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Jenvert, Rose-Marie. "The ribosome, stringent factor and the bacterial stringent response". Doctoral thesis, Stockholm : Wenner-Gren Institute for Experimental Biology, Stockholm University, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-6739.
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Bouakaz, Lamine. "Versatile Implementations of an Improved Cell-Free System for Protein Biosynthesis : Functional and structural studies of ribosomal protein L11 and class II release factor RF3. Novel biotechnological approach for continuous protein biosynthesis". Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Universitetsbiblioteket [distributör], 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-6325.
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Gilkes, Daniele M. "Multiple modes of MDMX regulation affect p53 activation". [Tampa, Fla.] : University of South Florida, 2008. http://purl.fcla.edu/usf/dc/et/SFE0002312.
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Petrov, Alexey. "Wiring the ribosome: functions of ribosomal proteins L3 and L10, and 5S rRNA". College Park, Md. : University of Maryland, 2006. http://hdl.handle.net/1903/4082.
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Thesis (Ph. D.) -- University of Maryland, College Park, 2006.Thesis research directed by: Cell Biology & Molecular Genetics. Title from t.p. of PDF. Includes bibliographical references. Published by UMI Dissertation Services, Ann Arbor, Mich. Also available in paper.
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Mandava, Chandra Sekhar. "Ribosomal Stalk Protein L12 : Structure, Function and Application". Doctoral thesis, Uppsala universitet, Struktur- och molekylärbiologi, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-157198.
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Ribosomal stalk proteins are known to play important role in protein synthesis. The ‘stalk’, an extended structure on the large subunit of the ribosome is composed mainly of two to three dimers of L12 and one L10 protein, which forms the base of the stalk. In E. coli, four copies of L12 molecules exist as dimer of dimers forming the pentameric L8 complex together with L10. This thesis is a collection of four interlinked studies on the structure, function and application of the ribosomal stalk protein L12. In the first study, we have mapped the interaction sites of the four major translation GTPase factors (IF2, EF-Tu, EF-G & RF3) on L12 molecule using heteronuclear NMR spectroscopy. Surprisingly, all these factors produced an overlapping interaction map spanning two α-helices on the C terminal domain of L12, thereby suggesting a general nature of the interaction between L12 and the GTPase factors. L12 is known to stimulate GTPase activity of the elongation factors EF-Tu and EF-G. Here, we have clarified the role of L12 in IF2 mediated initiation of protein synthesis. Our data suggest that rapid subunit association requires a specific interaction between the L12 protein on the 50S and IF2·GTP on the 30S preinitiation complex. We have also shown that L12 is not a GAP for IF2 and GTP hydrolysis triggers IF2 release from the 70S initiation complex. The next question we have addressed is why multiple copies of L12 dimer are needed on the ribosome. For this purpose, we created a pure E. coli strain JE105, where the terminal part of rplJ gene coding for the binding site of one L12 dimer on protein L10 was deleted in the chromosomal locus. Using ribosomes with single L12 dimer we have observed that the rate of the initiation and elongation involving IF2 and EF-G gets most compromised, which in turn decreases the growth rate of the bacteria. This study also indicates that L12 can interact with different GTPase factors in a specialized manner. Lastly, we have developed an application making advantage of the multiple L12 dimers on the ribosome. By inserting a (His)6-tag at the C-terminus of the L12 protein we have created a novel E. coli strain (JE28), where all ribosomes are tetra-(His)6-tagged. Further, we have developed a single step method for purification of the active (His)6-tagged ribosomes from JE28.
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Simmons, Mary Kecia Rigsby. "Genetic characterization of ribosomal protein L10 in Saccharomyces cerevisiae". College Park, Md. : University of Maryland, 2005. http://hdl.handle.net/1903/2659.
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Thesis (M.S.) -- University of Maryland, College Park, 2005.Thesis research directed by: Cell Biology & Molecular Genetics. Title from t.p. of PDF. Includes bibliographical references. Published by UMI Dissertation Services, Ann Arbor, Mich. Also available in paper.
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Pereira, Larissa Miranda. "Clonagem, expressão, purificação e caracterização estrutural da proteína ribossomal L10 humana recombinante". Universidade de São Paulo, 2009. http://www.teses.usp.br/teses/disponiveis/85/85131/tde-22092011-101810/.
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A proteína ribossomal L10 (RP L10) é uma forte candidata a ser incluída na classe de proteínas supressoras de tumor. Também denominada QM, a proteína em questão é conhecida por participar da ligação das subunidades ribossomais 60S e 40S e da tradução de mRNAs. Possui massa molecular entre 24 a 26 kDa e ponto isoelétrico (pI) 10,5. A seqüência da proteína QM é bastante conservada em mamíferos, plantas, invertebrados, insetos e leveduras indicando que esta possui funções críticas na célula. Com função supressora de tumor, a proteína RP L10 foi estudada em linhagens de tumor de Wilm (WT-1) e em células tumorais de estômago, nas quais se observou uma diminuição na quantidade de seu mRNA. Mais recentemente a RP L10 foi encontrada em baixas quantidades nos estágios iniciais de adenoma de próstata e com uma mutação em câncer de ovário, indicando uma participação no desenvolvimento destas doenças. Como proteína, já foi descrito que esta interage com as proteínas c-Jun e c-Yes, inibindo a ação ativadora de fatores de crescimento e divisão celular. Este trabalho tem um papel importante no estabelecimento da expressão desta proteína solúvel, para estudos posteriores que tenham como objetivo avaliar a ação de regiões específicas que atuam na ligação das subunidades ribossomais 60S e 40S e tradução, bem como nas regiões que se ligam a proto-oncogenes. O cDNA para proteína QM foi amplificado por PCR e clonado no vetor de expressão periplásmica p3SN8. A proteína QM foi expressa em E.coli BL21 (DE3) no citoplasma e periplasma bacteriano e na melhor condição, a expressão de QM de bactérias transformadas pelo plasmídeo recombinante p1813_QM em 25°C ou 30°C, a proteína foi obtida solúvel e com quantidad es muito pequenas de contaminantes. Os ensaios de estrutura secundária demonstraram que a proteína QM tem predominância de a-hélice, mas quando do seu desenovelmento, essa condição muda e a proteína passa a ter característica de folhas β.The ribosomal protein L10 (RP L10) is a strong candidate to be included in the class of tumor suppressor proteins. This protein, also denominated as QM, is known to participate in the binding of ribosomal subunits 60S and 40S and the translation of mRNAs. It has a molecular weight that varies between 24 and 26 kDa and an isoelectric point of (pI) 10.5. The sequence of the protein QM is highly conserved in mammals, plants, invertebrates, insects and yeast which indicates its critical functions in a cell. As a tumor suppressor, RP L10 has been studied in strains of Wilm\'s tumor (WT-1) and tumor cells in the stomach, where was observed a decrease in the amount of its mRNA. More recently, the RP L10 was found in low amounts in the early stages of prostate adenoma and showed some mutation in ovarian cancer, what indicates its role as a suppressor protein in the development of these diseases. It has also been described that this protein interacts with c-Jun and c-Yes inhibiting growth factors and consequently, cell division. This work has an important role on the establishment of soluble expression of QM to give base information for further studies on expression that aim to evaluate the specific regions where it acts binding the 60S and 40S ribossomal subunits and translation, as well as its binding to proto-oncogenes. The cDNA for QM protein was amplified by PCR and cloned into periplasmic expression vector p3SN8. The QM protein was expressed in E. coli BL21 (DE3) in the region of cytoplasm and periplasm, the best condition was obtained from the expression of the recombinant plasmid QM p1813_QM at 25°C or 30°C, the soluble protein was obtained with small amounts of contaminants. The assays of secondary structure showed that the QM protein is predominantly alpha-helix, but when it loses the folding, this condition changes and the protein is replaced by β- sheet feature.
8
Burnett, Tracey A. "Analysis of the novel surface protein P159 and the ribosomal protein L7/L12 of mycoplasma hyopneumoniae". Access electronically, 2005. http://www.library.uow.edu.au/adt-NWU/public/adt-NWU20051104.145934/index.html.
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Simoff, Ivailo. "Ribosomal proteins L5 and L15 : Functional characterisation of important features, in vivo". Doctoral thesis, Stockholms universitet, Wenner-Grens institut, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-27731.
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Protein synthesis is a highly regulated and energy consuming process, during which a large ribonucleoprotein particle called the ribosome, synthesizes new proteins. The eukaryotic ribosome consists of two unequal subunits called: small and large subunits. Both subunits are composed of ribosomal RNA (rRNA) and ribosomal proteins (r-proteins). Although rRNAs build the matrix of the ribosome and carries out catalysing of the peptide-bond formation between amino acids, r-proteins also appear to play important structural and functional roles. The primary role of r-proteins is to initiate the correct tertiary fold of rRNA and to organize the overall structure of the ribosome. In this thesis, I focus on two proteins from the large subunit of the eukaryotic ribosome: r-proteins L5 and L15 from bakers yeast S. cerevisiae. Both r-proteins are essential for ribosome function. Their life cycle is primarily associated with rRNA interactions. As a consequence, the proteins show high sequence homology across the species borders. Furthermore, both L5 and L15 are connected to human diseases, which makes the study their role in ribosome biogenesis and ribosome function important. By applying random- and site-directed mutagenesis, coupled with functional complementation tests, I aimed to elucidate functionally regions in both proteins, implicated in transport to the cell nucleus, protein-protein interactions and/or rRNA binding. The importance of individual and multiple amino acid exchanges in the primary sequence of rpL5 and rpL15 were studied in vivo. The obtained results show that S. cerevisiae rpL15 was tolerant to amino acid exchanges in the primary sequence, whereas rpL5 was not. Consequently, A. thaliana rpL15 could substitute for the function of wild type rpL15, whereas none of the tested orthologous proteins to rpL5 could substitute yeast rpL5 in vivo. These observations further emphasize the importance of studying r-proteins as separate entities in the ribosome context.
10
Fu, Yang. "Identification and Characterization of Novel Ribosomal Protein-binding RNA motifs in Bacteria". Thesis, Boston College, 2014. http://hdl.handle.net/2345/3795.
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Thesis advisor: Michelle M. MeyerAs the factory responsible for producing proteins, ribosomes are of great importance. In bacteria, ribosomes are composed of three ribosomal RNAs (rRNA) of different sizes, and around 50 ribosomal proteins (r-protein). During ribosome biogenesis in bacteria, synthesis of rRNAs and r-proteins are both tightly regulated and coordinated to ensure robust growth. In particular, a group of cis-regulatory RNA elements located in the 5' untranslated regions or the intergenic regions in r-protein operons are responsible for the regulation of r-protein biosynthesis. Based on the fact that RNA-regulated r-protein biosynthesis is essential and universal in bacteria, such unique and varied regulatory RNAs could provide new targets for antibacterial purpose. In this thesis, we report and experimentally verify a novel r-protein L1 regulation model that contains dual L1-binding RNA motif, and for the first time, a S6:S18 dimer-binding RNA structure in the S6 operon. We also describe Escherichia coli-based and Schizosaccharomyces pombe-based reporter systems for in vivo characterization of RNA-protein interactions. So far, both in vivo systems failed to report RNA-protein interactions, and thus need further tuning. In addition, we performed phage-display to select for regulatory RNA-binding small peptides and examined their effects on bacteria viability. One selected peptide, N-TVNFKLY-C, caused defective growth when overexpressed in E. coli. Yet, further studies must be conducted to verify the possibility that bacteria were killed by direct RNA-peptide interaction that disrupted the native r-protein regulation
Thesis (MS) — Boston College, 2014
Submitted to: Boston College. Graduate School of Arts and Sciences
Discipline: Biology
11
PEREIRA, LARISSA M. "Clonagem, expressao, purificacao e caracterizacao estrutural da proteina ribossomal L10 humana recombinante". reponame:Repositório Institucional do IPEN, 2009. http://repositorio.ipen.br:8080/xmlui/handle/123456789/9478.
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Made available in DSpace on 2014-10-09T12:27:09Z (GMT). No. of bitstreams: 0Made available in DSpace on 2014-10-09T13:57:22Z (GMT). No. of bitstreams: 0
Dissertacao (Mestrado)
IPEN/D
Instituto de Pesquisas Energeticas e Nucleares - IPEN-CNEN/SP
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Klyashtornyy, Vladislav. "Principles of protein nucleic acid : recognition on the examples of the ribosomal protein L1 and the cold shock domain of YB-1 protein". Thesis, Evry-Val d'Essonne, 2012. http://www.theses.fr/2011EVRY0039/document.
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Cette thèse est une étude structurale sur l’interaction entre 2 protéines modèles et des acides nucléiques : la protéine L1 (navette ribosome/ARN messagers) et le sous domaine CSD de YB-1, protéine régulatrice de la transcription et traduction. Deux méthodes sont utilisées : i) diffraction des RX par des cristaux de complexes L1:ARN ribosomal ou messager et ii) modélisation et dynamique moléculaire pour l’interaction CSD avec des homo-ribo- ou homo-deoxyribo-nucléotides simple brin. Les méthodes sont décrites avec leurs forces et limites. Les résultats sur L1-rARN/ARN éclairent les mécanismes de régulation de la traduction en montrant des différences d’affinité pour l’ARN des sous domaines I et II de L1. L’analyse de mutants de L1 dans le site de liaison à l’ARN du sous domaine I éclairent la nature des liaisons non covalentes sous tendant l’affinité de ce sous domaine pour l’ARN et souligne l’importance de la structure de L1, de sa « complémentarité » avec l’ARN et de liaisons hydrogènes non accessibles au solvant. Les travaux de modélisation et de dynamique moléculaire sur l’interaction CSD:acides nucléiques montrent que la séquence nucléotidique module l’affinité de ce complexe, l’oligonucléotide de type oligoG donnant le complexe le plus stable suivi des séquences de type oligoU et oligoA puis des oligoT et oligoC. L’orientation du brin d’ARN par rapport au CSD impacte aussi la stabilité du complexe. Une analyse des surfaces d’interaction et de la nature des liaisons intermoléculaires, montre que des principes similaires guident l’interaction L1:ARN et CSD:acides nucléiques : géométrie complémentaire des partenaires et liaisons hydrogène protégées du solvantThis thesis is a structural study on the interaction between two model proteins and nucleic acids: the L1 protein (shuttle ribosome/mRNA) and the CSD subdomain of YB-1, a protein that regulates transcription and translation. Two methods are used: i) X-ray diffraction by crystals of L1:ribosomal or messenger RNA complexes and ii) molecular modeling and dynamics for the CSD interaction with homo-ribo or homo-deoxyribo- single-stranded nucleotide. The methods are described with their strengths and limitations. Results on L1-rARN/ARN enlighten the mechanisms regulating translation by showing differences in affinity for RNA of the subdomains I and II of L1. Analyses of L1 mutants in the RNA binding site from the subdomain I illuminate the nature of non-covalent bonds subtending the affinity of this subdomain for RNA and stress the importance of the structure of L1, its "complementarity" with RNA and of hydrogen bonds not accessible to the solvent. Molecular modeling and dynamics of the CSD:nucleic acids interaction shows that the nucleotide sequence modulates the affinity of the complex, oligoG giving the most stable complex followed by oligoU and then oligoA or oligoT and oligoC. The orientation of the RNA strand relative to the CSD also impacts the stability of the complex. An analysis of the interaction surfaces and of the nature of intermolecular bonds, shows that similar principles guide the L1: RNA and CSD: nucleic acids interactions, i.e. a complementary geometry between partners and presence of hydrogen bonds protected from the solvent
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Vanet, Anne. "Etude de l'expression et de la fonction d'une methyltransferase modifiant une proteine particuliere (l11), du ribosome d'escherichia coli". Paris 7, 1994. http://www.theses.fr/1994PA077101.
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Le but de cette these est d'etudier l'expression et la fonction de la methyltransferase de la proteine ribosomique l11 d'escherichia coli. Elle comprend une introduction qui traite de toutes les modifications du ribosome d'une part, et de l'expression genetique de l11 d'autre part. Le deuxieme chapitre presente les resultats obtenus durant cette these: le gene prma qui a ete sous-clone et sequence est bien le gene de structure de la l11-methyltransferase. Ce gene est cotranscrit avec panf, determinant genetique specifiant la permease du pantothenate. Le gene prma n'est pas essentiel a la survie de la bacterie. L'etude de deux souches portant des mutations dans le gene structurale de cette l11-methyltransferase a ete faite. Les resultats en annexe exposent plus particulierement le role de la proteine fis dans l'activation des operons stables d'escherichia coli
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Elhag, Gasmalla Abdelwahab. "Molecular characterization of full-length cDNAs for nuclear-encoded chloroplast ribosomal proteins L12, L24 and L27 of Nicotiana tabacum". Diss., The University of Arizona, 1991. http://hdl.handle.net/10150/185581.
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Poly(A)⁺ mRNA isolated from Nicotiana tabacllm (cv. Petite havana) leaves was used to prepare a cDNA library in the expression vector Agtll. The library was screened with antibodies raised against proteins of chloroplast 50S ribosomal subunits. Full length cDNAs for three nuclear-encoded tobacco chloroplast large ribosomal subunit proteins were identified and sequenced. The deduced protein sequences are homologous to E. coli ribosomal proteins L12 (involved in GTP hydrolysis), L24 (a ribosomal RNA binding protein) and L27 (a constituent of peptidyltransferase ). The full-length cDNA encoding tobacco chloroplast ribosomal protein L12 is 773 nucleotides long, and encodes a mature protein of 133 amino acids and a transit peptide of 53 amino acids. The amino terminus of the mature protein was confirmed by protein sequencing of the first 12 amino acids. The deduced amino acid sequence of tobacco L12 protein has a high degree of identity with chloroplast ribosomal protein L12 of spinach (70%) and E. coli (51 % ). A full-length cDNA encoding tobacco chloroplast ribosomal protein L24 is 862 nucleotides long and encodes a mature protein of 157 amino acids and a putative transit peptide of 30 amino acids. The deduced amino acid sequence of tobacco L24 protein has a high degree of identity with chloroplast ribosomal protein L24 of pea (73%) and E. coli (35%). The fusion protein from the clone coding the tobacco L24 ribosomal protein was bound to nitrocellulose filters and used as affinity matrix to purify the antibody to the L24 protein. Monospecific antibody to L24 was used to identify, by Western blotting, the L24 ribosomal protein among purified proteins of the large subunit of the chloroplast ribosome. A full-length eDNA encoding tobacco ribosomal protein L27 is 882 nucleotides long and encodes a mature protein of 128 amino acids and a putative transit peptide of 51 amino acids. The deduced amino acid sequence of tobacco L27 protein has a high degree of identity with E. coli ribosomal protein L27 (64%) in the overlapping region between the two proteins. Besides the transit peptide, both ribosomal proteins L24 and L27 sequences have a carboxyl-terminal extension. Using Northern blot analysis, unique full size cytoplasmic mRNAs were observed for the three different proteins. For each of the three proteins (L12, L24, L27), at least two cDNAs with identical coding sequence and different 3'-non-coding sequences were identified. Southern blot analysis of genomic DNA indicated the presence of more than one gene for each of the three proteins. Furthermore, genomic clones likely to represent two different genes were isolated for tobacco ribosomal protein L27.
15
Willumeit, Regine. "Lokalisierung der Proteine L1, S6 und S10 des E.-coli-Ribosoms mit spinabhängiger Neutronenkleinwinkelstreuung /". Geesthacht : GKSS, 1996. http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&doc_number=007390140&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA.
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GAUVIN, SEGANTIN SYLVIANE. "Expression du gene rpl21 codant pour la proteine l21 du ribosome plastidiale de l'epinard : etude de deux elements du promoteur". Université Joseph Fourier (Grenoble), 1996. http://www.theses.fr/1996GRE10213.
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Deux elements du promoteur du gene rpl21 (sequence ct et site s2) codant pour la proteine l21 du plaste d'epinard ont ete etudies. Leur role dans la regulation de l'expression du gene rpl21 a ete etudie en transgenie et par des experiences d'interactions in vitro adn-proteines. La sequence oligopyrimidique ct est essentielle a l'expression du gene rpl21 in vivo. Le site s2 est responsable d'une activation de l'expression in vivo du gene rpl21 au niveau des feuilles uniquement. Cette activation est subordonnee a la fixation d'un facteur feuille-specifique (s2f), et a des interactions proteines-proteines avec d'autres facteurs lies au promoteur rpl21
17
Sanejouand, Yves-Henri. "Etude theorique des mouvements internes de grande amplitude de la decaalanine et du fragment c-terminal de la proteine ribosomale l7/l12". Paris 11, 1990. http://www.theses.fr/1990PA112136.
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La plasticite des proteines joue un role majeur dans l'expression de leur fonction. Or, les deplacements amples de groupes d'atomes a l'interieur des proteines sont souvent difficiles a etudier experimentalement. Par exemple, on ne sait dire ce qui distingue entre eux les sous-etats conformationnels mis en evidence par frauenfelder. Pour preciser l'interpretation de ce type de donnee experimentale, les methodes de dynamique moleculaire seraient ideales si le calcul de trajectoires de proteines d'environ 100 nsec etait possible. La methode de dynamique moleculaire confinee que nous avons developpee repose sur la description que donne la theorie des modes normaux des mouvements amples et lents d'une proteine. Elle permet de calculer des trajectoires beaucoup plus longues que d'ordinaire. Cependant, un comportement anharmonique meconnu perturbe le deroulement des trajectoires calculees par notre methode, meme dans le cas d'un polypeptide, une decaalanine, ne subissant aucun changement de conformation. Pour preciser les voies de developpement ulterieur de notre methode, nous avons consacre la troisieme partie de notre these a l'etude d'un mouvement ample et lent a l'interieur d'une petite proteine, le fragment c-terminal de la proteine ribosomale l7/l12
18
Gopinathan, Lakshmi Vanden Heuvel John P. "Regulation of Peroxisome proliferator-activated receptor [alpha] by Ribosomal protein L11, murine double minute 2, and E6-associated protein". 2008. http://etda.libraries.psu.edu/theses/approved/WorldWideIndex/ETD-3573/index.html.
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Huang, Shuo-Yen, i 黃碩彥. "Interactions between Ribosomal Proteins and Endoplasmic Reticulum (ER): The role of large subunit ribosomal proptein L19 in making rough ER and ribosome assembly". Thesis, 2003. http://ndltd.ncl.edu.tw/handle/51579057066224244798.
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碩士國立陽明大學
遺傳學研究所
91
During the process of protein translocation, the nascent polypeptide chain is recognized by signal recognition particles (SRP) which carry the ribosome-nascent polypeptide complex (RNC) to reside on the ER membrane. In the previous studies, our laboratory has found that human large subunit ribosomal protein L7 specifically bound to the ER membrane. This thesis is focused on the finding of another contact point from ribosome to the ER. Based on the 2.4-angstrom high-resolution structure of Archaea (Haloarcula marismortui) 50S ribosome, and the data of cryo-EM reconstitution of eukaryotic RNC-Sec61 complex structure, human ribosomal protein L19 has tentatively been suggested as one of the contact points from ribosome to ER. Thus, in this thesis, L19 was cloned and expressed in both prokaryotic and eukaryotic expression vectors. As the result shown, we have confirmed that L19 also has the ability to bind ER. We also found that recombinant L19 has made into ribosome assembly in 293T cell. During the process, we observed that L19 was co-localized with L7 in forming of the nuclear body-like microbodies outside the nucleoli. The observations predicted that the nuclear body-like microbodies may be a precursor of ribosome assembly. In the last part of this thesis, we have made a recombinant ribosome-containing modified L19 protein which carried a heart muscle kinase (HMK) recognition sequence (RRASV) at the C-terminal end of L19 protein. We examined whether this recombinant ribosome is able to be detected by kinase reaction or not, and the result was negative, suggesting that the C-terminal end of L19 is not exposed on surface.
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Chi, Hsiao-Lan, i 紀筱嵐. "Nuclear Import of Eukaryotic Ribosomal Proteins: Cellular trafficking of human ribosomal protein L10 between the cell nucleus and the plasma membrane". Thesis, 2007. http://ndltd.ncl.edu.tw/handle/89076727203258272443.
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碩士國立陽明大學
生命科學暨基因體科學研究所
95
In the eukaryotic ribosome biogenesis, the ribosomal proteins must be imported into the nucleus for assembly. In general, proteins which are capable of entering the nucleus usually contain a nuclear localization signal (NLS). In this study, we first used all available NLS prediction programs to search the presence of NLS in all eukaryotic ribosomal proteins, and found RPS4, RPS20, RPL10, RPL17, RPL18 and RPL31 do not contain any predicted NLS. To verify the nature of such ribosomal proteins, we used a flag-tagging approach to see whether these proteins are able to reach nucleus or not. The results show that FLAG-S4, FLAG-L17, and FLAG-L31 have made into the nucleus, whereas FLAG-S20 resides at cytoplasm; furthermore, of particularly interest is that FLAG-L10 and FLAG-L18 have been located at the plasma membrane. Accordingly, we have continued to investigate the nature of RPL10 with respect to it cellular distribution. The mutant FLAG-L10D183K carrying a deletion of a putative PDZ domain binding motif (PBM) at the C-terminal end allows the protein to be transported from the membrane to the nucleus, suggesting that the nuclear entry of RPL10 could be membrane-binding dependent. Interestingly, during examination of the cellular distribution of FLAG-L10, we also found that on rare occasions, FLAG-L10 can be located within the nucleus and nucleoli in dividing cells. This implies that the nuclear import of RPL10 could be cell cycle dependent. By transfecting a FLAG-L10 gene into synchronized cells, we have found that FLAG-L10 reaches the nucleus and nucleoli during the G1 phase. To understand the mechanism behind such an unusual phenomenon of nuclear uptake, we intend to use a GST-pull down assay to search for possible proteins that may facilitate the nuclear import or involve in the plasma membrane association of RPL10.
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Ping-HanChung i 鍾秉翰. "Ribosomal protein L19 regulates CCND1 protein expression and cell cycle progression through interacting with the internal ribosome entry site located on the 5’UTR of CCND1 mRNA". Thesis, 2012. http://ndltd.ncl.edu.tw/handle/75338023090296390942.
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碩士國立成功大學
生物資訊與訊息傳遞研究所
100
Ribosome is composed of rRNAs, ribosomal proteins, and many non-ribosomal factors to conduct the translation function. Traditionally, ribosomal proteins were considered as co-factors to execute the protein translation. But, numerous studies have demonstrated that ribosomal proteins not only play as co-factors of translational complex but also regulate the protein synthesis of specific mRNAs. RPL19 is a component of ribosome large subunit which belonged to the L-19E super-family and conserved among eukaryotes. In previous study, RPL19 was reported to have an impact on cyclin D1 protein expression but not on other cell cycle regulators, which indicated RPL19 may be a regulator of specific cell cycle regulators. During cell cycle progression, internal ribosome entry site (IRES) was reported to mediate the translational regulation of many cell cycle regulators. Since cyclin D1 expression was reported to be regulated by RPL19 and the 5’UTR of cyclin D1 mRNA carries a potential IRES element, the hypothesis was reported that RPL19 may regulate the expression of cyclin D1 through IRES. To address it, cells were synchronized and following experiments were conducted. First, western blot analysis showed that RPL19 expression level remained unchanged during cell cycle progression. However, RNA-IP showed that RPL19 interacted with cyclin D1 mRNAs at G1/S boundary. Bicistronic reporter assay showed that the 5’UTR of cyclin D1 had strong IRES activity and was regulated by RPL19. IRES-mediated translation regulation is often facilitated with the help of IRES trans-acting factors (ITAFs). RPL19 cooperated with a known ITAF, hnRNP A1, to regulate the IRES activity of cyclin D1. Furthermore, we observed that down-regulation of RPL19 significantly decreased the proliferation rate of HeLa cells. To sum up, we identified that RPL19, a ribosomal protein, can cooperate with hnRNPA1 to regulate cell cycle progression through regulating the IRES activity of cyclin D1.
22
Hamman, Brian D. "The conformational dynamics and subunit equilibrium of Escherichia coli ribosomal protein L7/L12". Thesis, 1994. http://hdl.handle.net/10125/9378.
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23
Yu-ZhenWu i 吳榆蓁. "To identify the functional role of ribosomal protein L19 (RPL19) in the cancer development". Thesis, 2019. http://ndltd.ncl.edu.tw/handle/fcfc5j.
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24
Wu, Jing-Yiing, i 吳京穎. "The Interaction between the Ribosomal Proteins and Endoplasmic Reticulum(ER)：The role of large subunit ribosomal proteins L17 and L26 in making rough ER". Thesis, 2004. http://ndltd.ncl.edu.tw/handle/01768869824988472328.
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碩士國立陽明大學
遺傳學研究所
92
The interaction between the ribosome and ER (endoplasmic reticulum) has been revealed by cryo-electron microscopy at 15.4Å resolution. The information predicts that four contact points, namely L19, L25, L26 and L35 of ribosome, provide the major attachments to the ER. So far, no direct biochemical evidence has been given in respect to the attachments. This thesis intends to investigate the binding of human ribosomal protein L17 and L26 to the ER. In this study I have demonstrated that the phosphorylation- tagged L17 and that of L26 can be assembled into recombinant ribosomes, and maintain a normal functions in translation. In addition I have detected that the using phosphorylation probing C-terminal regions of L17 and that of L26 expose on the surface of the ribosome. In test of purified ribosomal proteins binding the rough ER it shows that the L17 and L26 can bind to ER by the microsome floating assay. Furthermore, in a cross-linking experiment I have observed that L17 does not crosslink to the components of translocon protein complex, but rather associates with other high molecular weight proteins of ER. This result of this study has provided a useful information in understanding the mechanism of protein translocation.
25
Lu, Nan Chi, i 呂南畿. "Crystallization Studies of Rhizopus oryzae Aspartic Protease, Helicobacter pylori Ribosomal Protein L7/L12 and Corynebacterium glutamicum Citrate Synthase". Thesis, 2005. http://ndltd.ncl.edu.tw/handle/36475413530930947866.
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碩士國立清華大學
分子與細胞生物研究所
93
Rhizopus oryzae aspartic protease is the endopeptidase that depends on aspartic acid residues for their catalytic activity. The intensity of the bitterness is proportional to the number of hydrophobic amino acids and basic amino acids in the hydrolysate. Rhizopus oryzae aspartic protease has a high specificity for hydrophobic amino acids and hence has a great potential for debittering. In this study, we aimed to determine the X-ray crystallographic structure of aspartic protease from Rhizopus oryzae. Crystals grew in the conditions using 25 % PEG MME 2000, 0.2 M ammonium sulfate, 0.1 M sodium-acetate (pH 4.2) as precipitant at 20 ℃. Crystals diffracted beyond a resolution of 1.1 Å and were found to belong to space group P41212, with unit-cell parameters of a＝b＝68.8 Å, c＝132.2 Å, α＝β＝γ＝900. Attempts to solve the phases with heavy-atom soaking using the multiple-wavelength anomalous diffraction (MAD) method were nonetheless failed. This structure was later solved by Jai-shin Liu with molecular replacement method. The other crystallization studies were focused on ribosomal protein L7/L12 of Helicobacter pylori (HP1199) and citrate synthase of Corynebacterium glutamicum. Needle-like crystals of HP1199 were obtained that lacked diffraction, while citrate synthase is still under crystallization trails.
26
Drygin, Denis. "Studies of the complex of ribosomal protein L1 with its binding site in 23S rRNA: Modification -interference, mutagenesis and crosslinking". 2002. https://scholarworks.umass.edu/dissertations/AAI3039352.
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Interaction of ribosomal protein L1 and the 23S rRNA plays an important role in both the structure and biological activity of the Escherichia coli ribosome. We have minimized the binding site for protein L1 on the 23S rRNA to a 32-nucleotide fragment consisting of helix 77, helix 78, and the conserved sequences that interconnect them. Filter-binding, modification-interference and manganese rescue experiments were used do demonstrate (1) that the absence of a 2′-OH group at position 2122 can disrupt protein L1-23S rRNA interaction, but only if certain other deoxyribonucleotides are present in the transcript and (2) that the Rp phosphoryl oxygens preceding U2122 and A2176 in the rRNA molecule play a role in Ll-23S rRNA interaction through magnesium ion coordination, possibly by participating in magnesium bridges with the protein. The crystal structure of protein L1 from Thermus thermophilus, which closely resembles Escherichia coli L1, consists of two domains that are divided by a deep cleft. It has been suggested that the binding site for RNA is located within this interdomain cleft. Using site-directed mutagenesis it was possible to identify a cluster of conserved amino acids that are crucial for protein-RNA interactions (F37, D42, T216, G218), as well as several amino acids that help to stabilize the complex (K36, P137, N138, K140, H171, K176, M217). All of the mutagenized amino acids are located on the surface of the interdomain cleft. To orient L1 relative to the RNA, crosslinking studies were performed using photoreactive moieties incorporated into the L1 binding site and protein L1 itself. A 4-thiouridine residue at position 2172 and 2-azidoadenosine ligated to the 3′-end of the minimized binding site were shown to form a “zero length” crosslink with protein L1. Whereas the azidophenacyl group attached to position 40 of the protein was demonstrated to map a portion of loop 76/77 on 23S rRNA.