Plants produce a wide variety of natural products that can be exploited for medicinal purposes. Paclitaxel is a key anti-cancer drug originally isolated from the bark of Taxus spp. that is currently approved for use in the treatment of breast, lung and non-small cell cancers, AIDS-related Kaposi's sarcoma and coronary artery disease. Worldwide demand for paclitaxel is high and plant cell culture (PCC) is an attractive production route. Cultured cambial meristematic cells (CMCs) provide a good platform from which to increase drug production, as they possess superior growth properties on an industrial scale compared to typical dedifferentiated cell culture. Elicitors, such as methyl-jasmonate (MeJA), can up-regulate paclitaxel production in PCC, however the effect is only transient. Identification and characterisation of the key transcriptional regulators that control MeJA induced metabolic reprogramming can provide potential tools to manipulate Taxus CMC culture to produce more paclitaxel. Roche454 sequencing was employed to establish the basic transcriptomic profile of Taxus cuspidata CMCs, which was then utilized as a reference to observe the transcriptional profile of CMCs at three time points after MeJA elicitation (0.5, 2 and 12 h). Analysis of the transcriptional regulatory network identified 19 transcription factors (TFs) that were significantly up-regulated at an early time point (0.5 h) after elicitation. These TFs came from five families – AP2, MYB, NAC, bHLH and WRKY – that are well known to regulate secondary plant metabolism. An Arabidopsis thaliana transient expression assay (TEA) was employed to investigate the regulatory activity of these 19TFs against 10 paclitaxel biosynthetic promoters. The TEA screen identified 79 significant interactions with every promoter interacting with at least three TFs, which could activate or repress activity. A MYB TF was identified that could up-regulate eight out of the ten promoters tested, indicating it maybe a potential overall regulator of paclitaxel biosynthesis. In vitro electromobility shift assays established the possible binding site for this TF as an AC element, with the consensus sequence of A(A/C)C. Repressors of promoter activity were also identified, for example an AP2 TF which contains the well-established ERF associated amphiphilic repression (EAR) motif. The activity of the EAR domain was explored in vivo using a TEA assay and site directed mutagenesis mutants. Activity was lost when the mutation occurred within the domain suggesting the TF was working as an active repressor. TFs can work individually or in combination to achieve metabolic reprogramming after MeJA elicitation. One of the best characterised examples of plant combinatorial control is between particular sub classes of MYB and bHLH TFs. However investigation into possible interactions between the T. cuspidata MYB and bHLH TFs in vivo using yeast two hybrid and TEAs found few combinations that led to a significant change in regulatory activity. The regulatory activity of WRKY TFs was shown to be post-translationally controlled when the TEAs were treated with MeJA, however the mechanism by which this occurs remains to be elucidated. The interactions identified between the 19 TFs and the paclitaxel biosynthetic promoters can be exploited in the future to produce superior Taxus CMC lines with increased paclitaxel yields.

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第17780号 / 医博第3806号 / 新制||医||999(附属図書館) / 30587 / 京都大学大学院医学研究科医学専攻 / (主査)教授 妻木 範行, 教授 武藤 学, 教授 松田 道行 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

This thesis focuses on the functional and structural characterization of FtsH proteases in Synechocystis PCC 6803. One of the aims was to determine localization and subunit organization of FtsH homologues in Synechocystis cells using GST and GFP tagged FtsH derivatives. The main result of the thesis is identification of two FtsH hetero-oligomeric complexes and one homo-oligomeric complex in Synechocystis cells. The large part of the thesis is aimed at establishing the role of the first hetero-oligomeric complex, FtsH2/FtsH3, in quality control of Photosystem II and at identification of a mechanism, how its substrate proteins D1 and D2 are recognized. Another part is dedicated to characterization of the second hetero-oligomeric complex, FtsH1/FtsH3, which consists of two essential FtsH homologues and which is here identified as an important regulatory element in maintaining iron homeostasis.

La formation des trois feuillets embryonnaires primordiaux et leur régionalisation selon les axes embryonnaires sont des étapes cruciales au cours du développement précoce. Dans ce contexte, nous avons montré que XDSCR6, un inducteur du mésoderme et des axes embryonnaires qui présente des propriétés dorsalisantes, interagit physiquement et fonctionnellement avec le facteur de transcription XSTAT3. Au cours des étapes précoces du développement, XSTAT3 est active pendant la gastrulation et l'activation anormale de cette protéine dans la région dorsale induit la ventralisation des tissus embryonnaires. Par ailleurs, nous avons montré que XDSCR6 et XSTAT3 présentent des rôles antagonistes in vivo au cours de la mise en place des axes embryonnaires. Cet antagonisme peut être expliqué par le fait que XDSCR6 régule négativement l'activité transcriptionnelle de XSTAT3 en modulant sa méthylation sur les résidus lysine. L'ensemble de nos résultats a permis de déterminer l'importance cruciale de cette modification post-traductionnelle dans les propriétés ventralisantes de XSTAT3. Par ailleurs, nous avons montré que la méthyltransférase XEZH2 méthyle et active XSTAT3 in vivo. Des travaux antérieurs de l'équipe avaient montré que les propriétés dorsalisantes de XDSCR6 reposent sur sa capacité à inhiber l'activité épigénétique répressive de XEZH2 sur les gènes du mésoderme dorsal. Ainsi, nos travaux suggèrent que XDSCR6 est un modulateur transcriptionnel situé à l'interface entre certains régulateurs chromatiniens et des facteurs de transcription pendant la mise en place des axes embryonnaires. / One of the most challenging questions in developmental biology is to understand how a totipotent zygote differentiates into an organism containing all cell lineages. The formation of the three germ layers and the establishment of embryonic axis are fundamental events during early development. In this context, we demonstrated that XDSCR6, a mesoderm and embryonic axis inducer that exhibits dorsalizing properties, physically and functionally interacts with the transcriptional factor XSTAT3. During early development, XSTAT3 is active throughout gastrulation step and its abnormal activation in dorsal region leads to embryonic tissues ventralization. Furthermore, we showed that XDSCR6 and XSTAT3 have antagonistic roles in vivo during axis formation. This antagonism can be explained by the fact that XDSCR6 negatively regulates the transcriptional activity of XSTAT3 by interfering with its methylation on lysine residues. Moreover, this post-translational modification plays a crucial role in the ventralization abilities of XSTAT3. In a previous study, it has been shown that XDSCR6 negatively regulates the XEZH2 repressive epigenetic activity on dorsal mesoderm genes. Thus, we propose that XDSCR6 is a transcriptional modulator acting between epigenetic regulators and transcriptional factors during embryonic axis formation.

Orientador: Celso Eduardo Benedetti / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-11T01:25:29Z (GMT). No. of bitstreams: 1 Barbosa_RosiclerLazaro_D.pdf: 3769373 bytes, checksum: ba15f76eb9d63f64834d030ffed2482a (MD5) Previous issue date: 2008 / Resumo: O gene XF0767 de Xylella fastidiosa está localizado num operon composto por mais quatro genes classificados como proteínas hipotéticas (XF0768-XF0767-XF0766-XF0765-XF0764). Este operon está conservado em uma série de bactérias associadas a plantas, incluindo Agrobacterium tumefaciens, Mezorhizobium loti e Sinorhizobium meliloti. A região upstream ao códon de iniciação deste operon possui seqüências canônicas correspondentes a sítios -35 e ¿10 de regiões promotoras reguladas por fatores sigma70. O objetivo deste trabalho foi caracterizar o sistema de regulação do operon pela proteína XF0767, nomeada BigR (biofilm growth-associated repressor), visando à compreensão deste sistema e sua importância para a bactéria. A proteína BigR se liga na seqüência repetida invertida (9-4-9) localizada na região ¿10 do promotor do operon XF0768-0764, denominada BigRbox. BigR inibe a atividade do operon reprimindo a expressão do gene repórter GFP em Escherichia coli, Agrobacterium tumefaciens e Xylella fastidiosa. Mutações no BigRbox dos promotores de Xylella e Agrobacterium afetam a ligação do repressor e abole a transcrição do gene repórter. Esses dados indicam, portanto, que BigR compete com a RNA polimerase pelo mesmo sítio de ligação ao DNA, revelando assim o mecanismo de regulação do operon. BigR apresenta similaridade com fatores transcricionais de bactérias contendo domínio HTH (helix-turn-helix) de ligação ao DNA. Apesar de BigR ter sido inicialmente classificada como uma proteína da família SmtB/ArsR, as quais regulam operons relacionados à resistência a metais, nossos dados indicam que BigR não atua como sensor de metal. A adição de cádmio, ferro e cobre na mistura de ligação causam uma aparente dissociação do complexo DNA/BigR, entretanto, estudos in vivo na presença de metais não evidenciaram nenhuma alteração na expressão do gene repórter. Mutantes deficientes em BigR também não apresentam diferença de crescimento na presença de metais. O gene XF0768 codifica uma proteína nomeada BLH (beta-lactamase-like hydrolase) por pertencer à superfamília das metalo-beta-lactamases. Dada a presença de BigR e BLH no operon de Xylella e Agrobacterium, a atividade do operon foi analisada em diferentes condições como crescimento das células repórter in planta, co-cultivo com bactérias endofíticas e deficiência nutricional. Entretanto, uma maior atividade do operon em Xylella e Agrobacterium foi detectada apenas na condição de biofilme. Células de Agrobacterium aderidas em raiz de tabaco também apresentaram maior expressão do gene repórter quando comparadas às células em suspensão. Mutantes de Agrobacterium deficientes em BigR (bigR-) apresentam maior expressão do gene repórter, confirmando que BigR age como o repressor transcricional do operon. A quantificação da formação de biofilme das células mutante e selvagem revelou uma maior densidade de biofilme no mutante bigR- em superfície de vidro e também maior quantidade de células aderidas em raiz de tabaco, indicando que o operon pode estar envolvido com o processo de adesão ou desenvolvimento do biofilme bacteriano. Do ponto de vista estrutural, foi mostrado que a proteína BigR truncada no N-terminal (?BigR) encontra-se estruturada na forma de trímero, diferindo do observado para as proteínas com domínio HTH que em geral formam dímeros e monômeros. BigR é estável termicamente, começando a perder estrutura à 74oC, mas retendo um sinal residual de a-hélice até 90oC. Tratamentos com altas concentrações de (NH4) SO 2 4 interferiram na ligação da proteína ao DNA alvo e no conteúdo de estrutura secundária sem alterar, contudo, sua estabilidade térmica. A purificação e cristalização da proteína ?BigR resultou na coleta de alguns conjuntos de dados da proteína nativa e derivada, através de soaking ou marcada com SeMet. Apesar dos dados obtidos serem de boa qualidade, até o momento, não foi possível a resolução da estrutura cristalográfica desta proteína / Abstract: The XF0767 gene from Xylella fastidiosa is located in an operon composed by a set of genes (XF0768-XF0767-XF0766-XF0765-XF0764) of unknown function. This operon is conserved in a number of plant-associated bacteria including Agrobacterium tumefaciens, Mezorhizobium loti e Sinorhizobium meliloti. The DNA region upstream of the operon has canonical sequences corresponding to ¿35 and ¿10 elements found in sigma70-regulated promoters. The aim of this work was to elucidate the biological function of the protein encoded by XF0767, named BigR (biofilm growth-associated repressor), as a transcriptional regulator and its importance to the bacteria. BigR binds to an inverted repeat sequence (9-4-9) located in the ¿10 region of the XF0768-0764 operon promoter. This sequence was named BigRbox. BigR repressed transcription of its own operon upon binding to the BigRbox in Xylella fastidiosa and Agrobacterium tumefaciens. Mutations in the BigRbox significantly affected the repressor binding and abolished transcription of the reporter gene in both bacteria, indicating that BigR compete with the RNA polymerase for the same promoter site. BigR is similar to HTH transcriptional factors of the SmtB/ArsR family, which control tolerance and detoxification of heavy metals in prokaryotes. Despite the similarities, BigR does not appear to function as a metal sensor, as initially predicted. Although binding of BigR to its target DNA was diminished in the presence of cadmium, copper and iron, operon regulation in response to metals was not demonstrated in vivo. In addition, Agrobacterium mutants deficient in BigR did not show changes in growth rates in the presence of metals. BLH is an unusual beta-lactamase-like hydrolase coded by the XF0768 gene. To gain insights into the possible function of the operon, the activity of reporter cells was observed in the presence of different compounds and conditions including in planta growth, effect of endophytic competition and nutrient deficiency. Significantly, an increased operon activity was observed in Xylella and Agrobacterium biofilms. Agrobacterium cells attached to tobacco roots also showed high levels of reporter gene expression in comparison to cells in suspension. A. tumefaciens mutants deficient in the BigR showed constitutive expression of the operon, confirming that BigR acts as a transcriptional repressor. Biofilm quantification showed increased biofilm formation in glass surfaces as well as in tobacco roots, indicating that the operon may play a role in cell adherence or biofilm development. Structurally, the truncated BigR protein (?BigR) is a trimmer in solution, as opposed to most HTH regulators known, which are usually found as dimmers or monomers. BigR is stable at high temperatures (74oC); however, treatments with high concentrations of ammonium sulfate interfere with the protein secondary structure and its DNA binding capacity, without affecting its thermal stability. Good quality X-ray diffraction data were collected for the native and derivative ?bigR protein; however, structure resolution was not possible probably due to problems with the crystals / Doutorado / Genetica de Microorganismos / Doutor em Genetica e Biologia Molecular

LYL1 (Lymphoblastic leukemia-derived sequence 1) est un facteur de transcription basic hélice-boucle-hélice (bHLH) exprimé dans les lymphocytes B, les cellules myéloïdes et les cellules endothéliales (CE). Les souris déficientes pour Lyl1 (Lyl1-/-) sont viables et chez la souris adulte, LYL1 a un rôle majeur dans la maturation des vaisseaux sanguins nouvellement formés et dans le contrôle de la perméabilité vasculaire basale, suggérant l'importance de LYL1 dans le maintien de la quiescence et/ou stabilisation des CE. Les vaisseaux sanguins représentent une barrière entre le sang et le tissu conjonctif. Ils peuvent également jouer le rôle de niche vasculaire contenant des progéniteurs des différentes cellules murines (par exemple, des cellules hématopoïétiques, des cellules β-pancréatiques, des cellules neuronales, des cellules hépatiques et des cellules adipeuses). Les deux tissus adipeux, blancs et bruns (WAT et BAT), sont très vascularisés. Jusqu'à présent, rien n'était connu sur le rôle de LYL1 dans le tissu adipeux. Les résultats présentés dans cette thèse montrent que l'augmentation significative du poids corporel des mâles Lyl1-/- par rapport aux souris sauvages (WT), sous régime normal, n'est pas associée à des troubles métaboliques. Ils présentent également un poids plus élevé de tissus adipeux (WAT et BAT) et de plus grandes gouttelettes lipidiques. In vivo, la perte de Lyl1 accélère le processus de différenciation des cellules souches adipeuses (CSA), puisque les adipocytes blancs et bruns sont matures et actifs plus tôt. De plus, les CSA sont moins nombreuses dans les tissus adipeux, ce qui confirme que la perte de Lyl1 favorise la différenciation des CSA vers adipocytes matures. Nous avons également démontré que Lyl1 est exprimée dans les CSA et les pré-adipocytes, suggérant un rôle direct dans LYL1 dans la différenciation adipocytaire. D'autre part, les vaisseaux des WAT des souris Lyl1-/- sont mal recouverts de cellules murales et plus perméables, suggérant que la niche vasculaire des tissus adipeux pourrait être perturbée. Sous alimentation riche en graisses (HFD), le poids corporel et le poids du tissu adipeux sont plus faibles chez les souris Lyl1-/- par rapport à WT. De plus les souris Lyl1-/- présentent de plus petites gouttelettes lipidiques que les WT, sous HFD. Ces résultats préliminaires, suggèrent que les souris Lyl1-/- pourraient être protégées contre l'obésité induite par l'alimentation. Cependant d'autres expériences sont nécessaires pour valider ces résultats. Il existe probablement un mécanisme de compensation qui se met en place chez les souris Lyl1-/- sous HFD. Ce travail a démontré que, sans Lyl1, la différenciation adipocytaire est accélérée et que la niche vasculaire adipocytaire est perturbée. / LYL1 (Lymphoblastic leukemia-derived sequence 1) is a basic helix-loop-helix (bHLH) transcriptional factor, which is expressed in B lymphocytes, myeloid cells and endothelial cells (EC). Lyl1 deficient (Lyl1-/-) mice are viable and in adult mice, LYL1 has an active role in the maturation of newly formed blood vessels and is also involved in the control of basal vascular permeability, suggesting that LYL1 is required for the maintenance of EC quiescence and stabilization. Blood vessels provide a barrier between connective tissue and blood. They also have been described as “vascular niche” containing progenitors of different murine cells (e.g. hematopoietic cells, pancreatic β-cells, neuronal cells, liver cells and adipose cells). Both white and brown adipose tissues (WAT and BAT) are highly vascularized. Up to now, nothing was known concerning the role of LYL1 in adipose tissue. The results presented in this thesis revealed that the significant increase in body weight of Lyl1-/- males compared to their wild type (WT) littermates under chow diet is not due to any metabolic disorders. They also showed higher adipose tissue weights (BAT and WAT) and bigger lipid droplets. In vivo Lyl1 deficiency cause early differentiation process of adipose stem cells (ASCs) since both white and brown adipocytes are mature and active faster. In addition, ASCs are less numerous in Lyl1-/- adipose tissues, which confirm that Lyl1 deficiency favors the differentiation of ASCs towards mature adipocytes. We also demonstrated that Lyl1 is expressed both in ASCs and pre-adipocytes, suggesting a direct role of LYL1 in adipocyte differentiation. On the other hand, the vessels in Lyl1-/- WAT are poorly covered with mural cells and more permeable, proposing that adipose stem cell vascular niche could be disturbed. Under high fat diet (HFD), total body weight and adipose tissue weight are lower in Lyl1-/- mice compared to WT. Moreover smaller lipid droplets were observed in Lyl1-/- mice under HFD. These preliminary results suggest that Lyl1-/- mice could be protected from diet-induced obesity. However more experiments are needed to validate these results. Probably there is a compensatory type of mechanism going on under HFD in Lyl1-/- mice. This work demonstrated that under Lyl1 deficiency adipocyte differentiation process becomes faster and adipose tissue vascular niche could be disturbed.

Loss of hearing affects more than 10 % of the population, and one newborn in a thousand is born with defects of the inner ear. Transcriptional factors involved in the development of inner ear are important in our understanding of the causes of inner ear defects. ISLET1 is one of these factors. ISLET1 expression is detected in the sensory and neuronal cells of the inner ear. It participates in otocyst formation, and the specification and differentiation of cells of cochlea and vestibular system. The functional role of ISLET1 during inner ear development was investigated. Its role was studied by using Pax2-Isl1 transgenic mice that overexpress Islet1 under the control of the Pax2 promoter. Two transgenic lines were generated, Pax2-Isl1/300 and Pax2- Isl1/52. Two copies of the Pax2-Isl1 transgene were inserted to Pax2-Isl1/300 genome and one copy was inserted to the Pax2-Isl1/52 genome. Defects in sense of hearing were detected in both lines and circling behavior, a defect of balance, was detected in the Pax2-Isl1/300 transgenic mice. We observed high postnatal lethality in heterozygote transgenic mice. Pax2-Isl1/52 homozygote mutation is lethal at embryonic day 10 (E10,5). Pax2-Isl1/300 homozygote letality couldn't be detected because of the inability to breed heterozygote mutated mice of this line....

Role of Nkx2.5 on development and electrophysiology of the mouse heart Prague 2015 Bc. Peter Hámor ABSTRACT The objective of this thesis is to investigate the role of Nkx2.5 gene dosage on electrophysiology of the mouse heart in prenatal stage of its development, in which the physiological functions of the heart fail to function properly. The main goal of this work is to search for differences in conduction of electric impulses through the embryonic mouse heart according to their genotype. Special method of capturing the conduction of electric impulse through myocardium was used for this purpose, called optical mapping. Thanks to this method I was able to construct images and videos capturing transition of the impulse with marked beginning of the activation and its direction in the heart. These outputs, or optical maps, help to define anomalies and defects compared with a normal functioning heart. The thesis focuses on the expression of the transcription factor Nkx2.5 and regulatory components related with the correct formation and physiology of the heart until 9.5 days post coitum. Individuals in this developmental stage were optically mapped and compared according to their genotypes - homozygous non-mutant, heterozygote and homozygous mutant mouse embryos exhibited some degree of similarity, while other...

Les modèles de Markov d’ordre 2 (HMM2) sont des modèles stochastiques qui ont démontré leur efficacité dans l’exploration de séquences génomiques. Cette thèse explore l’intérêt de modèles de différents types (M1M2, M2M2, M2M0) ainsi que leur couplage à des méthodes combinatoires pour segmenter les génomes bactériens sans connaissances a priori du contenu génétique. Ces approches ont été appliquées à deux modèles bactériens afin d’en valider la robustesse : Streptomyces coelicolor et Streptococcus thermophilus. Ces espèces bactériennes présentent des caractéristiques génomiques très distinctes (composition, taille du génome) en lien avec leur écosystème spécifique : le sol pour les S. coelicolor et le milieu lait pour S. thermophilus / Second-order Hidden Markov Models (HMM2) are stochastic processes with a high efficiency in exploring bacterial genome sequences. Different types of HMM2 (M1M2, M2M2, M2M0) combined to combinatorial methods were developed in a new approach to discriminate genomic regions without a priori knowledge on their genetic content. This approach was applied on two bacterial models in order to validate its achievements: Streptomyces coelicolor and Streptococcus thermophilus. These bacterial species exhibit distinct genomic traits (base composition, global genome size) in relation with their ecological niche: soil for S. coelicolor and dairy products for S. thermophilus. In S. coelicolor, a first HMM2 architecture allowed the detection of short discrete DNA heterogeneities (5-16 nucleotides in size), mostly localized in intergenic regions. The application of the method on a biologically known gene set, the SigR regulon (involved in oxidative stress response), proved the efficiency in identifying bacterial promoters. S. coelicolor shows a complex regulatory network (up to 12% of the genes may be involved in gene regulation) with more than 60 sigma factors, involved in initiation of transcription. A classification method coupled to a searching algorithm (i.e. R’MES) was developed to automatically extract the box1-spacer-box2 composite DNA motifs, structure corresponding to the typical bacterial promoter -35/-10 boxes. Among the 814 DNA motifs described for the whole S. coelicolor genome, those of sigma factors (B, WhiG) could be retrieved from the crude data. We could show that this method could be generalized by applying it successfully in a preliminary attempt to the genome of Bacillus subtilis