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Insights Into the Decoding Mechanism from Studies of Mutant RibosomesMcClory, Sean P. January 2013 (has links)
No description available.
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Studies on ribosomal oxygenasesSekirnik, Rok January 2014 (has links)
The 2OG oxygenases comprise a superfamily of ferrous iron dependent dioxygenases with multiple biological roles, including in hypoxia sensing, transcriptional control, and splicing control. It was recently proposed that 2OG oxygenases catalyse the hydroxylation of ribosomal proteins in prokaryotes (ycfD) and in humans (NO66 and MINA53), raising the possibility that 2OG oxygenases also control translation. The work described in this thesis concerned investigations on the biochemical and functional aspects of prokaryotic and mammalian ribosomal protein hydroxylases (ROX) in vitro and in cells. An efficient chromatographic system linked to mass spectrometric analysis (LC-MS) was developed for studying the masses of individual ribosomal proteins (>90% coverage of ribosomal proteome) to ±1 Da accuracy. It was demonstrated that ycfD catalyses the hydroxylation of R81 on L16 in E. coli, in a manner dependent on atmospheric oxygen levels. YcfD deletion results in growth phenotype at low temperatures and in minimal medium, and in decreased global translation rates in minimal medium; ycfD deletion does not affect translational accuracy and ribosome assembly. Furthermore, ycfD-deletion results in increased sensitivity to the antibiotics chloramphenicol and lincomycin. Consistent with a 2OG-oxygenase mediated mechanism of antibiotic resistance, chloramphenicol sensitivity of the E. coli wild-type strain could be increased by inhibiting the activity of ycfD by removing co-factors required for catalytic activity (Fe(II) and O2), and, at least in part, by using a ycfD inhibitor, IOX1, which inhibits ycfD with IC<sub>50</sub> of 38 μM in vitro. The therapeutic potential of a post-translational modification mediating antibiotic resistance provides an opportunity for medicinal targeting of ribosome-modifying enzymes, for example ycfD, which may be more ‘druggable’ than the ribosome itself. In co-treatment with an existing antibiotic, such as chloramphenicol, a small molecule inhibitor would achieve a potentiated antibiotic effect. Structural aspects of ROX hydroxylation were pursued by characterising a thermophilic ROX-substrate complex; a ycfD homologue was identified in the thermophilic bacterium Rhodothermus marinus and shown to be a thermophilic 2OG oxygenase ycfD<sub>RM</sub>, acting on R82 of ribosomal protein L16<sub>RM</sub>. The activity of ycfD<sub>RM</sub> in cells was limited at high growth temperature and oxygen solubility was demonstrated as a likely limiting factor of ycfD<sub>RM</sub> activity, thus identifiying a potential 2OG oxygenase oxygen sensor in prokaryotes. A crystal structure of ycfD<sub>RM</sub> in complex with L16RM substrate fragment was determined to 3.0 Å resolution. Structural analyses suggested that ycfD<sub>RM</sub> contains 30% more hydrophobic interactions and 100% more salt-bridge interactions than ycfD<sub>EC</sub>, suggesting that these interactions are important for thermal stabilisation of ycfD<sub>RM</sub>. The structures reveal key interactions required for binding of ribosomal proteins. Substantial structural changes were observed in the presence of the substrate fragment, which implies induced-fit binding of the L16<sub>RM</sub> substrate. The work has informed further structural studies on the evolutionarily related human ROX, NO66 and MINA53, for which substrate structures have been obtained since the completion of the work. The LC-MS analysis of ribosomal proteins was extended to mouse and human cells to demonstrate that the human ROX homologue of ycfD, MINA53, hydroxylates the 60S ribosomal protein rpL27a in cells. It was demonstrated that rpL27a hydroxylation is widespread and found in all mouse organs analysed, as well as in cancer cell lines and in clinical cancer tissues. A partial or complete reduction of rpL27a hydroxylation was observed in a number of clinically identified MINA53 mutations from the COSMIC database of cancer mutations. Structural analysis suggested that mutations occur more frequently at structurally important regions of MINA53, including the βIV-βV insert in the core fold of MINA53. The identification of inhibiting clinical mutations suggests that rpL27a hydroxylation level could be used as a cancer mark, and in the future for selective inhibition by ribosomal antibiotics. The work presented in this thesis demonstrates that it is possible to selectively inhibit modified ribosomes; an inhibitor of unhydroxylated rpL27a could therefore, at least in principle, be active against the sub-set of tumours with inactivating mutation(s) of MINA53, but not normal tissue. Future work should therefore focus on identifying a selective inhibitor of unhydroxylated eukaryotic ribosomes which could be applied for treatment of cancers harbouring deactivating MINA53 mutations. The same approach could be applied to other ribosome modifications (to rRNA, ribosomal proteins, and ribosome-associate factors) that are different in cancer compared to normal cells.
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Vazba eIF3 v komplexu s eIF5 a eIF1 na ribosomální podjednotku 40S je doprovázena dramatickými strukturními změnami / Binding of eIF3 in complex with eIF5 and eIF1 to the 40S ribosomal subunit is accompanied by dramatic structural changesZeman, Jakub January 2019 (has links)
In eukaryotic translation, eukaryotic initiation factors (eIFs) are at least as important as the ribosome itself. Some of these factors play different roles throughout the entire process to ensure proper assembly of the preinitiation complex on mRNA, accurate selection of the initiation codon, errorless production of the encoded polypeptide and its proper termination. Perhaps, the most important factor integrating signals from others and coordinating their functions on the ribosome is eIF3. In Saccharomyces cerevisiae, eIF3 is formed by five subunits. All these subunits contain structural motifs responsible for contact with ribosomal proteins and RNAs. In addition to these highly structured parts, the rest of eIF3 is unstructured and very flexible. Therefore, despite the recent progress thanks to the use of a cryo-electron microscopy, a precise structure and position of eIF3 on the 40S ribosomal subunit are still not known. Also, the presence of eIF3 on 80S during early elongation and its role in reinitiation and readthrough are not fully understood. In order to crack mysteries of yeast eIF3, we used x-ray crystallography, chemical cross- linking coupled to mass spectrometry, and various biochemical and genetic assays. We demonstrated that eIF3 is very compactly packed when free in solution. This...
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Funciones del factor de inicio de la traducción eucariota 5A2 en el cáncer de pulmónMartínez Férriz, Arantxa 12 May 2023 (has links)
[ES] Las poliaminas son metabolitos esenciales para el crecimiento de las células eucariotas y su metabolismo está frecuentemente desregulado en cáncer. Una de las dianas moleculares de las poliaminas es el factor de elongación de la traducción eIF5A, una proteína esencial y conservada evolutivamente.
eIF5A es la única proteína conocida que contiene el aminoácido hipusina, que deriva de la poliamina espermidina. En humanos existen dos isoformas, eIF5A1 y eIF5A2. EIF5A2 se encuentra en el cromosoma 3q26, una región frecuentemente amplificada en muchos tumores y que está altamente expresada en varios tipos de cáncer, incluyendo el cáncer de pulmón no microcítico (CPNM). eIF5A2 es esencial para el mantenimiento de la proliferación celular y su inhibición la suprime en algunos tumores.
Recientemente se ha correlacionado la sobreexpresión de eIF5A2 con la invasión y como biomarcador de mal pronóstico en algunos cánceres, y se ha observado que eIF5A2 induce la transición epitelio-mesenquimal (EMT) en CPNM. La EMT es un proceso complejo y reversible que induce la diferenciación de las células epiteliales a células mesenquimales migrantes con capacidad de invasión. Numerosos estudios han demostrado que la EMT está relacionada con la progresión del cáncer, metástasis y mal pronóstico en tumores. Por tanto, la determinación de un método eficaz para inhibir la EMT en CPNM podría mejorar significativamente los tratamientos actuales.
La naturaleza altamente selectiva de la hipusinación de eIF5A2 y su susceptibilidad a la inhibición farmacológica sugieren que eIF5A2 es una diana terapéutica muy atractiva. Actualmente, se dispone de un análogo de poliamina, GC7, que se utiliza para inhibir la hipusinación y se ha demostrado que frena el crecimiento de células cancerosas.
El presente trabajo de tesis doctoral tiene como objetivo caracterizar el papel patológico de eIF5A2 en el desarrollo del CPNM. Para ello, hemos estudiado, mediante modificaciones genéticas por silenciamiento y sobreexpresión, el papel de eIF5A2 en la proliferación, motilidad e invasión celular utilizando líneas celulares de CPNM. Así mismo, se ha estudiado el efecto del inhibidor GC7 en líneas celulares de CPNM y modelos murinos para determinar si previene o revierte la EMT, y reduce la migración y la invasión de células de CPNM. Por último, se ha analizado la correlación entre la expresión de eIF5A2, las variables clínico-patológicas y la supervivencia de los pacientes en una colección de muestras de pacientes con CPNM.
Los resultados obtenidos sugieren la existencia de una regulación entre las isoformas eIF5A1 y eIF5A2 para compensar la expresión de ambos homólogos. Además, nuestros datos apuntan a una coordinación temporal y posicional entre las vías de TGFß1 y eIF5A2 para impulsar la traducción de proteínas requerida para el reordenamiento del citoesqueleto y la motilidad de las células cancerosas invasivas. Hemos demostrado con modelos de ratón in vivo, que los tumores generados mediante xenotrasplante de células que sobreexpresan eIF5A2 tienen mayor capacidad invasiva. Finalmente, mostramos la existencia de una correlación positiva entre la expresión de eIF5A2 y el marcador de proliferación Ki67 en tejido de tumores de CPNM, y que la tasa de supervivencia es menor en aquellos pacientes que expresan niveles elevados de eIF5A2.
Los resultados obtenidos en este trabajo confirman que eIF5A2 podría ser empleado como un biomarcador de mal pronóstico en CPNM y su inhibición farmacológica podría emplearse como una posible herramienta terapéutica, sola o en combinación con otros fármacos, en aquellos casos en los que eIF5A2 se encuentre sobreexpresado. / [CA] Les poliamines són metabòlits essencials per al creixement de les cèl·lules eucariotes i el seu metabolisme està frequentment desregulat en càncer. Una de les dianes moleculars de les poliamines és el factor d'elongació de la traducció eIF5A, una proteïna essencial i conservada evolutivament.
eIF5A és l'única proteïna cel·lular coneguda que conté l'aminoàcid hipusina, que deriva de la poliamina espermidina. En humans hi ha dues isoformes, eIF5A1 i eIF5A2. EIF5A2 es troba al cromosoma 3q26, una regió freqüentment amplificada en molts tumors, i que està altament expressada en diferent tipus de càncer, incloent el càncer de pulmó no microcític (CPNM). eIF5A2 és essencial per al manteniment de la proliferació cel·lular i la seva inhibició la suprimeix en alguns tumors.
Recentment s'ha correlacionat la sobreexpressió d'eIF5A2 amb la invasió i com a biomarcador de mal pronòstic a alguns càncers i s'ha observat que eIF5A2 indueix la transicició epiteli-mesenquima (EMT) en CPNM. L'EMT és un procés complex i reversible que indueix la diferenciació de les cèl·lules epitelials a cèl·lules mesenquimals migrants amb capacitat d'invasió. Nombrosos estudis han demostrat que l'EMT està relacionada amb la progressió del càncer, la metàstasi i el mal pronòstic en molts tumors. Per tant, la determinació d'un mètode eficaç per inhibir l'EMT a CPNM podria millorar significativament els règims dels tractaments actuals.
La naturalesa altament selectiva de la hipusinació d'eIF5A2 i la susceptibilitat a la inhibició farmacològica fan d'aquesta proteina una diana terapèutica molt atractiva. Actualment, es disposa d'un anàleg de poliamina, anomenat GC7, que s'utilitza per inactivar la reacció d'hipusinació i s'ha demostrat que inhibeix el creixement de cèl·lules canceroses.
Aquest treball de tesi doctoral té com a objectiu caracteritzar el paper patològic d'eIF5A2 en el desenvolupament del CPNM. Per això, hem estudiat, mitjançant modificacions genètiques per silenciament i sobreexpressió, el paper d'eIF5A2 en la proliferació, la motilitat i la invasió cel·lular utilitzant línies cel·lulars de càncer de pulmó. Així mateix, s'ha estudiat l'efecte de l'inhibidor GC7 en línies cel·lulars de CPNM i models murins per determinar si augmenta la quimiosensibilitat de les cèl·lules, prevé o reverteix l'EMT i redueix la migració i la invasió de cèl·lules de CPNM. Finalment, s'ha analitzat la correlació entre l'expressió d'eIF5A2, les variables clinicopatològiques i la supervivència dels pacients en una col·lecció de mostres de pacients amb CPNM.
Els resultats obtinguts suggereixen que hi ha una regulació entre les isoformes eIF5A1 i eIF5A2 per compensar l'expressió dels dos homòlegs. A més, les nostres dades apunten a una coordinació temporal i posicional entre les vies de TGFß1 i eIF5A2 per impulsar la traducció requerida de proteïnes per als reordenaments del citosquelet i les característiques de motilitat de les cèl·lules canceroses invasives. Hem demostrat amb models de ratolí in vivo que els tumors generats mitjançant xenotrasplantament de cèl·lules que sobreexpressen eIF5A2 tenen més capacitat invasiva. Finalment, mostrem l'existència una correlació positiva entre l'expressió d'eIF5A2 i el marcador de proliferació Ki67 en teixit de tumors de CPNM, i que la taxa de supervivència és menor en aquells pacients que expressaven alts nivells d'eIF5A2.
Els resultats obtinguts en aquest treball confirmen que eIF5A2 podria ser emprat com un biomarcador de mal pronòstic a CPNM i la seva inhibició farmacològica podria utilitzar-se com una possible eina terapèutica, sola o en combinació amb altres fàrmacs, en aquells casos en què eIF5A2 es trobe sobreexpressat. / [EN] Polyamines are essential metabolites for eukaryotic cells growth, and their metabolism is frequently deregulated in cancer. One of the molecular targets of polyamines is the translation elongation factor eIF5A, an essential and evolutionarily conserved protein.
eIF5A is the only protein known that contains the amino acid hypusine, which is derived from the polyamine spermidine. In humans there are two isoforms, eIF5A1 and eIF5A2. EIF5A2 is located on chromosome 3q26, a region frequently amplified in different types of cancer, including non-small cell lung cancer (NSCLC). eIF5A2 is essential for the maintenance of cell proliferation and its inhibition suppresses it in many tumors.
Recently, eIF5A2 overexpression has been correlated with invasion and as a biomarker of poor prognosis in some cancers, and it has been observed that eIF5A2 induces epithelial-mesenchymal transition (EMT) in NSCLC. EMT is a complex and reversible process that induces the differentiation of epithelial cells into migrant mesenchymal cells with invasive capacity. Numerous studies have shown that EMT is related to cancer progression, metastasis, and poor prognosis in many tumors. Therefore, the determination of an effective method to inhibit EMT in NSCLC could significantly improve current treatment regimens.
The highly selective nature of eIF5A2 hypusination and its susceptibility to pharmacological inhibition make this process a very attractive therapeutic target. Currently, a polyamine analog, called GC7, is available and is used to inactivate the hypusination reaction and has been shown to inhibit cancer cell growth.
The objective of this doctoral thesis is to characterize the pathological role of eIF5A2 in the development of NSCLC. For this, we have studied, through genetic alterations by silencing and overexpression, the role of eIF5A2 in cell proliferation, motility and invasion using lung cancer cell lines. Likewise, the effect of the GC7 inhibitor in NSCLC cell lines and murine models has been studied to determine if it increases the chemosensitivity of cells, prevents or reverses EMT, and reduces migration and invasion of NSCLC cells. Finally, the correlation between the expression of eIF5A2, clinicopathological variables and patient survival has been analyzed in a collection of samples from patients with NSCLC.
The results obtained suggest the existence of a regulation between the eIF5A1 and eIF5A2 isoforms to compensate the expression of both homologues. Furthermore, our data point to a temporal and positional coordination between the TGFß1 and eIF5A2 pathways to drive the required translation of proteins for cytoskeletal rearrangements and motility characteristics of invasive cancer cells. We have demonstrated with in vivo mouse models that tumors generated by xenotransplantation of cells that overexpress eIF5A2 have a greater invasive capacity. Finally, we show the existence of a positive correlation between the expression of eIF5A2 and the proliferation marker Ki67 in NSCLC tumor tissue, and that the survival rate is lower in those patients who expressed high levels of eIF5A2.
The results obtained in this work confirm that eIF5A2 could be used as a biomarker of poor prognosis in NSCLC and its pharmacological inhibition could be used as a possible therapeutic tool, alone or in combination with other drugs, in those cases in which eIF5A2 is found overexpressed. / Martínez Férriz, A. (2023). Funciones del factor de inicio de la traducción eucariota 5A2 en el cáncer de pulmón [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/193293
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