces their dissociation. This compex in RNA quality control, targeting RNAs that cause ribosomal stalling. In this thesis the importance of several functional sites of the Dom34-Hbs1 complex for the degradation of these RNA sis investigated. Details of and therelationship between RNA quality control pathways in which the complex functions are further investigated. Finally, a new role of this complex, dissociating inactive ribosomes and there by making their subunits available to re-enter the translation cycle is described
Iratni, Rabah. "Régulation de l'expression de l'opéron ribosomique rrn des plastes d'épinard." Université Joseph Fourier (Grenoble), 1994. http://www.theses.fr/1994GRE10229.
Повний текст джерелаGoldfeder, Mauricio Barbugiani. "Caracterização funcional da proteína Cwc24p de Saccharomyces cerevisiae." Universidade de São Paulo, 2008. http://www.teses.usp.br/teses/disponiveis/46/46131/tde-26112008-170559/.
Повний текст джерелаIn eukaryotes, the ribosome biogenesis involves a large number of factors, that are responsible for the rRNAs maturation and for their association with ribosomal proteins. The pre-rRNA processing pathway is very complex and includes many steps of nucleotide modifications and endo- and exonucleolytic cleavage reactions. The nucleotide modifications are directed by snoRNPs that are formed by snoRNAs and proteins, divided in two major groups, of box H/ACA (which direct pseudouridilation), or of box C/D (methylation). Although the snoRNP U3 presents the snoRNA sequences and the proteins characteristics of box C/D class, it is not involved in methylation, but rather in the early cleavages of pre-rRNA 35S. U3 snoRNA is transcribed from two intron-containing genes in yeast, snR17A and snR17B. Although the assembly of the U3 snoRNP has not been precisely determined, at least some of the core box C/D proteins are known to bind pre-U3 cotranscriptionally, thereby affecting splicing and 3\'-end processing of this snoRNA. We identified the interaction between the box C/D assembly factor Nop17p and Cwc24p, a novel yeast RING-finger protein which had been previously isolated in a complex with the splicing factor Cef1p. Here we show that, consistently with the protein interaction data, Cwc24p localizes to the cell nucleus, and its depletion leads to the accumulation of both U3 pre-snoRNAs. U3 snoRNA is involved in the early cleavages of 35S pre-rRNA, and the defective splicing of pre-U3 detected in cells depleted of Cwc24p causes the accumulation of the 35S precursor rRNA. These results led us to the conclusion that Cwc24p is involved in pre-U3 snoRNA splicing, indirectly affecting pre-rRNA processing.
Raoelijaona, Raivoniaina. "Compréhension des rôles des complexes Nob1/Pno1 et RPS14/Cinap dans la maturation cytoplasmique de la petite sous-unité ribosomique (pré-40S) chez les eucaryotes." Thesis, Bordeaux, 2019. http://www.theses.fr/2019BORD0221/document.
Повний текст джерелаRibosomes are translational machineries universally responsible of protein synthesis. In eukaryote, ribosome assembly is a complex and highly regulated process that requires coordinated action of more than 200 biogenesis factors. Ribosome assembly is initiated in the nucleolus, continues in the nucleoplasm and terminates in the cytoplasm. The cytoplasmic maturation events of the small ribosomal subunit are associated with sequential release of the late assembly factors and concomitant maturation of the pre-rRNA. During final maturation of the small subunit, the pre-18S rRNA is cleaved off by the endonuclease Nob1, which activity is coordinated by its binding partner Pno1. Detailed information on pre-ribosomal particle architectures have been provided by structural snapshots of maturation events. However, key functional aspects such as the architecture required for pre-rRNA cleavage have remained elusive. In order to better understand these late steps of cytoplasmic pre-40S maturation, we first redefine the domain organization of Nob1, then study its binding mode with Pno1 using different tools such as sequence analysis, structure prediction and biochemical experiments and, we then performed functional assay to elucidate the role played by Pno1 during the pre-18S rRNA maturation.Our results have shown that eukaryotic Nob1 adopts an atypical PIN domain conformation: two fragments (res 1-104 and 230-255) separated by an internal loop, which is essential for Pno1 recognition. We also found out that Pno1 inhibits Nob1 activity likely by masking the cleavage site. Our findings further support the recently published cryo-EM structure of the pre-40S, where Nob1 displays an inactive conformation. Moreover, 18S rRNA 3’-end cleavage has to happen and this implies structural rearrangement or requirement of some accessory proteins such as Cinap, an atypical kinase involved in pre-18S processing. Studying the interplay between proteins localized in the pre-40S platform (RPS14, RPS26, Nob1/Pno1 complex) has shown that Cinap is able to form a trimeric complex with Nob1 and its binding partner Pno1. Furthermore, Cinap can recognize RPS26 in a RPS14-dependent manner, which had already been studied with its yeast counterpart. It is important to note that RPS26 is the ribosomal protein replacing Pno1 in the mature ribosome. Our finding clearly suggests a mechanism where RPS26 recruitment to the ribosome requires Pno1 dissociation. This exchange would be carried out by Cinap. Therefore, we can suggest a simplified model as follow: upon binding with Pno1, the newly formed complex (Cinap/Pno1) will trigger a conformational change, which will allow the endonuclease Nob1 to reach its substrate (D-site) and perform its cleavage resulting in mature 18 rRNA generation
Cepeda, Leidy Paola Paez. "Caracterização da função molecular de Nop53 e de seu papel no controle do exossomo em Saccharomyces cerevisiae." Universidade de São Paulo, 2017. http://www.teses.usp.br/teses/disponiveis/46/46131/tde-22112017-140024/.
Повний текст джерелаAbstract Nop53 is a nucleolar, conserved and essential protein in the yeast Saccharomyces cerevisiae, involved in the biogenesis of the large ribosomal subunit 60S. The main phenotype of the depletion of Nop53 in yeast cells is the accumulation of the prerRNA processing intermediate 7S, which is also the substrate of the exosome complex for the formation of the mature rRNA 5:8S. Nop53 directly interacts with the exosome subunit Rrp6, and with the subunit Mtr4 of the TRAMP complex, an exosome co-activator. The main objective of this work was the analysis of the interaction between Nop53 and the exosome and the identication of the mechanism through which Nop53 regulates the exosome activity. The results shown here demonstrate that the depletion of Nop53 leads to a more stable association of the exosome with the pre-60S ribosome particle, as determined by co-immunoprecipitation of proteins with one of the exosome core subunits, and by fractionation of complexes through glycerol gradients. These results suggested that Nop53 could play a role in the release of the exosome after the formation of the mature rRNA 5:8S. This hypothesis was conrmed through the co-immunoprecipitation of pre-rRNA 7S with the exosome in the absence of Nop53. In addition to the interaction with the exosome subunit Rrp6, as shown here, Nop53 also interacts with core subunits of the complex. Interestingly, overexpression of one of these subunits, Rrp43, partially complements the depletion of Nop53. These results led to the conclusion that Nop53 may recruit the exosome to the pre-60S particle for the maturation of the pre-rRNA 7S to the mature 5:8S, but Nop53 may also be involved in the release of the exosome, possibly through its interaction with the helicase Mtr4.
Gill, Hardeep. "The Effect of Aluminium Industry Effluents on Sediment Bacterial Communities." Thèse, Université d'Ottawa / University of Ottawa, 2012. http://hdl.handle.net/10393/23423.
Повний текст джерелаBhattacharyya, Souvik. "Fidelity Of Translation Initiation In E. coli : Roles Of The Transcription-recycling Factor RapA, 23S rRNA Modifications, And Evolutionary Origin Of Initiator tRNA." Thesis, 2016. https://etd.iisc.ac.in/handle/2005/2574.
Повний текст джерелаCSIR
Bhattacharyya, Souvik. "Fidelity Of Translation Initiation In E. coli : Roles Of The Transcription-recycling Factor RapA, 23S rRNA Modifications, And Evolutionary Origin Of Initiator tRNA." Thesis, 2016. http://etd.iisc.ernet.in/handle/2005/2574.
Повний текст джерелаTranslation 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.
Muralidhara, Chaitanya. "Matrix and tensor decomposition methods as tools to understanding sequence-structure relationships in sequence alignments." 2010. http://hdl.handle.net/2152/9818.
Повний текст джерелаtext
Dey, Debayan. "Crystal Structures of Native and AdoMet Bound rRNA Methyltransferase from Sinorhizobium meliloti : Structural Insights into rRNA Recognition. Evolutionary, Structural and Functional Studies on Nucleoid-Associated Proteins HU and IHF." Thesis, 2016. http://etd.iisc.ac.in/handle/2005/4062.
Повний текст джерелаJasiński, Maciej. "Oddziaływanie syntetycznych oligomerów z rybosomowym RNA." Doctoral thesis, 2017. https://depotuw.ceon.pl/handle/item/2127.
Повний текст джерелаSyntetyczne oligomery kwasów nukleinowych, inaczej oligonukleotydy, to krótkie (zazwyczaj od kilku do kilkudziesięciu nukleotydów) nici kwasów nukleinowych o potencjalnych zastosowaniach terapeutycznych i diagnostycznych. Początek badań nad oddziaływaniami syntetycznych oligonukleotydów z RNA żywych organizmów przypada na koniec lat osiemdziesiątych XX wieku. Obecnie, najczęściej wykorzystywane są oligomery będące modyfikacjami naturalnych kwasów nukleinowych, które cechują się podwyższoną stabilnością w środowisku komórkowym i większą stabilnością tworzonych kompleksów. W przedstawionej pracy badane były oddziaływania oligomerów 2'-O-metylowanego RNA i peptydowego kwasu nukleinowego (PNA) z ważnym funkcjonalnie fragmentem rybosomowego RNA (rRNA) - tzw. miejscem A, które pełni kluczowe funkcje w procesie translacji. Odpowiada ono m.in. za zgodność sekwencji powstających w rybosomie łańcuchów polipeptydowych białek z informacją zawartą w matrycy mRNA. Opisane w pracy badania objęły porównanie właściwości modeli prokariotycznego i eukariotycznego rybosomalnego miejsca A oraz scharakteryzowanie oddziaływań oligonukleotydów 2'-O-metylowanego RNA i PNA z modelowymi fragmentami rRNA. W badaniach wykorzystane zostały obliczenia dynamiki molekularnej, oraz metody eksperymentalne: spektroskopia absorpcyjna i fluorescencyjna, izotermiczne miareczkowanie kalorymetryczne i elektroforeza żelowa. Wstępne badania z wykorzystaniem dynamiki molekularnej ujawniły brak odpowiednich narzędzi do analizy symulacji struktur kwasów nukleinowych. W związku z tym, stworzony został program do analizy struktur kwasów nukleinowych pod kątem charakterystycznych dla nich oddziaływań krótko- i dalekozasięgowych występujących między nukleotydami. Przeprowadzone w ramach pracy badania to część szerszego projektu, którego celem jest stworzenie nowych związków terapeutycznych, opartych o syntetyczne oligonukleotydy. Związki te, wiążąc się z wysoką specyficznością do funkcjonalnych miejsc rybosomów będą zapobiegały syntezie białek bakteryjnych. Przedstawiana praca składa się z pięciu części. W części pierwszej przedstawiono budowę i właściwości 2'-O-metylowanego RNA oraz PNA, oraz omówiono szerzej biologiczny aspekt pracy. Druga część stanowi opis wykorzystywanych metod obliczeniowych i doświadczalnych. W części trzeciej przedstawiony został program do analizy trajektorii dynamiki molekularnej kwasów nukleinowych MINT (ang. Motif Identifier for Nucleic Acids Trajectories). W części czwartej opisane zostały wyniki teoretycznych i doświadczalnych badań modeli prokariotycznego i eukariotycznego rRNA oraz oddziaływań oligonukleotydów 2'-O-metylowanego RNA z tymi modelami. Część piąta poświęcona jest badaniom możliwości wykorzystania obliczeń dynamiki molekularnej do przewidywania właściwości strukturalnych i stabilności termicznej kompleksów PNA z RNA.
Vazin, Mahsa. "Transcript Termination by RNA polymerase I in the fission yeast, Schizosaccharomyces pombe." Thesis, 2013. http://hdl.handle.net/10214/7289.
Повний текст джерелаNellimarla, Srinivas. "Structure Function Relationships in the 5' ETS of the Schizosaccharomyces pombe pre-rRNA." Thesis, 2012. http://hdl.handle.net/10214/3886.
Повний текст джерелаThis study was supported by the Natural Sciences and Engineering Research Council of Canada.
Γερμπανάς, Γεώργιος. "Επίδραση των πολυαμινών στη δομή και λειτουργία του 5s ριβοσωματικού RNA". 2006. http://nemertes.lis.upatras.gr/jspui/handle/10889/469.
Повний текст джерелаΣτα βακτήρια, η μεγάλη ριβοσωματική υπομονάδα αποτελείται από δύο είδη RNA, το 23S και το 5S rRNA, καθώς και 33 πρωτεΐνες. Ο σχηματισμός του πεπτιδικού δεσμού και η απελευθέρωση της πεπτιδικής αλυσίδας επιτελούνται στη μεγάλη υπομονάδα, όπου εδράζεται το καταλυτικό κέντρο της πεπτιδυλοτρανσφεράσης (PTase). Εκτός αυτού, η μεγάλη υπομονάδα περιλαμβάνει το κέντρο προσδέσεως των μεταφραστικών παραγόντων, το οποίο πυροδοτεί τη GTPase δραστηριότητα των G-πρωτεϊνικών παραγόντων, που εμπλέκονται στη μετατόπιση των υποστρωμάτων και άλλες ριβοσωματικές λειτουργίες. Έχει υποτεθεί ότι το 5S rRNA παίζει ουσιώδη ρόλο στη συγκρότηση του κέντρου της PTase και στη μετάδοση σημάτων μεταξύ του καταλυτικού κέντρου και των ριβοσωματικών συστατικών που διεκπεραιώνουν τη μετατόπιση των υποστρωμάτων. Το ιοντικό περιβάλλον φαίνεται να επηρεάζει καθοριστικά τη διαμόρφωση του 5S rRNA. Για παράδειγμα, έχει βρεθεί ότι οι πολυαμίνες δεσμεύονται εκλεκτικά στο 5S rRNA και επηρεάζουν τη δραστικότητα του έναντι του διμεθυλο-θεϊκού, ενός αντιδραστηρίου-ιχνηθέτη της τριτοταγούς δομής του RNA. Αρχικά ελέγξαμε αν υπάρχουν εξειδικευμένες θέσεις πρόσδεσης των πολυαμινών στο 5S rRNA. Στη συνέχεια, με σκοπό να ελέγξουμε αν η πρόσδεση των πολυαμινών επηρεάζει τη λειτουργία του 5S rRNA, 70S ριβοσώματα προγραμματισμένα με πολύ-ουριδυλικό σχηματίσθηκαν από 50S υπομονάδες, ολικά ή εκλεκτικά φωτοσημασμένες με ένα φωτοδραστικό ανάλογο της σπερμίνης και από 30S ακατέργαστες υπομονάδες. Αυτά τα ριβοσώματα είχαν την ικανότητα να δεσμεύουν AcPhe-tRNA ελαφρώς ισχυρότερα, σε σύγκριση με ριβοσώματα συγκροτημένα από φυσικά συστατικά, μη περιέχοντα πολυαμίνες. Το γεγονός αυτό υποδηλώνει ότι η πρόσδεση πολυαμινών στο 5S rRNA επηρεάζει, σε μικρό βαθμό, τη λειτουργία του παράγοντα επιμήκυνσης EF-Tu. Συζευγμένα, όμως, τα εν λόγω ριβοσώματα με tRNAPhe στην Ε-θέση και AcPhe-tRNAστην Ρ-θέση, επέδειξαν ισχυρότερη καταλυτική δραστικότητα και αυξημένη ικανότητα για μετατόπιση των υποστρωμάτων. Τα αποτελέσματα αυτά εισηγούνται σημαντική εμπλοκή των πολυαμινών στο λειτουργικό ρόλο του 5S rRNA κατά την κατάλυση και μετατόπιση των υποστρωμάτων.
In bacteria, the large ribosomal subunit comprises two RNA species, 23S and 5S rRNA, and 33 proteins. Peptide bond formation and peptide release are catalyzed by the large subunit, where the peptidyltransferase (PTase) center is located. In addition to this center, which triggers the GTPase activities of G-protein factors involved in translocation and other ribosomal functions. It has been hypothesized that 5S rRNA plays essential role in assembling the PTase center and mediating signal transmissions between this center and the translocation machinery. Furthermore, the ionic environment seems to affect the conformation of 5S rRNA. For instance, polyamines have been found to bind specifically to 5S rRNA and influence the 5S rRNA reactivity towards dimethyl-sulfate (DMS), a chemical probe of RNA tertiary structure. Initially we examined whether there are specific sites for binding of polyamines. To test whether the binding of polyamines influence the function of 5S rRNA poly(U)-programmed 70S ribosomes were reconstituted from 50S subunits, totally or specifically photolabelled in their 5S rRNA with a photoreactive analogue of spermine, and native 30S subunits. These ribosomes were found to enzymatically bind AcPhe-tRNA better than ribosomes reconstituted from native components. This means, that furnishing 5S rRNA with spermine slightly influences the elongation factor EF-Tu function. However, equipped with tRNAPhe at the A-site and AcPhe-tRNA at the P-site, these ribosomes exhibited higher catalytic activity and enhanced tRNA translocation efficiency. These results suggest an essential impact of polyamines on the functional role of 5S rRNA in catalysis and translocation of translation substrates.