Le processus de maturation et de dégradation des ARNm chez les bactéries implique différentes ribonucléases (RNases). Une endoribonucléase a été découverte en 2009 chez Bacillus subtilis appelée RNase Y. Cette RNase joue un rôle central en catalysant la réaction de clivage initiatrice, un clivage endonucléolytique. Les fragments d'ARN issus du clivage par la RNase Y deviennent alors plus sensibles à la dégradation, en 5' et 3', par les exonucléases. En combinant ces différentes techniques, il s'est avéré que la RNase Y semble s'organiser sous forme d'un oligomère ayant une forme en anneau. Cet oligomère est homogène en microscopie, globulaire et structuré en SAXS. Le domaine ID lui n'est pas complètement déstructuré comme le révèle son analyse en SAXS. Il contient des éléments de structure secondaire de type hélice α et ne possède pas de structure tertiaire, comme le concluent respectivement les analyses en CD et RMN. L'analyse en SAXS de la forme dimérique de la RNase Y révèle que le dimère est structuré mais qu'il possède une forme allongée. Les tests d'activité in vitro sur la forme dimérique et oligomérique montre que ces deux formes sont activent. Les images collectées en cryo-microscopie nous permettrons d'obtenir une structure de meilleure résolution de l'oligomère, qui semble être constitué de 8 dimères de RNase Y. / Messenger RNA decay and processing in bacteria involve a set of various ribonucleases (RNases). In Bacillus subtilis, a newly discovered endoribonuclease called RNase Y was shown to play a central role in mRNA decay by catalyzing the initial endonucleolytic cleavage reaction. Its action releases several RNA pieces that are more sensitive to degradation by exoribonucleases. By combination of these different approaches, it was found that RNase Y seems to be organized in a oligomeric form with a ring shape. This oligomer is homogenous in microscopy, globular and structured in SAXS. The intrinsically disordered domain is not completely disordered as we can conclude with the SAXS analysis. It contains some secondary structural elements (α helix) but it has no tertiary structure as we can conclude with CD and NMR analysis respectively. SAXS analysis of the RNase Y dimeric form show that this dimeric form is structured but have a very elongated shape. In vitro activity tests on both oligomeric and dimeric form reveal that these two forms are active. Oligomer cryomicroscopy pictures collected will allow us to get a structure with a better resolution. At the moment, this oligomer seems to be composed by eight RNase Y dimer.

Orientador: Lucia Galvão de Albuquerque / Resumo: As características de qualidade de carne, por serem de difícil mensuração, raramente são contempladas em programas de melhoramento genético. Porém, é necessário conhecer sobre os genes e os mecanismos moleculares que controlam essas características, isso poderá auxiliar na avaliação de animais de forma precoce. Objetivo desse estudo foi identificar e analisar genes e isoformas de mRNA diferencialmente expressos no tecido do músculo Longissimus thoracis de bovinos da raça Nelore, fenotipicamente divergentes para características cor da carne, marmoreio e maciez da carne (avaliada através das metodologias de WBSF e MFI) usando dados de RNA-Seq. Além disso, esse estudo visa a identificação dos efeitos de variantes estruturais em “splice sites” de transcriptos diferencialmente expressos em animais fenotipicamente divergentes para as características de color e marmoreio da carne. Uma média de 37 mil transcritos foram detectados sendo expressos no músculo de bovinos Nelore. Foram identificados 40 e 28 isoformas de mRNA (p-valor < 0,001) diferencialmente expressas para os fenótipos de WBSF e MFI, respectivamente. Além disso, foram identificados sendo diferencialmente expressos os mRNAs [WBSF (SYNPO-201) e MFI (ANKRD23-202)], e entre outras isoformas de mRNA relacionadas a genes que afetam a velocidade de degradação das fibras musculares durante o processo de envelhecimento da carne, como e.g. [para WBSF (MYOT, CASQ1, TPM2, MB e SYNM) e para MFI (FGFRL1 e NEB)]. Na análise de enriquec... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The measurement of meat quality traits are costly, because of that it is rarely included in breeding programs. However, it is necessary to know about the genes and the molecular mechanisms that control these traits, this may help in the evaluation of animals at an early stage.Thus, the identification of mRNA isoforms and the associated splice variants affecting meat quality traits in Nellore cattle could allow to better understanding the genetic architecture of these complex traits. The objective of this study was to identify and analyze genes and mRNA isoforms differentially expressed in the Longissimus thoracis muscle tissue of Nellore cattle, phenotypically divergent for meat color, marbling and meat tenderness (evaluated using WBSF and MFI methodologies) traits, using RNA-Seq data. In addition, to identify structural variants affecting splice sites of differencially expressed mRNA isoforms for marbling and meat color traits. An average of 37 thousand transcripts were detected in the Nellore muscle transcriptomic analysis. A total of 40 and 28 mRNA isoforms (p-value |<| 0.001) were differentially expressed between divergent groups for WBSF and MFI phenotypes, respectively. The differentially expressed mRNA isoforms [WBSF(MYL1, MYL3, MYH1 and MYBPC2) and MFI (MYL6) traits], which are myosin encoders, was the family with most abundantly number of mRNA isoforms detected as diferencially expressed. In addition, we identified as DE [WBSF (SYNPO-201 isoform) and for MFI (ANKRD23... (Complete abstract click electronic access below) / Doutor

<p>  </p> <p>Adenosine-to-Inosine (A-to-I) mRNA editing is a post-transcriptional modification of specific sites within the mRNA that has only recently been observed in filamentous fungi. In the wheat scab fungus <em>Fusarium graminearum,</em> this phenomenon has shown to be facilitated by FgTad2 and FgTad3, homologs of Adenine Deaminase Acting on tRNA (ADAT). Interestingly, these two proteins are constitutively expressed in all different life stages<em>, </em>in contrast to only the sexual stage-specific nature of A-to-I mRNA editing in <em>F. graminearum</em>. To understand the molecular mechanisms regulating this process, six candidate co-factor genes were identified which interact with FgTad2 and/or FgTad3, specifically during sexual reproduction. Deletion mutants of four candidate co-factor genes were successfully generated. All four mutants displayed normal asexual development of <em>F. graminearum</em>, but four mutants also altered sexual function. Those four mutant led to formation of morphologically normal perithecia and ascospores, but the perithecia failed to discharge ascospores. More interestingly, in <em>FGSG_10943 </em>deletion mutant, most of these ascospores germinated precociously within the perithecium. I also observed, that among the candidate co-factor genes which are specifically expressed during sexual reproduction, <em>FGSG_10943</em> was significantly upregulated during the later stage of sexual development. This gene is restricted in nature to only a few orders of fungi in the class Sordariomycetes that form dark pigmented ascocarps, particularly Hypocreales and Glomerellales. Taken together, these results indicate that the four candidate co-factor genes are dispensable for vegetative growth of the fungus and involved in ascospore discharge. <em>FGSG_10943</em> appears to be involved in autoinhibition of ascospores inside the perithecia and interact with FgTad2 during sexual reproduction to mediate A-to-I mRNA editing in <em>F. graminearum</em>.</p>

Adaptation to variations in oxygen concentration is a conserved mechanism in all metazoans as this process is central for the maintenance of cell and tissue homeostasis. Two major and highly conserved processes contribute to hypoxia-induced gene reprogramming. The first one relies on the transcriptional activation of gene expression by the Hypoxia Inducible Factors (HIFs) leading to the upregulation of a large panel of genes. The second one corresponds to a strong modification of the translation program. While the mechanisms underlying HIF-dependent transcriptional activation have been well characterized, the ones governing translation reprogramming are only partially understood. 
To uncover how mRNA translation takes place at low oxygen tension, we used Drosophila as our research model since both Drosophila flies and S2 cells are highly resistant to low O2. We first demonstrate that several genes are efficiently translated under hypoxia in Drosophila S2 cells. By a gene reporter-based approach, we demonstrate that Ldh mRNA 3’UTR is sufficient to promote reporter mRNA association to polysomes in hypoxia. A deletion analysis of Ldh 3’UTR leads to the identification of a ACAAA-rich sequence important for polysomal association and translation in hypoxia.Cap-binding factors play a key role in controlling translational initiation. We have shown that the cap-binding translation initiation factor eIF4EHP (4EHP) plays a dual role on translation under hypoxic conditions. Despite having a general repressive function on global translation under normoxic and hypoxic conditions, we demonstrated that 4EHP also positively controls the translation of specific mRNAs under hypoxia. Inactivation of 4ehp reduces LDH protein synthesis and impairs reporter mRNA translation in hypoxia. Deletion of 4ehp inhibites the translation of several candidate genes harboring a ACAAA motif in 3’UTR under hypoxia, suggesting that 4EHP is required for hypoxic translation of mRNAs carrying ACAAA-rich motifs. Most interestingly, we observed that 4EHP is strongly enriched in polysomal fractions in hypoxia, further supporting a role of this initiation factor in hypoxic translation. The reduction of 4ehp expression also impairs Drosophila development under hypoxic conditions. Taken together, our results indicate that specific mRNAs can bypass the translational blockade imposed by hypoxic conditions. This process is controlled by mRNA 3’UTR “CA” rich element and is positively regulated by the translation initiation factor 4EHP. / L'adaptation aux variations de la concentration en oxygène est un mécanisme conservé chez tous les métazoaires car ce processus est central pour le maintien de l'homéostasie cellulaire et tissulaire. Deux processus hautement conservés contribuent à la reprogrammation génétique induite par l'hypoxie. Le premier repose sur l'activation transcriptionnelle de l'expression génique par les facteurs inductibles de l'hypoxie (HIF) conduisant à l’induction d'un large panel de gènes. Le second correspond à une forte modification du programme traductionnel. Alors que les mécanismes sous-jacents à l'activation transcriptionnelle dépendante de HIF ont été bien caractérisés, ceux qui régissent la reprogrammation de la traduction ne sont que partiellement compris.Pour découvrir comment la traduction de l'ARNm se déroule à faible tension d'oxygène, nous avons utilisé la drosophile comme modèle d’étude, car les mouches Drosophila melanogaster et les cellules S2 issue de cet organisme sont très résistantes à de faibles teneurs en O2. Nous avons tout d’abord démontré que plusieurs gènes sont efficacement traduits en hypoxie dans les cellules S2 de drosophile. Par une approche basée sur l’utilisation de gènes rapporteurs, nous avons démontré que la région 3’ Non traduite (3’UTR) de l’ARNm Ldh est suffisante pour promouvoir l’association de l’ARNm du rapporteur aux polysomes en conditions hypoxiques. Une analyse par délétion de la région 3’UTR de l’ARNm Ldh a conduit à l’identification d’une séquence riche en ACAAA importante pour l’association polysomale et la traduction en hypoxie. La reconnaissance de la coiffe joue un rôle clé dans le contrôle de l'initiation de la traduction Nous avons montré que le facteur d'initiation de la traduction eIF4EHP (4EHP), qui se lie à la coiffe, joue un double rôle sur la traduction dans des conditions hypoxiques. Bien qu'il ait une fonction répressive sur la traduction générale dans des conditions normoxiques et hypoxiques, nous avons démontré que 4EHP contrôle aussi positivement la traduction d'ARNm spécifiques dans des conditions hypoxiques. L'inactivation de 4ehp réduit la synthèse de la protéine LDH et altère la traduction de l'ARNm rapporteur contenant la partir 3’UTR du messager Ldh en hypoxie. La délétion de 4ehp peut atténuer la traduction de plusieurs gènes candidats contenant un motif ACAAA dans leur région 3’UTR 3' en hypoxie, ce qui suggère que 4EHP est nécessaire pour la traduction hypoxique des ARNm portant des motifs riches en ACAAA. De façon intéressante, nous avons observé que 4EHP est fortement enrichi dans les fractions polysomales en hypoxie, ce qui confirme le rôle de ce facteur d'initiation dans la traduction en hypoxie. La réduction de l'expression de 4ehp altère également le développement de la Drosophile dans des conditions hypoxiques. Ensemble, nos résultats indiquent que des ARNm spécifiques peuvent contourner le blocage traductionnel imposé par les conditions hypoxiques. Ce processus est contrôlé par l'élément riche en "CA" situé dans la partie 3'UTR de l’ARNm et est régulé positivement par le facteur d'initiation de la traduction 4EHP. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Brominated flame retardants (BFR) such as hexachlorocyclopentadienyl-dibromocyclooctane (HCDBCO), bis(2-ethylhexyl)tetrabromophthalate (BEHTBP), 1,2-bis(2,4,6-tribromophenoxy)ethane (BTBPE) and decabromodiphenylethane (DBDPE) are contaminants of environmental concern. These BFRs are replacement alternatives for some of the major production BFRs, which have been restricted from the marketplace due to their adverse health effects. Their presence in environmental matrices, including wild birds, suggests they should be tested for possible toxic effects. BFR alternatives have been detected in the eggs of colonial fish-eating birds, suggesting maternal transfer during ovogenesis and the potential for these chemicals to bioaccumulate through the food chain. However, information regarding the toxicity of HCDBCO, BEHTBP, BTBPE and DBDPE exposure in birds is lacking. This thesis consisted of a combined in vitro/in ovo approach to determine: 1) the concentration-dependent effects of these four BFR alternatives in chicken embryonic hepatocytes (CEH), and 2) the dose-dependent effects of HCDBCO and BTBPE in chicken embryos following injection into the air cell of eggs prior to incubation. Changes in the mRNA expression levels of genes previously found to be responsive to other BFRs were assessed in CEH and liver tissue, in addition to examining overt toxicity (i.e. cytotoxicity, pipping success). None of the BFRs tested were cytotoxic up to 60 µM HCDBCO, 60 µM BEHTBP, 1.4 µM BTBPE or 0.2 µM DBDPE in CEH. Injection doses up to 50 µg/g egg HCDBCO and 10 µg/g egg BTBPE had no effect on embryonic pipping success. The accumulation of HCDBCO and BTBPE was variable in liver and did not follow a linear uptake pattern with respect to injection dose, due in part to difficulties with the solubility of these chemicals in the dimethyl sulfoxide (DMSO) vehicle. In, CEH, HCDBCO caused a decrease in CYP1A4/5 mRNA at all concentrations tested, while CYP2H1 and CYP3A37 were induced only at 10 µM. In contrast, only TTR mRNA was down-regulated in hepatic tissue at all injection concentrations of HCDBCO. The highest concentration of BTBPE induced CYP1A4/5 mRNA to 115- and 18-fold in CEH, and 6.5- and 1.8-fold in liver tissue. In vitro and in ovo exposure to BTBPE caused a concentration-dependent decrease in DIO3 mRNA, while CYP3A37 was down-regulated 2-fold at 10 µg/g in liver tissue. In CEH, DBDPE induced CYP1A4/5 mRNA to a maximum of 29- and 59-fold at 0.2 µM, and increases in DIO1 mRNA and decreases in CYP3A37 mRNA were also observed. None of the gene targets were responsive to BEHTBP exposure in CEH. This is the first study to report on the toxicological and molecular effects of HCDBCO, BEHTBP, BTBPE and DBDPE in an avian species. Using this combined in vitro/in ovo approach has permitted the characterization of these four BFR alternatives by defining possible mechanisms of biological action in a model avian species, the chicken.

Nicotine's rewarding effects are mediated through distinct subunits of nAChRs, encoded by different nicotinic cholinergic receptor (CHRN) genes and expressed in discrete regions in the brain. In the present study, we aimed to test the associations between rare variants at CHRN genes and nicotine dependence (ND), and alcohol dependence (AD). A total of 26,498 subjects with nine different neuropsychiatric disorders in 15 independent cohorts, which were genotyped on Illumina, Affymetrix, or PERLEGEN microarray platforms, were analyzed. Associations between rare variants (minor allele frequency (MAF) <0.05) at CHRN genes and nicotine dependence, and alcohol dependence were tested. The mRNA expression of all Chrn genes in whole mouse brain and 10 specific brain areas was investigated. All CHRN genes except the muscle-type CHRNB1, including eight genomic regions containing 11 neuronal CHRN genes and three genomic regions containing four muscle-type CHRN genes, were significantly associated with ND, and/or AD. All of these genes were expressed in the mouse brain. We conclude that CHRNs are associated with ND (mainly) and AD, supporting the hypothesis that the full catalog of ND/AD risk genes may contain most neuronal nAChRs-encoding genes.

京都大学 / 0048 / 新制・課程博士 / 博士(医科学) / 甲第21694号 / 医科博第98号 / 新制||医科||7(附属図書館) / 京都大学大学院医学研究科医科学専攻 / (主査)教授 竹内 理, 教授 Shohab YOUSSEFIAN, 教授 藤渕 航 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

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