A la différence des mammifères, les plantes ne possèdent pas de cellules spécialisées dans la défense face aux pathogènes. Chaque cellule végétale peut déclencher une réponse immunitaire. Pour interagir avec succès avec la plante, les pathogènes doivent alors supprimer ou contourner les défenses de l’hôte. Afin d’y parvenir, les bactéries pathogènes disposent des effecteurs, des protéines qui peuvent être injectées dans la cellule végétale. De nombreux effecteurs sont connus pour cibler les organites lors de l’infection, confirmant l’importance du chloroplaste et de la mitochondrie dans les mécanismes de défense des cellules végétales. Dans ces conditions, il demeure vital pour la plante de garder la main sur l’expression des gènes des organites afin d’assurer une réponse proportionnée au risque encouru sans pénaliser la croissance de façon disproportionnée. A la différence de l’expression des gènes nucléaires, la régulation de l’expression des gènes des organites se fait principalement lors d’étapes très complexes de maturation post-transcriptionnelle. Parmi les protéines impliquées dans ces étapes de maturation, on trouve les protéines pentatricopeptide repeat (PPR). Les protéines PPR sont impliquées dans de nombreuses étapes de maturation des ARN des organites, comme l’édition C vers U ou l’épissage. Elles sont également présentes chez d’autres eucaryotes, mais n’ont jamais été étudiées chez les bactéries. L’hypothèse testée dans le cadre de la thèse est que ces protéines PPR, qu’elles soient d’origine exogène ou endogène, sont impliquées dans des modifications de l’expression des gènes des organites en condition de stress biotique. Afin de tester notre hypothèse, nous nous sommes intéressés à PGN (Pentatricopeptide repeat protein for Germination on NaCl) chez la plante modèle A. thaliana. Caractérisée par Laluk et al. (2011), le mutant KO montre une sensibilité accrue au nécrotrophe Botrytis cinerea, et l’expression du gène codant pour cette protéine est induite après infection. Nous avons mis en évidence des défauts d’édition dans la séquence non codante en amont de nad6 et dans cox2, deux gènes mitochondriaux. Leur édition ne varie cependant pas en condition d’infection par Botrytis cinerea. Dans la même optique, à la suite d’un crible bio-informatique, nous nous sommes intéressés à deux protéines PPR bactériennes que nous avons trouvées chez les phytopathogènes Erwinia amylovora et Ralstonia solanacearum. Probablement obtenues par les bactéries par transfert horizontal de gènes, il s’agit de la première caractérisation de PPR bactériennes à notre connaissance. Ces protéines possèdent des caractéristiques d’effecteurs, c’est—dire des protéines injectées par la bactérie dans la plante durant l’infection. Si nous n’avons pas vu de modification du transcriptome des organites de la plante provoqué par la surexpression de ces protéines PPR exogènes, nous avons cependant mis en évidence une baisse significative du taux d’incidence de la maladie provoquée par E. amylovora en l’absence d’un gène fonctionnel codant pour sa PPR chez la plante hôte Malus domestica « Golden delicious ». Pour la PPR d’E. amylovora comme celle de R. solanacearum, nous avons également trouvés plusieurs interactants en double hybride levure chez A. thaliana, représentant de nombreuses cibles putatives à étudier. Afin de réaliser ces expérimentations et d’obtenir ces résultats, nous avons eu besoins d’outils particuliers. Nous avons donc développé un pipeline spécifique d’analyse de données de séquençage d’ARN ainsi qu’une méthode améliorée de prédiction des zones de fixation des protéines PPR, ouvrant la voie à une caractérisation simplifiée de nombreuses protéines. / Compared to mammals, plants do not have highly specialized cells involved in defense against pathogens. Each plant cell is able to start an immune response. To interact successfully with plants, pathogens have to block or bypass host defenses. To do so, phytopathogenic bacteria can use effectors, which are basically bacterial proteins injected in the plant cell during infection. Several effectors are known to target organelles during infection, supporting the idea that chloroplasts and mitochondria are key players in plant cell defense. As a reason, it remains necessary for the plant to keep organellar gene expression under control in order to ensure a response in proportion to the risk, without penalizing growth. Unlike nuclear gene expression, organellar gene expression regulation goes through highly complex post-transcriptional maturation steps. Among proteins involved in these events, PPR proteins (for pentatricopeptide repeat) are known to be very important. PPR proteins are involved in several RNA maturation steps in organelles, like C to U editing or splicing. They are studied in several eukaryotes, but not in bacteria. During my PhD studies, the hypothesis is exogenous or endogenous PPR proteins are involved in organellar gene expression modifications during biotic stress. To test our hypothesis, we work on PGN (Pentatricopeptide repeat protein for Germination on NaCl) in plant model A. thaliana. Characterized by Laluk et al. (2011), the KO mutant displays an enhanced sensitivity to the necrotrophic pathogen Botrytis cinerea, and PGN gene expression is induced after infection. We find two editing defects for the KO mutant, in nad6 5’ non coding sequence and in cox2 coding sequence. However, editing at these two sites does not vary in wild type plants during Botrytis cinerea infection.Using a bioinformatic screen, we find several bacterial PPR proteins. Two of them are encoded by bacterial plant pathogens: Erwinia amylovora and Ralstonia solanacearum. To our knowledge, these proteins, putatively obtained through horizontal gene transfer, are the first bacterial PPR proteins to be characterized. They also share similarities with bacterial effectors. If overexpression of these bacterial PPR proteins in A. thaliana does not unveil organellar transcriptome modifications, we show a decrease of the incidence rate of the disease caused by E. amylovora in the host plant Malus domestica “Golden delicious” without a functional gene coding for the PPR protein. For both Erwinia and Ralstonia PPR, we find several interactants in A. thaliana using Yeast Two Hybrid, each of them representing a potential target that could be studied. In order to perform these experiments and obtain these results, we needed very specific tools. During the PhD studies, we develop an RNAseq analysis pipeline and an enhanced method to predict PPR binding sites, opening the way to an easier characterization of several PPR proteins.

Plants are continuously exposed to different abiotic and biotic stresses in their natural environment. Their capacity to survive depends on the capacity to perceive external signal and quality amount a defence response for protection from the stress perceived. The purpose of this project was to study the impact of combined abiotic stress and biotic stress on the outcome of the disease inducing Arabidopsis thaliana – Pseudomonas syringae interaction. This study included a focus on the role of ABA in these interactions and also whether 3´-O-β D- ribofuranosyl adenosine (hereafter it called ‘400’ compound), a novel adenosine derived compound induced during compatible interactions, was involved. The later involved the targetted disruption of a putative 400 biosynthetic pathway involving analysis of knockout mutants of enzymes; APD-ribose diphosphatase NAD binding / hydrolases of the NUDIX class, glucosyl transferases, ribosyltransferases, a ribose-phosphate pyrophosphokinase3 and galactosyltransferases. Unfortunately, none of these targeted interventions modified the host response to Pseudomonas infection, nor altered levels of 400 in challenged leaves. The primary research investigated the interaction between abiotic and biotic stresses in Arabidopsis plants focussing on the modulation of plant defence against multiple, and possibly antagonistic, stress responses and the role plant hormones play in this process. We showed that high light caused enhanced susceptibility to the already virulent Pseudomonas syringae DC3000pvsp61. The pathways contributing to this enhanced susceptibility were largely ABA independent. Subsequent characterization of transgenic lines expressing the soluble Arabidopsis abscisic acid receptors, PYRABACTIN RESISTANCE1-LIKE4-6 provided compelling evidence for a role for these receptors in DC3000 virulence strategies, but they contribute to a lesser extent to the enhanced susceptibility under high light. This was corroborated genetically by using mutants of the immediately downstream targets of PYLs, the type two protein phosphatase, specifically the triple mutant hab1-1/abi2-1/abi1-2. A number of epitope and fluorescent constructs were generated to facilitate future studies of the role of ABA signaling. Targetted profiling suggested that SA dynamics were altered under DC3000 challenged Arabidopsis grown under high light. Furthermore, differential accumulation of flavonoids suggested these may also play a role in attenuating host defences under high light. Finally we provide evidence based on comparative analysis of that the photoreceptors phytochrome double mutant phyA-211/phyB-9 and cry1/cry2 behave antagonistically in Arabidopsis response to DC3000. Overall our studies support the conclusion that plants abiotic stress (HL) response takes precedence over biotic stress (DC3000) responses and that abiotic stress is detrimental to plant immunity. The luciferase transgenic PYL lines showed high level of expression of ClucP::PYL5 plant tissues challenged 2hpi of DC3000 (OD600: 0.15) in comparison with C1lucP::PYL6. This result opposes to what RT-PCR reported; which was that three PYLs genes display similar expression level at 6hpi of hrpA or 18hpi of DC3000. The epitope tags of CaMV::HA transgenic plants showed HA-tagged signal with stunted phenotype in a range of PYL4, 5 and 6 plants but none of the plants displayed any differences in susceptibility to DC3000. Although, RT-PCR assay showed high levels of expression in the three PYLs, 6hpi of hrpA but no signal was detected in B8eGFP::PYL5 transgenic line either followed the DC3000 and hrpA infection or by examined plant seedlings at early stages under confocal microscopy.

Genotypes adapted to contrasting environments are expected to behave differently when placed in common controlled conditions, if their sensitivity to environmental cues or intrinsic growth behaviour are set to different thresholds, or are limited at distinct levels. This allows natural variation to be exploited as an unlimited source of new alleles or genes for the study of the genetic basis of quantitative trait variation. My doctoral work focuses on analysing natural variation for shoot growth and response to the environment in A. thaliana. Natural variation analyses aim at understanding how molecular genetic or epigenetic diversity controls phenotypic variation at different scales and times of plant development and under different environmental conditions, and how selection or demographic processes influence the frequency of those molecular variants in populations for them to get adapted to their local environment. As such, the analysis of A. thaliana natural variation can be addressed using a variety of approaches, from genetics and molecular methods to ecology and evolutionary questions. During my PhD, I got the chance to tackle several of those aspects through my contributions to three independent projects which have in common to exploit A. thaliana natural variation. The first one is the analysis of the pattern of polymorphism from a set of 102 A. thaliana accessions at the MOT1 gene coding for a molybdate transporter (an essential micronutrient) and responsible for contrasted growth and fitness among accessions in response to Mo availability in the soil. I showed at different geographical scales that MOT1 pattern of polymorphisms is not consistent with neutral evolution and shows signs of diversifying selection. This work helped reinforce the hypothesis that in some populations, mutations in MOT1 have been selected to face soils rich in Mo and potentially deleterious despite their negative effect on Mo-limiting soils. The second project consists in the characterisation and functional analysis of two putative receptor-like kinases (RLKs) identified from their effect on shoot growth specifically under mannitol-supplemented media and not in response to other osmotic constraints. The function of such RLKs in A. thaliana, which is not known to synthesize mannitol was intriguing at first but, through different experiments, we built the hypothesis that those RLKs could be activated by the mannitol produced by some pathogens such as fungi and participate to plant defensive response. The third project, in collaboration with Michel Vincentz's team from CBMEG (Brasil) and Vincent Colot (IBENS, Paris), consists in the analysis of the occurrence of natural epigenetic variants of the QQS gene in different populations from Central Asia and their possible phenotypic and adaptive consequences. Overall, these analyses of the genetic and epigenetic molecular variation leading to the biomass phenotype(s) in interaction with the environment provide clues as to how and where in the pathways adaptation is shaping natural variation.

Une meilleure compréhension de la physiologie de la semence des céréales constitue certainement un moyen pour améliorer et développer de nouvelles variétés capables de correspondre aux besoins économiques et écologiques du moment. Les rédoxines constituent des marqueurs intéressants pour appréhender la qualité technologique et germinative du grain de blé en particulier. Le criblage des banques de données a permis d’isoler des isoformes de ces rédoxines. Cette étude a confirmé l’implication des thiorédoxines dans la réduction des protéines de réserve du blé et de maïs. Elle a permis de mettre en évidence un autre rôle de certains isoformes de thiorédoxines h dans la formation de polymères de hauts poids moléculaires. L'inhibition de l’expression de gènes par interférence ADN montre que les thiorédoxines et les glutarédoxines sont impliquées dans la protection contre le stress oxydatif chez le blé. De même, l'application d’un stress biotique simulé par la laminarine a permis de discriminer l'implication de différents marqueurs du stress, et de montrer en particulier que la 1-Cys-Prx peut être considérée comme un indicateur de l'état redox du grain pendant la germination. La mise en place d’une méthode simple et efficace de transformation des céréales via Agrobacterium, constitue un moyen pour comprendre davantage le rôle de ces rédoxines dans la gestion des stress, et les éventuelles conséquences sur la qualité technologique du grain. / A better understanding of the physiology of seed cereal constitutes certainly a means to improve and develop new varieties capable of corresponding to the actual economic and ecological needs. Redoxins are interesting markers to apprehend the technological and germinative quality of wheat seed in particular. The screening of data banks allowed isolating isoforms of these redoxins. This study confirmed the implication of thioredoxins in the reduction of storage proteins in wheat and corn seeds. It allowed to bring to light another role of some thioredoxins h isoforms in the formation of high molecular weights polymers. The inhibition of the expression of genes by DNA interference shows that thioredoxins and glutaredoxins are involved in the protection against oxidative stress in wheat. Also, the application of a biotic stress simulated by laminarin allowed to discriminate the implication of various stress markers, and to highlight in particular that the 1-Cys-Prx can be considered as an indicator of the redox state of the grain during germination and seedling. The implementation of a simple and effective method of transformation of cereal via Agrobacterium constitutes a means to understand more on the role of these redoxins in the management of the stress, and the possible consequences on the technological quality of the seed.

Sugarcane (Saccharum spp) is an important commercial crop cultivated widely in tropical and subtropical countries. Primarily sugarcane is used to produce sugar and recently it is proven to be a valuable resource for bioethanol, biodiesel, bioplastic and bioelectricity. Smut is one of the most serious sugarcane disease and occurs in sugarcane fields all over the world. The disease is caused by the biotrophic fungus Sporisorium scitamineum. The fungus induces metabolic changes in the plant leading to the production of a whip-like structure where fungal sporogenesis take place. The objective of this study was to analyse the reactive oxygen species (ROS) production, antioxidant enzymes activity and expression of genes associated with the ROS metabolism in smut susceptible (IAC66-6) and resistant sugarcane genotypes (SP80-3280). In addition, this work assessed the relationship between antioxidant enzymes and sensitivity of S. scitamineum to exogenous hydrogen peroxide (H2O2). This thesis is presented in the format of two chapters (chapters 2 and 3). In the second chapter, the results revealed that there were variations in the antioxidant system as well as in the ROS production in resistant sugarcane genotype, whereas few changes occurred in the susceptible genotype inoculated with S. scitamineum. Microscopic analysis revealed that S. scitamineum teliospore germination and appressorium formation were delayed during early infection in the smut resistant genotype, which coincided with H2O2 accumulation. In chapter 3, the results demonstrated that S. scitamineum is highly resistant to exogenous H2O2. At 2 mM exogenous H2O2 concentration the fungus presented an effective antioxidant system in response to the secondary products of oxidative stress. Furthermore, S. scitamineum when exposed for a long time at 2 mM exogenous H2O2 concentration it can acquire an adaptive response to H2O2. The results obtained in this study contributed to increase the understanding of this very complex interaction between sugarcane and S. scitamineum and it will be helpful toward understanding which aspects are involved in the resistance to S. scitamineum. These informations are important to create strategies for improving smut resistance in sugarcane. / Cana-de-açúcar (Saccharum spp) é uma importante cultura comercial amplamente cultivada em países tropicais e subtropicais. A cana-de-açúcar é principalmente utilizada para produzir açúcar e recentemente é considerada uma valiosa fonte para produção de bioetanol, biodiesel, bioplásticos e bioeletricidade. O carvão é uma das doenças mais graves da cana-de-açúcar e ocorrem em canaviais do mundo inteiro. A doença é causada pelo fungo biotrófico Sporisorium scitamineum. Este fungo induz mudanças metabólicas na planta, levando a formação de uma estrutura chamada chicote, onde ocorre a esporogênese. O objetivo desse estudo foi analisar a produção de espécies reativas de oxigênio (EROs), atividade de enzimas antioxidantes e a expressão de genes associados ao metabolismo de EROs em genótipos de cana-açúcar susceptível (IAC66-6) e resistente (SP80-3280). Além disso, este trabalho avaliou a relação entre as enzimas antioxidantes e sensibilidade de S. scitamineum a peróxido de hidrogênio (H2O2) exógeno. Esta tese está apresentada no formato de 2 capítulos (capítulos 2 e 3). No segundo capítulo, os resultados revelaram que ocorreram alterações no sistema antioxidante, bem como na produção de EROs no genótipo resistente, enquanto que poucas mudanças ocorreram no genótipo susceptível inoculado com S. scitamineum. Análises de microscopia revelaram que a germinação de teliósporos e a formação de apressórios de S. scitamineum atrasou durante o início da infeção no genótipo resistente ao carvão, coincidindo com o acúmulo de H2O2. No capítulo 3, os resultados demonstraram que S. scitamineum é altamente resistente a H2O2 exógeno. O fungo crescendo na concentração de 2 mM de H2O2 apresentou um eficiente sistema antioxidante em resposta a produtos secundários do estresse oxidativo. Além disso, quando S. scitamineum foi exposto a 2 mM de H2O2 exógeno, ele pode adquirir uma resposta adaptativa ao H2O2. Os resultados obtidos neste estudo contribuíram para aumentar o entendimento dessa complexa interação entre cana e S. scitamineum e será útil para a compreensão de quais aspectos estão envolvidos na resistência a este fungo. Estas informações são importantes para criar estratégias para o melhoramento de cana a essa doença.

Sugarcane (Saccharum spp) is an important commercial crop cultivated widely in tropical and subtropical countries. Primarily sugarcane is used to produce sugar and recently it is proven to be a valuable resource for bioethanol, biodiesel, bioplastic and bioelectricity. Smut is one of the most serious sugarcane disease and occurs in sugarcane fields all over the world. The disease is caused by the biotrophic fungus Sporisorium scitamineum. The fungus induces metabolic changes in the plant leading to the production of a whip-like structure where fungal sporogenesis take place. The objective of this study was to analyse the reactive oxygen species (ROS) production, antioxidant enzymes activity and expression of genes associated with the ROS metabolism in smut susceptible (IAC66-6) and resistant sugarcane genotypes (SP80-3280). In addition, this work assessed the relationship between antioxidant enzymes and sensitivity of S. scitamineum to exogenous hydrogen peroxide (H2O2). This thesis is presented in the format of two chapters (chapters 2 and 3). In the second chapter, the results revealed that there were variations in the antioxidant system as well as in the ROS production in resistant sugarcane genotype, whereas few changes occurred in the susceptible genotype inoculated with S. scitamineum. Microscopic analysis revealed that S. scitamineum teliospore germination and appressorium formation were delayed during early infection in the smut resistant genotype, which coincided with H2O2 accumulation. In chapter 3, the results demonstrated that S. scitamineum is highly resistant to exogenous H2O2. At 2 mM exogenous H2O2 concentration the fungus presented an effective antioxidant system in response to the secondary products of oxidative stress. Furthermore, S. scitamineum when exposed for a long time at 2 mM exogenous H2O2 concentration it can acquire an adaptive response to H2O2. The results obtained in this study contributed to increase the understanding of this very complex interaction between sugarcane and S. scitamineum and it will be helpful toward understanding which aspects are involved in the resistance to S. scitamineum. These informations are important to create strategies for improving smut resistance in sugarcane. / Cana-de-açúcar (Saccharum spp) é uma importante cultura comercial amplamente cultivada em países tropicais e subtropicais. A cana-de-açúcar é principalmente utilizada para produzir açúcar e recentemente é considerada uma valiosa fonte para produção de bioetanol, biodiesel, bioplásticos e bioeletricidade. O carvão é uma das doenças mais graves da cana-de-açúcar e ocorrem em canaviais do mundo inteiro. A doença é causada pelo fungo biotrófico Sporisorium scitamineum. Este fungo induz mudanças metabólicas na planta, levando a formação de uma estrutura chamada chicote, onde ocorre a esporogênese. O objetivo desse estudo foi analisar a produção de espécies reativas de oxigênio (EROs), atividade de enzimas antioxidantes e a expressão de genes associados ao metabolismo de EROs em genótipos de cana-açúcar susceptível (IAC66-6) e resistente (SP80-3280). Além disso, este trabalho avaliou a relação entre as enzimas antioxidantes e sensibilidade de S. scitamineum a peróxido de hidrogênio (H2O2) exógeno. Esta tese está apresentada no formato de 2 capítulos (capítulos 2 e 3). No segundo capítulo, os resultados revelaram que ocorreram alterações no sistema antioxidante, bem como na produção de EROs no genótipo resistente, enquanto que poucas mudanças ocorreram no genótipo susceptível inoculado com S. scitamineum. Análises de microscopia revelaram que a germinação de teliósporos e a formação de apressórios de S. scitamineum atrasou durante o início da infeção no genótipo resistente ao carvão, coincidindo com o acúmulo de H2O2. No capítulo 3, os resultados demonstraram que S. scitamineum é altamente resistente a H2O2 exógeno. O fungo crescendo na concentração de 2 mM de H2O2 apresentou um eficiente sistema antioxidante em resposta a produtos secundários do estresse oxidativo. Além disso, quando S. scitamineum foi exposto a 2 mM de H2O2 exógeno, ele pode adquirir uma resposta adaptativa ao H2O2. Os resultados obtidos neste estudo contribuíram para aumentar o entendimento dessa complexa interação entre cana e S. scitamineum e será útil para a compreensão de quais aspectos estão envolvidos na resistência a este fungo. Estas informações são importantes para criar estratégias para o melhoramento de cana a essa doença.

A soja constitui uma das culturas mais importantes mundialmente, tanto social quanto economicamente. Consequentemente, informações moleculares sobre processos de desenvolvimento, bem como conhecimento detalhado das interações entre condições estressoras e a resposta da planta a fatores ambientais são necessários. A identificação e caracterização de genes que respondem a condições ambientais específicas constituem um passo inicial no entendimento dos processos adaptativos. Proteínas ricas em glicina (GRPs) são polipeptídeos contendo um grande número do aminoácido glicina em sua estrutura primária. Os genes codificantes de GRPs são regulados ao longo do desenvolvimento e regulados por auxina, ABA, frio, ferimentos, luz, ritmo circadiano, salinidade, seca, patógenos e encharcamento. Entretanto, há pouca informação sobre GRPs de plantas e seus papéis no desenvolvimento e resposta a estresses. As GRPs podem ser divididas em quatro classes (I, II, III, IV) de acordo com sua estrutura primária e presença de domínios característicos. A classe IV é composta por proteínas ligantes de RNA. Domínios adicionais permitem dividir a classe IV de GRPs em quatro subclasses (IVa, IVb, IVc, IVd). A subclasse IVc é representada por proteínas contendo um cold-schock domain (CSD) e dedos de zinco CCHC tipo retrovirais. O objetivo do presente estudo foi: (i) identificar e caracterizar os genes codificantes de classe IV de GRPs, (ii) verificar a padrão de expressão dos genes codificantes da subclasse IVc de GRPs e (iii) produzir plantas de soja transgênicas expressando o gene AtGRP2, o qual foi mostrado estar envolvido na floração e desenvolvimento da semente em Arabidopsis, e também poderia desempenhar um papel na aclimatação ao frio. Um total de 47 genes codificantes da classe IV de GRPs foi identificado no genoma da soja: 19 da subclasse IVa, sete da IVb, seis da IVc e 15 da IVd. Análises in silico indicaram uma expressão preferencial de todos os genes codificantes da subclasse IVc em tecidos em desenvolvimento. Análises de RT-qPCR revelaram que plantas jovens e maduras exibem uma expressão mais alta em folhas do que em outros órgãos, com exceção dos genes GRP2L_4/5 que tiveram expressão mais alta em sementes. GRP2L_4/5 e GRP2L_2 foram induzidos em resposta a baixas temperaturas. Sob estresse com ABA a expressão de todos os genes foi reprimida em folhas e/ou raízes, com exceção do gene GRP2L_2 que foi induzido em raízes. Em resposta a infecção com Phakopsora pachyrhizi, a expressão de GRP2L_2 e GRP2L_3 foi mais alta e precoce no genótipo suscetível quando comparada com o resistente, enquanto que a resposta de GRP2L_4/5 e GRP2L_6 foi mais tardia no genótipo resistente. Ainda, embriões somáticos secundários das cultivares Bragg, IAS-5 e BRSMG 68 Vencedora de soja foram usados para introduzir o gene AtGRP2 no genoma da soja por bombardeamento e sistema bombardeamento/Agrobacterium. Seis eventos de transformação independentes foram confirmados por PCR. No presente momento as plantas estão em desenvolvimento em frascos de vidro. No presente estudo a classe IV de GRPs em soja foi identificada e caracterizada. Este é o primeiro passo para elucidar o papel destas proteínas em plantas. / Molecular information on plant developmental process, as well as detailed knowledge of the interaction between stress conditions and plant response to environmental factors are essential for understanding the adaptive response. Glycine-Rich Proteins (GRP) have the amino acid glycine well represented in their primary structure. The genes encoding GRPs are developmentally regulated and induced by auxin, ABA, cold, wound, light, circadian rhythm, salinity, drought, pathogens, and flooding. However, there is scarce information about plant GRPs and its role on development and stress response. The GRPs can be divided into four classes (I, II, II and IV) according to their primary structure and the presence of characteristic domains. Class IV is composed by RNA-binding proteins. Additional domains permit to split class IV GRPs into four subclasses (IVa, IVb, IVc and IVd). Subclass IVc is represented by proteins containing a Cold-Shock Domain (CSD) and retroviral-like CCHC zinc fingers. The goal of the present study was: (i) to identify and characterize the genes encoding class IV GRPs, (ii) to verify the relative expression of genes encoding subclass IVc GRPs and (iii) to produce transgenic soybean plants expressing the AtGRP2 gene, which was shown to be involved in Arabidopsis flower and seed development, and can also play a role in cold acclimation. A total of 47 genes encoding class IV GRPs were found in the soybean genome: 19 from IVa, seven from IVb, six from IVc and 15 from IVd subclasses. In silico analyses indicated a preferential expression of all genes encoding subclass IVc GRPs in tissues under development. RT-qPCR analyses revealed that both young and mature plants exhibit relative higher expression of subclass IVc GRPs in leaves than in other organs, with exception of GRP2L_4/5 genes that have higher expression in seeds. The GRP2L_4/5 and GRP2L_2 were up-regulated in response to low temperatures. Under ABA stress the expression of all genes was down-regulated in leaves and roots, with exception of GRP2L_2 gene that was up-regulated in roots. In response to Phakopsora pachyrhizi infection, GRP2L_2 and GRP2L_3 expression was higher and earlier in the susceptible genotype when compared with that of the resistant one, while GRP2L_4/5 and GRP2_6 respond later in the resistant genotype. Furthermore, secondary somatic embryos of Bragg, IAS-5 and BRSMG 68 Vencedora soybean cultivars were used to introduce the AtGRP2 gene into the soybean genome by particle bombardment and bombardment/Agrobacterium system. Six independent Bragg transformation events were confirmed by PCR. In the present moment the plants are under development in glass flasks. In the present study the soybean class IV GRPs were identified and characterized. This is the first step to elucidate the role of these proteins in plants.

A soja constitui uma das culturas mais importantes mundialmente, tanto social quanto economicamente. Consequentemente, informações moleculares sobre processos de desenvolvimento, bem como conhecimento detalhado das interações entre condições estressoras e a resposta da planta a fatores ambientais são necessários. A identificação e caracterização de genes que respondem a condições ambientais específicas constituem um passo inicial no entendimento dos processos adaptativos. Proteínas ricas em glicina (GRPs) são polipeptídeos contendo um grande número do aminoácido glicina em sua estrutura primária. Os genes codificantes de GRPs são regulados ao longo do desenvolvimento e regulados por auxina, ABA, frio, ferimentos, luz, ritmo circadiano, salinidade, seca, patógenos e encharcamento. Entretanto, há pouca informação sobre GRPs de plantas e seus papéis no desenvolvimento e resposta a estresses. As GRPs podem ser divididas em quatro classes (I, II, III, IV) de acordo com sua estrutura primária e presença de domínios característicos. A classe IV é composta por proteínas ligantes de RNA. Domínios adicionais permitem dividir a classe IV de GRPs em quatro subclasses (IVa, IVb, IVc, IVd). A subclasse IVc é representada por proteínas contendo um cold-schock domain (CSD) e dedos de zinco CCHC tipo retrovirais. O objetivo do presente estudo foi: (i) identificar e caracterizar os genes codificantes de classe IV de GRPs, (ii) verificar a padrão de expressão dos genes codificantes da subclasse IVc de GRPs e (iii) produzir plantas de soja transgênicas expressando o gene AtGRP2, o qual foi mostrado estar envolvido na floração e desenvolvimento da semente em Arabidopsis, e também poderia desempenhar um papel na aclimatação ao frio. Um total de 47 genes codificantes da classe IV de GRPs foi identificado no genoma da soja: 19 da subclasse IVa, sete da IVb, seis da IVc e 15 da IVd. Análises in silico indicaram uma expressão preferencial de todos os genes codificantes da subclasse IVc em tecidos em desenvolvimento. Análises de RT-qPCR revelaram que plantas jovens e maduras exibem uma expressão mais alta em folhas do que em outros órgãos, com exceção dos genes GRP2L_4/5 que tiveram expressão mais alta em sementes. GRP2L_4/5 e GRP2L_2 foram induzidos em resposta a baixas temperaturas. Sob estresse com ABA a expressão de todos os genes foi reprimida em folhas e/ou raízes, com exceção do gene GRP2L_2 que foi induzido em raízes. Em resposta a infecção com Phakopsora pachyrhizi, a expressão de GRP2L_2 e GRP2L_3 foi mais alta e precoce no genótipo suscetível quando comparada com o resistente, enquanto que a resposta de GRP2L_4/5 e GRP2L_6 foi mais tardia no genótipo resistente. Ainda, embriões somáticos secundários das cultivares Bragg, IAS-5 e BRSMG 68 Vencedora de soja foram usados para introduzir o gene AtGRP2 no genoma da soja por bombardeamento e sistema bombardeamento/Agrobacterium. Seis eventos de transformação independentes foram confirmados por PCR. No presente momento as plantas estão em desenvolvimento em frascos de vidro. No presente estudo a classe IV de GRPs em soja foi identificada e caracterizada. Este é o primeiro passo para elucidar o papel destas proteínas em plantas. / Molecular information on plant developmental process, as well as detailed knowledge of the interaction between stress conditions and plant response to environmental factors are essential for understanding the adaptive response. Glycine-Rich Proteins (GRP) have the amino acid glycine well represented in their primary structure. The genes encoding GRPs are developmentally regulated and induced by auxin, ABA, cold, wound, light, circadian rhythm, salinity, drought, pathogens, and flooding. However, there is scarce information about plant GRPs and its role on development and stress response. The GRPs can be divided into four classes (I, II, II and IV) according to their primary structure and the presence of characteristic domains. Class IV is composed by RNA-binding proteins. Additional domains permit to split class IV GRPs into four subclasses (IVa, IVb, IVc and IVd). Subclass IVc is represented by proteins containing a Cold-Shock Domain (CSD) and retroviral-like CCHC zinc fingers. The goal of the present study was: (i) to identify and characterize the genes encoding class IV GRPs, (ii) to verify the relative expression of genes encoding subclass IVc GRPs and (iii) to produce transgenic soybean plants expressing the AtGRP2 gene, which was shown to be involved in Arabidopsis flower and seed development, and can also play a role in cold acclimation. A total of 47 genes encoding class IV GRPs were found in the soybean genome: 19 from IVa, seven from IVb, six from IVc and 15 from IVd subclasses. In silico analyses indicated a preferential expression of all genes encoding subclass IVc GRPs in tissues under development. RT-qPCR analyses revealed that both young and mature plants exhibit relative higher expression of subclass IVc GRPs in leaves than in other organs, with exception of GRP2L_4/5 genes that have higher expression in seeds. The GRP2L_4/5 and GRP2L_2 were up-regulated in response to low temperatures. Under ABA stress the expression of all genes was down-regulated in leaves and roots, with exception of GRP2L_2 gene that was up-regulated in roots. In response to Phakopsora pachyrhizi infection, GRP2L_2 and GRP2L_3 expression was higher and earlier in the susceptible genotype when compared with that of the resistant one, while GRP2L_4/5 and GRP2_6 respond later in the resistant genotype. Furthermore, secondary somatic embryos of Bragg, IAS-5 and BRSMG 68 Vencedora soybean cultivars were used to introduce the AtGRP2 gene into the soybean genome by particle bombardment and bombardment/Agrobacterium system. Six independent Bragg transformation events were confirmed by PCR. In the present moment the plants are under development in glass flasks. In the present study the soybean class IV GRPs were identified and characterized. This is the first step to elucidate the role of these proteins in plants.

A soja constitui uma das culturas mais importantes mundialmente, tanto social quanto economicamente. Consequentemente, informações moleculares sobre processos de desenvolvimento, bem como conhecimento detalhado das interações entre condições estressoras e a resposta da planta a fatores ambientais são necessários. A identificação e caracterização de genes que respondem a condições ambientais específicas constituem um passo inicial no entendimento dos processos adaptativos. Proteínas ricas em glicina (GRPs) são polipeptídeos contendo um grande número do aminoácido glicina em sua estrutura primária. Os genes codificantes de GRPs são regulados ao longo do desenvolvimento e regulados por auxina, ABA, frio, ferimentos, luz, ritmo circadiano, salinidade, seca, patógenos e encharcamento. Entretanto, há pouca informação sobre GRPs de plantas e seus papéis no desenvolvimento e resposta a estresses. As GRPs podem ser divididas em quatro classes (I, II, III, IV) de acordo com sua estrutura primária e presença de domínios característicos. A classe IV é composta por proteínas ligantes de RNA. Domínios adicionais permitem dividir a classe IV de GRPs em quatro subclasses (IVa, IVb, IVc, IVd). A subclasse IVc é representada por proteínas contendo um cold-schock domain (CSD) e dedos de zinco CCHC tipo retrovirais. O objetivo do presente estudo foi: (i) identificar e caracterizar os genes codificantes de classe IV de GRPs, (ii) verificar a padrão de expressão dos genes codificantes da subclasse IVc de GRPs e (iii) produzir plantas de soja transgênicas expressando o gene AtGRP2, o qual foi mostrado estar envolvido na floração e desenvolvimento da semente em Arabidopsis, e também poderia desempenhar um papel na aclimatação ao frio. Um total de 47 genes codificantes da classe IV de GRPs foi identificado no genoma da soja: 19 da subclasse IVa, sete da IVb, seis da IVc e 15 da IVd. Análises in silico indicaram uma expressão preferencial de todos os genes codificantes da subclasse IVc em tecidos em desenvolvimento. Análises de RT-qPCR revelaram que plantas jovens e maduras exibem uma expressão mais alta em folhas do que em outros órgãos, com exceção dos genes GRP2L_4/5 que tiveram expressão mais alta em sementes. GRP2L_4/5 e GRP2L_2 foram induzidos em resposta a baixas temperaturas. Sob estresse com ABA a expressão de todos os genes foi reprimida em folhas e/ou raízes, com exceção do gene GRP2L_2 que foi induzido em raízes. Em resposta a infecção com Phakopsora pachyrhizi, a expressão de GRP2L_2 e GRP2L_3 foi mais alta e precoce no genótipo suscetível quando comparada com o resistente, enquanto que a resposta de GRP2L_4/5 e GRP2L_6 foi mais tardia no genótipo resistente. Ainda, embriões somáticos secundários das cultivares Bragg, IAS-5 e BRSMG 68 Vencedora de soja foram usados para introduzir o gene AtGRP2 no genoma da soja por bombardeamento e sistema bombardeamento/Agrobacterium. Seis eventos de transformação independentes foram confirmados por PCR. No presente momento as plantas estão em desenvolvimento em frascos de vidro. No presente estudo a classe IV de GRPs em soja foi identificada e caracterizada. Este é o primeiro passo para elucidar o papel destas proteínas em plantas. / Molecular information on plant developmental process, as well as detailed knowledge of the interaction between stress conditions and plant response to environmental factors are essential for understanding the adaptive response. Glycine-Rich Proteins (GRP) have the amino acid glycine well represented in their primary structure. The genes encoding GRPs are developmentally regulated and induced by auxin, ABA, cold, wound, light, circadian rhythm, salinity, drought, pathogens, and flooding. However, there is scarce information about plant GRPs and its role on development and stress response. The GRPs can be divided into four classes (I, II, II and IV) according to their primary structure and the presence of characteristic domains. Class IV is composed by RNA-binding proteins. Additional domains permit to split class IV GRPs into four subclasses (IVa, IVb, IVc and IVd). Subclass IVc is represented by proteins containing a Cold-Shock Domain (CSD) and retroviral-like CCHC zinc fingers. The goal of the present study was: (i) to identify and characterize the genes encoding class IV GRPs, (ii) to verify the relative expression of genes encoding subclass IVc GRPs and (iii) to produce transgenic soybean plants expressing the AtGRP2 gene, which was shown to be involved in Arabidopsis flower and seed development, and can also play a role in cold acclimation. A total of 47 genes encoding class IV GRPs were found in the soybean genome: 19 from IVa, seven from IVb, six from IVc and 15 from IVd subclasses. In silico analyses indicated a preferential expression of all genes encoding subclass IVc GRPs in tissues under development. RT-qPCR analyses revealed that both young and mature plants exhibit relative higher expression of subclass IVc GRPs in leaves than in other organs, with exception of GRP2L_4/5 genes that have higher expression in seeds. The GRP2L_4/5 and GRP2L_2 were up-regulated in response to low temperatures. Under ABA stress the expression of all genes was down-regulated in leaves and roots, with exception of GRP2L_2 gene that was up-regulated in roots. In response to Phakopsora pachyrhizi infection, GRP2L_2 and GRP2L_3 expression was higher and earlier in the susceptible genotype when compared with that of the resistant one, while GRP2L_4/5 and GRP2_6 respond later in the resistant genotype. Furthermore, secondary somatic embryos of Bragg, IAS-5 and BRSMG 68 Vencedora soybean cultivars were used to introduce the AtGRP2 gene into the soybean genome by particle bombardment and bombardment/Agrobacterium system. Six independent Bragg transformation events were confirmed by PCR. In the present moment the plants are under development in glass flasks. In the present study the soybean class IV GRPs were identified and characterized. This is the first step to elucidate the role of these proteins in plants.

Submitted by JÚLIO HEBER SILVA (julioheber@yahoo.com.br) on 2017-11-21T16:58:09Z No. of bitstreams: 2 Dissertação - Fabianna Ferreira dos Santos - 2017.pdf: 2021838 bytes, checksum: b3bb0be06a5e24c873bd447f07705f2e (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2017-11-22T10:22:27Z (GMT) No. of bitstreams: 2 Dissertação - Fabianna Ferreira dos Santos - 2017.pdf: 2021838 bytes, checksum: b3bb0be06a5e24c873bd447f07705f2e (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2017-11-22T10:22:27Z (GMT). No. of bitstreams: 2 Dissertação - Fabianna Ferreira dos Santos - 2017.pdf: 2021838 bytes, checksum: b3bb0be06a5e24c873bd447f07705f2e (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2017-10-31 / Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq / Upland rice is grown without irrigation and the availability of water is totally dependent on the occurrence of rainfall. The objective of this study was to evaluate the differential expression of genes previously identified as responsive in drought conditions in upland rice genotypes grown under controlled irrigation and water restriction conditions. Two water treatments were applied, irrigation during the whole experiment and the water restriction, where irrigation was suspended for five days from the beginning of the reproductive stage (R2 / R3), with subsequent replacement of 50% of evapotranspirated water by irrigated plants at the base of the column for 10 days, followed by adequate irrigation until the end of the plant cycle. At the end of the crop cycle, evaluations of the production components (number of full grains, number of empty grains and mass of 100 grains) and yield were performed. Productivity estimates of 24 genotypes ranged from 44 to 170 g column-1 in the irrigated treatment and from 4 to 86 g column-1 in the water deficiency condition. The genotypes Três Meses Branco, BRS Esmeralda, BRSGO Serra Dourada, Casca Branca, BRSMG Curinga, Bico Ganga and Rabo de Burro were among the most productive genotypes both in irrigated condition and in water deficiency condition. Of the 24 genotypes used in the experiment described above, 12 contrasting yields in water treatments were characterized for differential expression for two target genes. One gene integrates the antioxidative defense system (Superoxide dismutase cofactor Manganese - MnSOD) and the other is a glycosyltransferase that promotes the glycosylation of an anthocyanin molecule (anthocyanidin 3-O-beta-D-glucosyltransferase). ANOVA based on the gene expression data revealed genotypes, water treatments and collection time in the gene expression (p≤0.05). The MnSOD gene presented the highest level of expression in all genotypes in the condition of greatest water restriction (five days without irrigation), with higher levels of expression in the less productive genotypes under stress conditions. On the other hand, the glycosyltransferase gene presented a considerably reduced expression in the most critical condition of the stress, without clear indicative of differentiation among the most productive genotypes during stress. The two genes evaluated were clearly responsive (p≤0.05) to the most severe water stress, but did not explain the differences between the genotypes grouped in the productivity estimates with and without dry stress. Therefore, it is possible to conclude that, due to the complexity in the processes adaptive to drought, each genotype uses different mechanisms of molecular responses, and it is not possible to differentiate them only through the genes evaluated in this study. / O arroz de terras altas é cultivado sem irrigação e a disponibilidade de água é totalmente dependente da ocorrência de chuva. O objetivo desse estudo foi avaliar em genótipos de arroz de terras altas cultivados em condições controladas de irrigação e restrição hídrica a expressão diferencial de genes previamente identificados como responsivos em condições de seca. Foram aplicados dois tratamentos hídricos, o irrigado durante todo experimento e o de restrição hídrica, onde a irrigação foi suspensa por cinco dias a partir do início do estádio reprodutivo (R2/R3), com subsequente reposição de 50 % da água evapotranspirada pelas plantas irrigadas na base da coluna por 10 dias, seguido por irrigação adequada até o final do ciclo da planta. Ao término do ciclo da cultura foram realizadas as avaliações dos componentes de produção (número de grãos cheios, número de grãos vazios e massa de 100 grãos) e da produtividade. As estimativas de produtividade dos 24 genótipos variaram de 44 a 170 g coluna-1 no tratamento irrigado e de 4 a 86 g coluna- 1 na condição de deficiência hídrica. Os genótipos Três Meses Branco, BRS Esmeralda, BRSGO Serra Dourada, Casca Branca, BRSMG Curinga, Bico Ganga e Rabo de Burro figuraram dentre os mais produtivos tanto em condição irrigada quanto em condição de deficiência hídrica. Dos 24 genótipos utilizados no experimento descrito acima, 12 contrastantes quanto à produtividade nos tratamentos hídricos foram caracterizados quanto à expressão diferencial para dois genes-alvo. Um gene integra o sistema de defesa antioxidativo (Superóxido dismutase cofator Manganês – MnSOD) e o outro é uma glicosiltransferase que promove a glicosilação de uma molécula de antocianina (anthocyanidin 3-O-beta-D-glucosyltransferase). A ANOVA realizada a partir dos dados de expressão gênica revelou efeito dos genótipos, tratamentos hídricos e época de coleta na expressão gênica (p≤0.05). O gene MnSOD apresentou o maior nível de expressão em todos os genótipos na condição de maior restrição hídrica (cinco dias sem irrigação), com maiores níveis de expressão nos genótipos menos produtivos em condição de estresse. Já o gene glicosiltransferase apresentou uma expressão consideravelmente reduzida na condição mais crítica do estresse, sem indicativo claro de diferenciação entre os genótipos mais produtivos durante o estresse. Os dois genes avaliados foram claramente responsivos (p≤0.05) ao estresse hídrico mais severo, porém não explicaram as diferenças entre os genótipos agrupados quanto às estimativas de produtividade com e sem estresse de seca. Diante disso, é possível concluir que diante da complexidade nos processos adaptativos à seca, cada genótipo utiliza diferentes mecanismos de respostas moleculares, não sendo possível diferencia-los somente através dos genes avaliados nesse estudo.