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Thesis (Ph. D. in Plant Pathology)--University of California, Davis, Jan. 1954. / Includes bibliographical references (leaves 68-72). Also available via the World Wide Web. (Restricted to UC campuses).

No description available.

Our knowledge of the factors mediating ethylene-dependent and -independent ripening of climacteric fruit remains limited. Besides the known importance of ethylene roles, auxin has also been emerged as crucial to regulating ripening. Furthermore, the crosstalk between ethylene and auxin in tomato fruit ripening still awaits clarification. ERFs (Ethylene Responsive Factors) are transcription factors belonging to a large family acting downstream on ethylene signaling that direclty regulate ripening-related metabolisms, but their specific roles are still lacking. We present here a comprehensive expression profiling of tomato ERFs in wild-type and tomato ripening-impaired tomato mutants (Nr, rin and nor) indicating that out of the 77 ERFs present in the tomato genome, 27 show enhanced expression at the onset of ripening, while 28 display a ripening-associated decrease in expression, suggesting that different ERFs may have contrasting roles in fruit ripening. Members of subclass E, ERF.E1, ERF.E2 and ERF.E4, show dramatic down-regulation in the ripening mutants suggesting their expression might be instrumental to fruit ripening. The study illustrates the high complexity of the regulatory network interconnecting RIN and ERFs and identifies subclass E members as the most active ERFs in ethylene- and RIN/NOR-dependent ripening. Additionally, with the aim to shed more light into ethylene and auxin interplay, hormonal treatments were applied to tomato fruits and several ripening aspects were then evaluated such as the volatile profile. Overall, results elicited that auxin delay the onset of ripening further showing epistatic effects over the influence of ethylene. Several ripening-related genes, including components of the ethylene signaling, were affected by auxin suggesting potential crosstalk points between the two hormones. Moreover, ethylene appears as potentially part of the auxin regulation through inducing its conjugation. The modulation of hormone levels in tomato fruit throughout ripening can be useful to help designing approaches that both improve fruit quality and extend shelf life. / O conhecimento acerca dos fatores dependentes e independentes de etileno que regulam o amadurecimento de frutos climatéricos é ainda limitado. Além da importância conhecida do etileno, a auxina também tem sido apontada como crucial para o controle do amadurecimento. Mais ainda, há poucos estudos envolvendo o crosstalk entre etileno e auxina em frutos de tomateiro. ERFs (Ethylene Responsive Factors) são fatores de transcrição que atuam nos últimos níveis da via de sinalização de etileno, regulando diretamente metabolismos associados ao amadurecimento. Contudo, seus papéis específicos ainda são desconhecidos. O presente estudo revela o perfil detalhado de expressão de ERFs em tomate selvagem e nos mutantes cujo amadurecimento é comprometido (Nr, rin e nor) indicando que dos 77 ERFs presentes no genoma, 27 apresentam aumento de expressão no início do amadurecimento, enquanto 28 apresentam redução, sugerindo que diferentes ERFs possivelmente têm papéis distintos na regulação do amadurecimento. Membros da subclasse E, ERF.E1, ERF.E2 e ERF.E4, apresentam drástica redução de expressão nos mutantes Nr, rin e nor apontando que tais fatores devem atuar fortemente no amadurecimento. O estudo ilustra também a complexidade das vias de regulação envolvendo RIN e ERFs e ainda aponta os membros da subslasse E como os mais ativos ERFs atuando nas vias etileno-dependentes e RIN/NOR-dependentes. Indo além, com o objetivo de se aprofundar no crosstalk entre etileno e auxina, tratamentos hormonais foram aplicados em frutos de tomateiro e diversos parâmetros do amadurecimento foram avaliados. De uma maneira geral, a auxina retarda o amadurecimento e ainda parece sobrepor os efeitos indutórios do etileno. Genes relacionados ao amadurecimento, incluindo genes relacionados à via de sinalização de etileno, foram afetados pela auxina sugerindo potenciais pontos de crosstalk entre os dois hormônios. O etileno ainda parece regular o metabolismo de auxina no fruto via indução de conjugação pela ativação de GH3s. Compreender o papel dos hormônios no controle da maturação é essencial para o desenvolvimento de tecnologias que visam melhorar a qualidade pós-colheita de frutos.

The common tomato of our garden belongs to the natural order Solanaceae and the genus Lycopersicum. The name from lykos, a wolf, and persica a peach, is given to it because of the supposed aphrodisiacal qualities, and the beauty of the fruit. By culture and use it is a vegetable, botanically it is a fruit and among the fruits, it is a berry being indehiscent, pulpy, with one or more seeds that are not stones. Though the tomato was not recognized as a valuable food until about a century ago, its merit is now universally accepted. Often it is referred to as "the poor man's orange" for it is rich in vitamins and in malic and citric acids, possessing besides, a fine appetizing flavor. The popularity of the tomato in man's diet is due to the fact that it is a most rewarding crop for the home garden. It grows well practically everywhere, affording high nutritional values. The demand for and acceptance of fresh tomato fruit is based largely on its nutritional value, flavor, aroma, taste, and other characteristics, such as color and texture. These quality criteria are dependent primarily on the structure and chemical composition of the fruit. The importance of quality in tomatoes beyond that which can be expressed in calories per gram, or even in vitamin content, is generally accepted in the United States. In order to meet this increasing demand throughout the year tomatoes often have to be grown in the greenhouses. Therefore, in commercial greenhouses, the tomato has replaced lettuce as the principal crop and it is likely to remain as an important underglass crop. Flavor is a composite of taste and odor. Odor is produced by many aromatic substances which are present in fruit. Flavor itself is a very complex sensation. The physiological basis of flavor perception is extremely complex and not clearly understood. Flavor chemistry is a comparatively new field of research. Tomato fruit quality is determined mainly by the sugar acid ratio, pectins, color, and flavor. Among these color and flavor are probably the most useful criteria for estimating maturity of tomato fruit. Higher quality is associated with redness of color and prominence of flavor. The flavor of a fruit becomes pronounced when the sugar content is at its maximum and the color of the skin acquires the richest shade. Isolation of volatile components from natural products is often difficult. Typical flavor and aroma of tomato fruit is primarily due to its volatile components. Neither complete analysis for nor synthesis of tomato flavor has been accomplished due to the marathon of problems associated with the extraction, separation, and identification techniques. The primary aim of this investigation was to separate and identify some of the major flavor and aroma components in the developing tomato fruit and also to assess the influence of certain physiological and biochemical changes on the biosynthesis of these components during fruit growth.

Our knowledge of the factors mediating ethylene-dependent and -independent ripening of climacteric fruit remains limited. Besides the known importance of ethylene roles, auxin has also been emerged as crucial to regulating ripening. Furthermore, the crosstalk between ethylene and auxin in tomato fruit ripening still awaits clarification. ERFs (Ethylene Responsive Factors) are transcription factors belonging to a large family acting downstream on ethylene signaling that direclty regulate ripening-related metabolisms, but their specific roles are still lacking. We present here a comprehensive expression profiling of tomato ERFs in wild-type and tomato ripening-impaired tomato mutants (Nr, rin and nor) indicating that out of the 77 ERFs present in the tomato genome, 27 show enhanced expression at the onset of ripening, while 28 display a ripening-associated decrease in expression, suggesting that different ERFs may have contrasting roles in fruit ripening. Members of subclass E, ERF.E1, ERF.E2 and ERF.E4, show dramatic down-regulation in the ripening mutants suggesting their expression might be instrumental to fruit ripening. The study illustrates the high complexity of the regulatory network interconnecting RIN and ERFs and identifies subclass E members as the most active ERFs in ethylene- and RIN/NOR-dependent ripening. Additionally, with the aim to shed more light into ethylene and auxin interplay, hormonal treatments were applied to tomato fruits and several ripening aspects were then evaluated such as the volatile profile. Overall, results elicited that auxin delay the onset of ripening further showing epistatic effects over the influence of ethylene. Several ripening-related genes, including components of the ethylene signaling, were affected by auxin suggesting potential crosstalk points between the two hormones. Moreover, ethylene appears as potentially part of the auxin regulation through inducing its conjugation. The modulation of hormone levels in tomato fruit throughout ripening can be useful to help designing approaches that both improve fruit quality and extend shelf life. / O conhecimento acerca dos fatores dependentes e independentes de etileno que regulam o amadurecimento de frutos climatéricos é ainda limitado. Além da importância conhecida do etileno, a auxina também tem sido apontada como crucial para o controle do amadurecimento. Mais ainda, há poucos estudos envolvendo o crosstalk entre etileno e auxina em frutos de tomateiro. ERFs (Ethylene Responsive Factors) são fatores de transcrição que atuam nos últimos níveis da via de sinalização de etileno, regulando diretamente metabolismos associados ao amadurecimento. Contudo, seus papéis específicos ainda são desconhecidos. O presente estudo revela o perfil detalhado de expressão de ERFs em tomate selvagem e nos mutantes cujo amadurecimento é comprometido (Nr, rin e nor) indicando que dos 77 ERFs presentes no genoma, 27 apresentam aumento de expressão no início do amadurecimento, enquanto 28 apresentam redução, sugerindo que diferentes ERFs possivelmente têm papéis distintos na regulação do amadurecimento. Membros da subclasse E, ERF.E1, ERF.E2 e ERF.E4, apresentam drástica redução de expressão nos mutantes Nr, rin e nor apontando que tais fatores devem atuar fortemente no amadurecimento. O estudo ilustra também a complexidade das vias de regulação envolvendo RIN e ERFs e ainda aponta os membros da subslasse E como os mais ativos ERFs atuando nas vias etileno-dependentes e RIN/NOR-dependentes. Indo além, com o objetivo de se aprofundar no crosstalk entre etileno e auxina, tratamentos hormonais foram aplicados em frutos de tomateiro e diversos parâmetros do amadurecimento foram avaliados. De uma maneira geral, a auxina retarda o amadurecimento e ainda parece sobrepor os efeitos indutórios do etileno. Genes relacionados ao amadurecimento, incluindo genes relacionados à via de sinalização de etileno, foram afetados pela auxina sugerindo potenciais pontos de crosstalk entre os dois hormônios. O etileno ainda parece regular o metabolismo de auxina no fruto via indução de conjugação pela ativação de GH3s. Compreender o papel dos hormônios no controle da maturação é essencial para o desenvolvimento de tecnologias que visam melhorar a qualidade pós-colheita de frutos.

La tomate (Solanum lycopersicum) [...] présente de nombreux avantages : facilité de culture, temps de génération court, connaissances et ressources importantes, génome séquencé, facilité de transformation... Le développement du fruit est un procédé complexe hautement régulé et divisible en quatre étapes principales : la division cellulaire, l'expansion cellulaire, l’étape appelé « turning » et la maturation. Chaque étape est associée à un phénotype, qui lui-même découle de changements à différents niveaux cellulaires. [...]. Grâce aux récents progrès technologiques et en particulier au développement des «techniques omiques», comme la génomique, la transcriptomique, la protéomique, la métabolomique, les principaux composants cellulaires peuvent désormais être étudiés à haut densité. Dans ce contexte, l'objectif de mon doctorat était d'effectuer une analyse protéomique quantitative du développement du fruit de tomate puis d’intégrer les données «omiques» à la fois par des analyses statistiques et par la modélisation mathématique. Le premier chapitre rapporte les résultats de quantification du protéome de fruit de tomate réalisé en collaboration avec la plateforme PAPPSO (INRA, Gif-sur-Yvette). Des échantillons collectés à neuf stades de développement du fruit de tomate ont été extraits et le protéome quantifié, en absence de marquage, par chromatographie liquide couplée à la spectrométrie de masse (LC-MS/MS). Ensuite, j'ai cherché la méthode la plus adaptée, testant un ensemble de filtres sur les données, pour obtenir une quantification précise des protéines à partir des intensités ioniques (XIC). Au total, j’ai pu obtenir la quantification absolue de 2494 protéines en utilisant une méthode basée sur la modélisation de l'intensité des peptides. [...] Le deuxième chapitre est consacré aux résultats obtenus par analyses combinées d’«omiques» au cours du développement du fruit de tomate. La transcriptomique a été réalisée en collaboration avec Genotoul GeT (Toulouse) et le groupe Usadel (RWTH Aachen University, Allemagne). Grâce à l’ajout d’étalons internes, plus de 20000 transcrits ont été quantifiés de manière absolue à chacune des neuf étapes de développement. Cette quantification a ensuite été validée par comparaison avec des données de concentration de 71 transcrits précédemment obtenues par PCR quantitative. Enfin, nous avons cherché à intégrer les quatre niveaux de données - transcriptome, protéome, métabolome et activome- afin d‘identifier les principales variables associées au développement. Pour ces quatre niveaux, les analyses ont confirmé que l’entrée en maturation s’accompagne de changements majeurs et révélé une grande similarité entre la fin et le début du développement, notamment au niveau du métabolisme énergétique. Le troisième chapitre porte sur les résultats de modélisation de la traduction protéique obtenus grâce à la quantification absolue du transcriptome et du protéome. Afin d’expliquer la corrélation décroissante observée au cours du développement entre les concentrations en protéines et celles des transcrits correspondants, nous avons résolu un modèle mathématique de la traduction protéique basé sur une équation différentielle ordinaire et impliquant deux constantes de vitesse: pour la synthèse et la dégradation de la protéine. La résolution de cette équation, validée par un critère de qualité basé un intervalle de confiance fermé, a conduit à l'estimation de ces constantes pour plus de 1000 protéines. [...] Enfin le dernier chapitre décrit l’ensemble du matériel et des méthodes utilisées pour obtenir les différents résultats présentés dans le manuscrit. Dans le domaine de la biologie des systèmes, ce travail illustre comment l'intégration de multiples données «omiques» et la modélisation mécanistique basée sur la quantification absolue des «omiques» peut révéler de nouvelles propriétés des composants cellulaires. / The interest of the tomato (Solanum lycopersicum) fruit has spread in plant science where it is used as the model for fleshy fruit. The valuable advantages of the tomato fruit are numerous: an ease of culture, a short generation time, a high knowledge with important resources, a sequenced genome, an ease for transforming…. The development of tomato fruit is a complex regulated process, divided in four main steps: cell division, cell expansion, turning and ripening. Each step is characterized by a phenotype resulting from changes at different cellular levels. Thus, gene expression, protein abundance, enzyme activities, metabolic fluxes and metabolite concentrations show significant changes during these steps. Thanks to recent technologies advances and in particular the development of ‘omics techniques’, such as genomic, transcriptomic, proteomic, metabolomic, the main cell components can now be analysed by high-throughput. In this context, the objective of my PhD was to perform a quantitative proteomic analysis of the tomato fruit development and then integrate omics data both by statistical analyses and by mathematical modelling. The first chapter focused on results obtained for the quantitative proteomic developed in collaboration with the PAPPSO platform (INRA, Gif-sur-Yvette). Samples were harvested at nine stages of tomato fruit development, total proteome was extracted and quantified by label-free LC-MS/MS. Then I searched for the most appropriate method, testing a set of filters on the data, to obtain an absolute label-free protein quantification from ion intensities (XIC). Finally, I obtained the absolute quantification of 2494 proteins using a method based on peptides intensity modelling. The quantification of proteins by LC-MS/MS was then validated by comparison with 32 enzymatic capacities used as proxy for protein abundance. The second chapter was dedicated to the results of integrative omics analyses throughout tomato fruit development. First, transcriptomic has been performed in collaboration with Genotoul GeT (Toulouse) and Usadel‘lab (RWTH Aachen University, Germany). Using spikes in the experimental design, more than 20000 transcripts have been quantitatively determined at the nine stages of development. Then, this absolute quantification of the tomato transcriptome has been cross-validated with 71 transcripts previously measured by qRT-PCR. Finally, we integrated the four omics datasets- transcriptome, proteome, metabolome and activome – in order to identify key variables of the tomato fruit development. For the four levels, analyses confirmed that the entrance in maturation phase was accompanied by major changes, and revealed a great similarity between the end and the beginning of development, especially in the energy metabolism. The third chapter focuses on modelling results of the protein translation based on the absolute quantification of transcriptomic and proteomic. To explain the decreasing correlation observed between proteins and transcripts concentration throughout development, we proposed a mathematical model of protein translation based on an ordinary differential equation and involving two rate constants (for synthesis and degradation of the protein). The resolution of this equation, validated by a quality criteria based on a closed confidence interval, led to the estimation of the rate constants for more than 1000 proteins. These results were then compared with previous published data reported for plants and more widely in eukaryotic cells. Finally, the last chapter describes all the materials and methods used to obtain the results presented in the manuscript.In the systems biology context, this work illustrates how integration of multiple omics datasets and mechanistic modelling based on absolute omics quantification can reveal new properties of cellular component.