Non-coding RNAs are highly abundant regulators of gene expression in all kingdoms of life that often play important roles in vital cellular functions. In bacteria, small regulatory RNAs (sRNAs) usually act post-transcriptionally by regulating mRNAs through base pairing within ribosome binding sites (RBS), thereby inhibiting translation initiation. tisB encodes a toxin, TisB, whose synthesis is controlled by the sRNA IstR-1. Intriguingly, IstR-1 base pairs far upstream of the RBS but nevertheless inhibits translation initiation. The tisB mRNA is unusual in that ribosomes cannot access the RBS directly, but instead need an unstructured upstream region. This is precisely where IstR-1 exerts its inhibitory effect. We propose this region to serve as a ribosome loading site (standby site) which permits ribosomes to overcome the obstacle of inhibitory RBS-containing structures. Sequence-independent ribosome binding to the standby site allows for efficient relocation to the RBS structure when it is transiently open. Thus, standby sites are translation enhancer elements. I also characterized TisB-mediated toxicity. The hydrophobic protein TisB is targeted to the inner membrane and causes damage. This decreases the intracellular ATP concentration and entails decreased  replication, transcription and translation rates. It is likely that this toxin is involved in multidrug tolerance under certain conditions. We identified the sRNA MicF as a negative regulator of lrp expression. Lrp is a global transcription factor that controls genes involved in amino acid metabolism and transport of small molecules. Interestingly, Lrp also downregulates MicF. Thus, this study established that the mutual downregulation of MicF/Lrp creates a positive feedback loop which gives a switch-like behavior important for fast adaptations.

Dosage compensation is a mechanism that equalizes the expression of X-linked genes in those organisms in which males and females differ in the number of X chromosomes. In Drosophila melanogaster, dosage compensation is achieved by up-regulating the transcription of the single male X chromosome. This effect is mediated by a chromatin remodeling complex known as the Male Specific Lethal (MSL) complex or Dosage Compensation Complex (DCC). In female flies, dosage compensation is inhibited primarily because of the translational repression of the mRNA encoding one of the DCC subunits, MSL-2, by the female-specific RNA binding protein Sex-lethal (SXL). To inhibit translation, SXL binds to poly(U) stretches present in both the 5’ and 3’ UTRs of msl-2 mRNA. Sequences adjacent to those SXL-binding sites in the 3´UTR are also required for translation inhibition and are bound by co-repression. In this thesis work, we have designed an affinity chromatography assay to isolate the putative co-repressor(s), and have identified the protein Upstream of N-ras (UNR). Drosophila UNR (dUNR) is an ubiquitous, conserved protein that contains 5 cold shock domains (CSD) and a glutamine- (Q) rich amino- terminal extension. We show that dUNR is a necessary co-factor for SXL-mediated msl-2 repression. SXL recruits dUNR to the 3’ UTR of msl-2 mRNA, imparting a sex-specific function to this ubiquitous protein. Domain mapping experiments indicate that dUNR interacts with SXL and msl-2 mRNA through CSD1, and that the domains for translation inhibition and SXL interaction can be distinguished. Our data indicate that the Q-rich domain, together with CSDs 1 and 2, plays an important role in translational repression, and suggest that factors in addition to dUNR and SXL are required for repression of msl-2 mRNA. Using a combination of UNR immunoprecipitation and microarray analysis, we have identified the mRNAs that are bound to dUNR in male and female flies. Our results suggest that dUNR is not only a novel regulator of dosage compensation, but also a general post-transcriptional regulator of gene expression.

A família PUF é um conjunto de proteínas que se ligam a mRNA regulando sua estabilidade e tradução em processos chave do desenvolvimento. Entre as 25 proteínas de Arabidopsis contendo as repetições PUF, três delas, APUM-I, APUM-2 e APUM-3, apresentam ~90% de identidade e colocalizam temporal e espacialmente nos meristemas apical e axilares de caule, zona de elongação da raiz e no periciclo durante a formação de calos e de raízes laterais, além de estames e polens. Ensaios de RT-PCR mostraram que a relação de expressão entre eles é a mesma em todos os órgãos analisados. Além disso, plantas nocautes apum-1- e apum-2- não apresentam fenótipo alterado, sugerindo redundância funcional. Plantas com a expressão dessas proteínas afetadas por RNA antisense apresentaram folhas cloróticas e reduzidas, raízes mais curtas e menos ramificadas e baixa fertilidade, fenótipo semelhante ao de plantas que superexpressam KRP-2, um inibidor de CDK. O transcrito KRP-2 apresenta um elemento de ligação AraPum no 3\'-UTR sugerindo ser um possível alvo para APUM. Em adição, plantas antisense têm aumento de transcritos KRP-2 em relação a selvagens. Assim, foi proposto que essas proteínas agem coordenando a formação de folhas e raízes pela influência na tradução de KRP-2. A função ancestral das proteínas PUF de manter o ciclo celular em detrimento da diferenciação, parece ser conservada em plantas. / The PUF family is a group of conserved proteins that bind to rnRNAs regulating its stability and translation in key developrnental processes. Among the twenty five Arabidopsis proteins with PUF repeats, we found that three highly similar members, APUM-I, APUM-2 and APUM-3 (~90% identity) and co-localize spatially and temporally in the shoot apical and axillaries meristems, root elongation zone and pericycle during callus and lateral root formation, as well as stamens and pollens. RTPCR assays showed that these proteins have similar expression profiles in ali organs analyzed. Moreover, plant apum-1 and apum-2 knockouts have no detectably altered phenotype, suggesting a functional redundancy between them. Plants in which APUM-I, APUM-2 and APUM-3 expression were reduced through antisense RNA, showed chlorotic and reduced leaves, shorter and less ramificated roots and low fertility. This phenotype is similar to that of plants over-expressing the KRP-2 gene, a CDK inhibitor. An AraPum binding element at 3\'-UTR of the KRP-2 transcript suggests that it may be a possible target for APUM. In addition, in comparison to wild-type plants, antisense plants have increased KRP-2 transcripts levels. We proposed that APUM proteins act by coordinating leaf and root formation by way of influencing KRP-2 transiation. The ancestral function of PUF proteins in the maintenance of the cell cycle, to detriment of differentiation, seems to be conserved in plants.

No description available.

No description available.

Proteínas PUF regulam a estabilidade e a tradução através da ligação a seqüências específicas nas regiões 3\' não traduzidas (3\' UTR) dos mensageiros. A ligação é mediada por um domínio de ligação conservado constituído por 8 repetições de aproximadamente 36 aminoácidos cada. Experimentos realizados no sistema triplo-híbrido de levedura mostraram que os homólogos PUF de Arabidopsis APUM-1, APUM-2 e APUM-3 são capazes de ligar especificamente à seqüência chamada de Elemento de Resposta a NANOS (NRE) reconhecida pelo homólogo PUF de Drosophila. A utilização de bibliotecas de expressão de RNA em ensaios no sistema triplo-híbrido permitiu a identificação de seqüências de ligação consenso para as três proteínas APUM. Análises computacionais identificaram elementos de ligação a APUM em regiões 3\' UTR de importantes transcritos relacionados ao controle do meristema do caule e à manutenção das células totipotentes. Nós mostramos que os homólogos APUM-l, APUM-2 e APUM-3 reconhecem elementos de ligação a APUM nas regiões 3\' UTR dos transcritos WUSCHEL, CLAVATA-1, ZWILLE e FASCIATA-2. Ensaios de RT-PCR e Western blot semiquantitativos mostraram que a quantidade dos transcritos WUSHEL e CLAVATA-1 é alterada em plantas antisenso induzíveis para APUM-l, APUM-2 e APUM-3. A relevância biológica dessas interações foi observada através de ensaios de coimunoprecipitação, confirmando, portanto, o primeiro caso de regulação traducional descrito para os mensageiros WUSCHEL e CLAVATA-1. Análises computacionais adicionais para a identificação de outros homólogos PUF em Arabidopsis encontraram vinte e cinco proteínas possuindo repetições PUF. Entre elas, os homólogos APUM-4, APUM-S e APUM-6 apresentam alta similaridade com as proteínas APUM-l, APUM-2 e APUM-3, sendo capazes de ligar especificamente à seqüência NRE e aos elementos de ligação a APUM presentes nas regiões 3\' UTR dos transcritos WUSCHEL, CLAVATA-1, ZWILLE e FASCIATA-ts resultados indicam que vários homólogos PUF podem agir como reguladores traducionais em Arabidopsis através de um mecanismo molecular conservado entre as espécies, podendo abrir uma nova área de investigação da regulação de mRNA em plantas. / PUF proteins regulate stability and translation through sequence-specific binding to 3\' untranslated regions (UTR) oftarget mRNA transcripts. Binding is mediated by a conserved PUF domain which contains 8 repeats of approximately 36 amino acids each. Through three-hybrid assays, we have found that APUM-1, APUM-2 and APUM-3 Arabidopsis PUF homologs can bind specifically to the NANOS Response Element sequence (NRE) recognized by Drosophila PUF homologo Using Arabidopsis RNA libraries in three-hybrid screenings, we were able to identify APUM binding consensus sequences. A computational analysis allowed us to identify the APUM binding element within the 3\' UTR in many Arabidopsis transcripts, even in important mRNAs related to shoot and stem cell maintenance. We show that APUM-1, APUM-2 and APUM-3 are able to bind specifically to APUM binding elements in the 3\' UTR of WUSCHEL, CLAVATA-1, ZWILLE and FASCIATA-2 transcripts. RT-PCR and Western blot semiquantitatives assays showed altered WUSHEL and CLAVATA-1 amounts in APUM-1, APUM-2 and APUM-3 antisense plants. The biologic relevance of these interactions was observed with co-immunoprecipitation assay, which confirmed the first example of translational regulation to WUSCHEL and CLA VATA-1 transcripts. Computational analysis to identify others PUF homologs in Arabidopsis found twenty five proteins presenting PUF repeats. Among them, we found that APUM-4, APUM-S and APUM-6 homologs are very similar to APUM-1, APUM2 and APUM-3 and also are able to bind specifically to the NRE sequence and to APUM binding elements in the 3\' UTR of WUSCHEL, CLAVATA-1, ZWILLE and FASCIATA-2 transcripts. Our results indicate that the APUM proteins may act as regulators in Arabidopsis through an evolutionarily conserved mechanism, which may open up a new approach to investigate mRNA regulation in plants.

Axonal protein synthesis is rapidly regulated by extrinsic cues during neural wiring but the full landscape of proteomic changes and their translational control mechanisms remain unknown. The ability to investigate the nascent proteome on subcellular compartments has been hampered by the low sensitivity of existing methodology on quantity-limited samples combined with the difficulty of obtaining sufficient amounts of pure material. By combining pulsed Stable Isotope Labelling by Amino acids in Cell culture (pSILAC) with Single-Pot Solid-Phase-enhanced Sample Preparation (SP3), I have established an approach to characterize the nascent proteome from quantity-limited somaless retinal axons (~2μg) on an unparalleled rapid time-scale (5 min). The results show that a surprisingly large number of proteins (>350) is translated constitutively in axons, many of which are linked to neurological disease. Axons stimulated by different cues (Netrin-1, BDNF, Sema3A) each show a signature set of up/down newly synthesised protein (NSP) changes (>100) within 5 min. Remarkably, conversion of Netrin-1-induced responses from repulsion to attraction triggers opposite translational regulation for 73% of a common subset corresponding to >100 NSPs. Further, I show that pharmacological increase in cAMP, known to induce chemoattractive response, also leads to rapid and wide-scale remodelling of the nascent axonal proteome (~100 NSP changes). I find that the cAMP-elicited NSP changes underlie the attractive turning but are distinct from those induced by the physiological chemoattractant Netrin-1, suggesting that the same type of chemotropic response can be mediated by different protein synthesis-dependent mechanisms. Finally, I show that Sema3A, but not Slit1, triggers a physiological and non-canonical PERK-eIF2α-eIF2B signalling pathway required in neural wiring to elicit the rapid (< 15 min) local translation control of a specific subset of NSPs. Collectively my findings lead to the general conclusion that guidance molecules rapidly induce cue-specific remodelling of the nascent axonal proteome via distinct regulatory mechanisms.

Proteínas PUF regulam a estabilidade e a tradução através da ligação a seqüências específicas nas regiões 3\' não traduzidas (3\' UTR) dos mensageiros. A ligação é mediada por um domínio de ligação conservado constituído por 8 repetições de aproximadamente 36 aminoácidos cada. Experimentos realizados no sistema triplo-híbrido de levedura mostraram que os homólogos PUF de Arabidopsis APUM-1, APUM-2 e APUM-3 são capazes de ligar especificamente à seqüência chamada de Elemento de Resposta a NANOS (NRE) reconhecida pelo homólogo PUF de Drosophila. A utilização de bibliotecas de expressão de RNA em ensaios no sistema triplo-híbrido permitiu a identificação de seqüências de ligação consenso para as três proteínas APUM. Análises computacionais identificaram elementos de ligação a APUM em regiões 3\' UTR de importantes transcritos relacionados ao controle do meristema do caule e à manutenção das células totipotentes. Nós mostramos que os homólogos APUM-l, APUM-2 e APUM-3 reconhecem elementos de ligação a APUM nas regiões 3\' UTR dos transcritos WUSCHEL, CLAVATA-1, ZWILLE e FASCIATA-2. Ensaios de RT-PCR e Western blot semiquantitativos mostraram que a quantidade dos transcritos WUSHEL e CLAVATA-1 é alterada em plantas antisenso induzíveis para APUM-l, APUM-2 e APUM-3. A relevância biológica dessas interações foi observada através de ensaios de coimunoprecipitação, confirmando, portanto, o primeiro caso de regulação traducional descrito para os mensageiros WUSCHEL e CLAVATA-1. Análises computacionais adicionais para a identificação de outros homólogos PUF em Arabidopsis encontraram vinte e cinco proteínas possuindo repetições PUF. Entre elas, os homólogos APUM-4, APUM-S e APUM-6 apresentam alta similaridade com as proteínas APUM-l, APUM-2 e APUM-3, sendo capazes de ligar especificamente à seqüência NRE e aos elementos de ligação a APUM presentes nas regiões 3\' UTR dos transcritos WUSCHEL, CLAVATA-1, ZWILLE e FASCIATA-ts resultados indicam que vários homólogos PUF podem agir como reguladores traducionais em Arabidopsis através de um mecanismo molecular conservado entre as espécies, podendo abrir uma nova área de investigação da regulação de mRNA em plantas. / PUF proteins regulate stability and translation through sequence-specific binding to 3\' untranslated regions (UTR) oftarget mRNA transcripts. Binding is mediated by a conserved PUF domain which contains 8 repeats of approximately 36 amino acids each. Through three-hybrid assays, we have found that APUM-1, APUM-2 and APUM-3 Arabidopsis PUF homologs can bind specifically to the NANOS Response Element sequence (NRE) recognized by Drosophila PUF homologo Using Arabidopsis RNA libraries in three-hybrid screenings, we were able to identify APUM binding consensus sequences. A computational analysis allowed us to identify the APUM binding element within the 3\' UTR in many Arabidopsis transcripts, even in important mRNAs related to shoot and stem cell maintenance. We show that APUM-1, APUM-2 and APUM-3 are able to bind specifically to APUM binding elements in the 3\' UTR of WUSCHEL, CLAVATA-1, ZWILLE and FASCIATA-2 transcripts. RT-PCR and Western blot semiquantitatives assays showed altered WUSHEL and CLAVATA-1 amounts in APUM-1, APUM-2 and APUM-3 antisense plants. The biologic relevance of these interactions was observed with co-immunoprecipitation assay, which confirmed the first example of translational regulation to WUSCHEL and CLA VATA-1 transcripts. Computational analysis to identify others PUF homologs in Arabidopsis found twenty five proteins presenting PUF repeats. Among them, we found that APUM-4, APUM-S and APUM-6 homologs are very similar to APUM-1, APUM2 and APUM-3 and also are able to bind specifically to the NRE sequence and to APUM binding elements in the 3\' UTR of WUSCHEL, CLAVATA-1, ZWILLE and FASCIATA-2 transcripts. Our results indicate that the APUM proteins may act as regulators in Arabidopsis through an evolutionarily conserved mechanism, which may open up a new approach to investigate mRNA regulation in plants.

Evolutionär konservierte, kleine offene Leserahmen (upstream open reading frames, uORFs) sind translational aktive Kontrollelemente, die bevorzugt in Boten-Ribonukleinsäuren von Schlüsselgenen zur Regulation von Zellwachstum, Proliferation und Differenzierung vorkommen. In dieser Arbeit wurden Mäuse analysiert, die defizient für das uORF Initiationscodon des Transkriptionsfaktors CCAAT/enhancer binding protein beta (C/EBPbeta-Delta-uORF) sind. Proteinanalysen verschiedener Gewebe zeigten, dass C/EBPbeta-Delta-uORF Mäuse im Gegensatz zu Wildtyptieren nicht in der Lage sind, die kurze, auto-antagonistische C/EBPbeta LIP Isoform zu induzieren. Die verminderte LIP Expression verursachte eine gestörte Differenzierung knochenabbauender Osteoklasten und ging mit einer Zunahme von mineralisiertem Knochengewebe in C/EBPbeta-Delta-uORF Mäusen einher. Nach partieller Hepatektomie führte der Verlust der uORF-vermittelten Induktion von LIP in regenerierenden C/EBPbeta-Delta-uORF Lebern zu einer Überaktivierung C/EBPbeta-regulierter Akute Phase Gene. Im Vergleich zum Wildtyp wiesen Hepatozyten von C/EBPbeta-Delta-uORF Tieren einen verzögerten und abgeschwächten Wiedereintritt in die S-Phase des Zellzyklus auf. Genomweite Genexpressionsanalysen zeigten, dass die verminderte S-Phase Aktivität in regenerierenden C/EBPbeta-Delta-uORF Lebern mit einer persistierenden Repression von Zellzyklusgenen korrelierte, wobei insbesondere die verminderte Expression zahlreicher E2F-regulierter Gene auffällig wurde. Chromatinimmunpräzipitations- und Reportergenexperimente führten zur Entwicklung eines mechanistischen Modells, das eine isoformspezifische C/EBPbeta-Koregulation E2F-kontrollierter Zellzyklusgene vorschlägt. Die Analyse der C/EBPbeta-Delta-uORF Mäuse belegt erstmals die Funktionalität der uORF-gesteuerten translationalen Kontrolle im Säugetier und weist auf eine entscheidende Bedeutung dieses Kontrollmechanismus bei zahlreichen physiologischen und pathopysiologischen Prozessen hin. / Evolutionary conserved small upstream open reading frames (uORFs) are translational control elements predominantly prevalent in the 5'' mRNA regions of key regulatory genes of growth, proliferation, and differentiation. This thesis comprises the evaluation of mice deficient for the uORF initiation codon of the transcription factor CCAAT/enhancer binding protein beta (C/EBPbeta-Delta-uORF). Protein analysis of various tissues demonstrated that C/EBPbeta-Delta-uORF mice, in contrast to wildtype control animals (C/EBPbeta-WT), fail to induce translation of the truncated, auto-antagonistic C/EBPbeta LIP isoform. The reduced expression of LIP was associated with impaired differentiation of bone resorbing osteclasts and resulted in an increased bone volume of C/EBPbeta-Delta-uORF mice. After partial hepatectomy the loss of uORF-mediated LIP induction resulted in super activation of acute phase response genes in regenerating livers. Furthermore, C/EBPbeta-Delta-uORF hepatocytes showed a delayed and blunted re-entry into the cell cycle after partial hepatectomy as compared to C/EBPbeta-WT animals. Genome-wide transcript expression analyses revealed that the reduced S-phase activity in regenerating C/EBPbeta-Delta-uORF livers correlated with a persistent repression of cell cycle regulatory genes and showed a remarkable underrepresentation of genes regulated by the E2F family of transcription factors. Chromatinimmunoprecipitations and luciferase reporter gene assays allowed the development of a mechanistic model that suggests C/EBPbeta isoform-specific co-regulation of E2F-controled cell cycle genes. The analysis of C/EBPbeta-Delta-uORF mice validates the functionality of uORF-mediated translational control in vertebrates and suggests a comprehensive role of uORF regulation in physiology and the etiology of disease.

No description available.