The interaction between Arabidopsis and its natural downy mildew pathogen, Hyaloperonospora arabidopsidis (Hpa), provides a model for understanding how oomycetes colonize plants. Hpa is a model organism for many highly destructive oomycete pathogens and transcriptomics of this interaction have been well-documented. However, the material in these studies has been derived from infected leaves that contain a mix of pathogen-proximal and pathogen-distal plant cells. The most direct interactions between Arabidopsis and Hyaloperonospora arabidopsidis occur in haustoriated cells- where the pathogen can secrete effectors and acquire nutrients needed for successful colonization and reproduction. These cells are difficult to isolate due to their limited number and ephemeral nature. I have developed a method to isolate the translatome (i.e., mRNAs associated with ribosomes) of pathogen-proximal cells. This method utilizes translating ribosome immuno-purification technology (TRAP), regulated by both pathogen-responsive and tissue-specific promoters, to isolate mRNAs that are being translated in pathogen-proximal cells. Compared to "bulk" transcriptomics of material isolated from homogenized leaves, this method will enrich for transcripts that are differentially expressed, and translated, in pathogen-proximal cells. From this method, RNA was isolated in amount and quality sufficient for sequencing. This sequencing data will enable the discovery of plant genes that may be manipulated by the pathogen to suppress defense responses and extract nutrients. / Ph. D. / The interactions between plants and the pathogens that feed on them are complex and at times difficult to study. Among the many different types of plant pathogens, oomycetes (a class of fungus-like organisms) are especially destructive. Using Arabidopsis and its natural downy mildew pathogen, Hyaloperonospora arabidopsidis (Hpa) as model for understanding how oomycetes colonize plants, I hope to learn more about plant-pathogen interactions. Hpa is a model organism for many highly destructive oomycete pathogens and several aspects of this interaction have been well-documented. However, the material in these studies has been derived from infected leaves that contain a mix of plant cells that are both in direct contact with the pathogen, or from uninfected areas of the plant. The most direct interactions between Arabidopsis and Hpa occur in cells that have been invaginated with a pathogen feeding structure called a haustorium. These cells are difficult to isolate due to their limited number and ephemeral nature. I have developed a method to isolate the translatome (i.e., mRNAs that are being translated by and are associated with ribosomes) of pathogen-proximal cells. This method utilizes translating ribosome immuno-purification technology (TRAP), regulated by both pathogen-responsive and tissue-specific promoters, to isolate mRNAs that are being translated in pathogen-proximal cells. Compared to “bulk” transcriptomics of material isolated from homogenized leaves, this method will enrich for transcripts that are differentially expressed, and translated, in pathogen-proximal cells. From this method, RNA was isolated in amount and quality sufficient for sequencing. This sequencing data will enable the discovery of plant genes that may be manipulated by the pathogen to suppress defense responses and extract nutrients.

Yes / Maintenance of skeletal muscle mass and function is critical to health and wellbeing throughout the lifespan. However, disuse through reduced physical activity (e.g., sedentarism), immobilisation, bed rest or microgravity has significant adverse effects on skeletal muscle health. Conversely, resistance exercise training (RET) induces positive muscle mass and strength adaptations. Several studies have employed microarray technology to understand the transcriptional basis of muscle atrophy and hypertrophy after disuse and RET, respectively, to devise fully effective therapeutic interventions. More recently, rapidly falling costs have seen RNA-sequencing (RNA-seq) increasingly applied in exploring muscle adaptations to RET and disuse. The aim of this review is to summarise the transcriptional responses to RET or disuse measured via RNA-seq in young and older adults. We also highlight analytical considerations to maximise the utility of RNA-seq in the context of skeletal muscle research. The limited number of muscle transcriptional signatures obtained thus far with RNA-seq are generally consistent with those obtained with microarrays. However, RNA-seq may provide additional molecular insight, particularly when combined with data-driven approaches such as correlation network analyses. In this context, it is essential to consider the most appropriate study design parameters as well as bioinformatic and statistical approaches. This will facilitate the use of RNA-seq to better understand the transcriptional regulators of skeletal muscle plasticity in response to increased or decreased use.

Yes / The ability of skeletal muscle to adapt to eccentric contractions has been suggested to be blunted in older muscle. If eccentric exercise is to be a safe and efficient training mode for older adults, preclinical studies need to establish if older muscle can effectively adapt and if not, determine the molecular signatures that are causing this impairment. The purpose of this study was to quantify the extent age impacts functional adaptations of muscle and identify genetic signatures associated with adaptation (or lack thereof). The anterior crural muscles of young (4 mo) and older (28 mo) female mice performed repeated bouts of eccentric contractions in vivo (50 contractions/wk for 5 wk) and isometric torque was measured across the initial and final bouts. Transcriptomics was completed by RNA-sequencing 1 wk following the fifth bout to identify common and differentially regulated genes. When torques post eccentric contractions were compared after the first and fifth bouts, young muscle exhibited a robust ability to adapt, increasing isometric torque 20%-36%, whereas isometric torque of older muscle decreased up to 18% (P ≤ 0.047). Using differential gene expression, young and older muscles shared some common transcriptional changes in response to eccentric exercise training, whereas other transcripts appeared to be age dependent. That is, the ability to express particular genes after repeated bouts of eccentric contractions was not the same between ages. These molecular signatures may reveal, in part, why older muscles do not appear to be as adaptive to exercise training as young muscles.NEW & NOTEWORTHY The ability to adapt to exercise training may help prevent and combat sarcopenia. Here, we demonstrate young mouse muscles get stronger whereas older mouse muscles become weaker after repeated bouts of eccentric contractions, and that numerous genes were differentially expressed between age groups following training. These results highlight that molecular and functional plasticity is not fixed in skeletal muscle with advancing age, and the ability to handle or cope with physical stress may be impaired. / The full-text of this article will be released for public view at the end of the publisher embargo on 1 Nov 2024.

Resistenzen von Tumoren gegenüber der Behandlung mit Chemotherapeutika stellen ein wesentliches Hindernis für eine erfolgreiche Therapie in der onkologischen Klinik dar. Ein Verständnis der biologischen Mechanismen auf molekularer Ebene, die zu diesen Resistenzphänomenen führen, ist daher von entscheidender Bedeutung, um Strategien zu entwickeln, die darauf zielen, eine Therapieresistenz zu überwinden. Um diesem Ziel näher zu kommen, wurden im Verlaufe dieser Arbeit verschiedene Modelle aus unterschiedlichen Tumoren entwickelt und analysiert, die im Zellkultursystem Chemoresistenzen von neoplastischen Geweben simulieren. In einem ersten Schritt wurden diese in vitro Systeme zellbiologisch hinsichtlich dem Vorhandensein von verschiedenen, aus der wissenschaftlichen Literatur bekannten Resistenzmechanismen, charakterisiert. Hierbei konnte neben der verstärkten Expression von ABC-Transportern, wie P-Glykoprotein (P-Gp), "Breast Cancer Resistance Protein" (BCRP) sowie "canalicular Multispecific Organic Anion Transporter" (cMOAT), eine intrazelluläre Kompartimentierung von Zytostatika, Modulation der Aktivität von DNA-Topoisomerasen II (Topo II) sowie Veränderungen in der Aktivität von DNA-Reparatursystemen, wie z.B. dem DNA-Mismatch Repair System (DMM) oder der O6-Methyguanin-Methytransferase (MGMT) in resistenten Zellen wiedergefunden werden. Die Aktivierung dieser Mechanismen reichte jedoch nicht aus, das komplexe Geschehen von unterschiedlichen Kreuzresistenzen in den Zellen zu erklären. Es wurde daher gezielt nach neuen Resistenzmechanismen gesucht. Dafür wurden zwei unterschiedliche Strategien verfolgt: 1. Suche nach neuen Resistenz-assoziierten Faktoren auf Ebene der zellulären mRNA Expressionsprofile ("Transcriptomics"), sowie 2. Suche nach neuen Resistenz-assoziierten Faktoren auf Ebene der zellulären Proteinexpression ("Proteomics"). Mittels beider experimentellen Ansätze konnten mehrere Faktoren identifiziert werden, die potentiell neue Resistenzmechanismen in Tumorzellen vermitteln können. Für die Faktoren Glypican-3 (GPC3), DFNA5 und "Transporter associated with Antigen Presentation" (TAP) konnten funktionelle Analysen nachweisen, daß diese am Resistenzgeschehen beteiligt sind. Zur Überwindung von Chemoresistenzen, wurde neben dem Einsatz konventioneller chemischer Substanzen, eine gentherapeutische Strategie, die Ribozymtechnologie, gewählt. In dieser Arbeit wurden Ribozyme gegen GPC3 sowie die ABC-Transporter BCRP und cMOAT entwickelt. / Resistance to antitumor chemotherapy is a common problem in patients with cancer and a major obstacle to effective treatment of disseminated neoplasms. An understanding of the molecular mechanisms leading to these resistance phenomena is of vital interest to develop strategies to overcome therapy resistance in clinics. In order to gain further insides into the biological mechanisms mediating drug resistance, in this study various cell culture models derived from different origins were established and analyzed in detail. At first, these in vitro models were investigated concerning the activity of drug resistance mechanisms that were described in the scientific literature previously. By this approach the enhanced expression of the ABC-transporters P-glycoprotein (P-gp), "breast cancer resistance protein" (BCRP) and "canalicular multispecific organic anion transporter" (cMOAT) could be observed. In addition, an intracellular compartmentalization of the antineoplastic agents, a modulation of the activities of DNA-topoisomerases II (Topo II), and altered activities of DNA-repair systems, such as the DNA-mismatch repair system (DMM) or O6-methyguanine methyltransferase (MGMT) were detected. However, since the activation of these mechanisms do not explain all of the cross resistance pattern observed in these cell systems, other additional mechanisms must be operating in the drug-resistant cells. In order to identify potential new molecular mechanisms involved in drug resistance, in this study two different experimental strategies were performed: 1. Search of new resistance-associated factors on the level of the cellular mRNA expression profiles ("transcriptomics"), and 2. Search of new resistance-associated factors on the level of cellular protein expression ("proteomics"). By applying both experimental strategies, several cellular factors could be identified that potential play a role in drug resistance of tumor cells. Functional evidence was provided for glypican-3 (GPC3), DFNA5 and "transporter associated with antigen presentation" (TAP) to be involved in drug-resistant phenotypes. To overcome drug resistance, a gene therapeutic approach, a hammerhead ribozyme-based technology, was developed. In this study various ribozymes directed against GPC3 and the ABC-transporters BCRP and cMOAT were constructed.

<p dir="ltr">Neurotrauma encompasses a broad category of injuries affecting the central nervous system (CNS), which includes both the traumatic brain injury (TBI) and spinal cord injury (SCI). These injuries can result from various causes, including accidents, falls, sports-related incidents, and other traumatic events, affecting millions of individuals annually. Traumatic injuries are the leading cause of disability, and moreover are associated with elevated risk of developing cognitive impairments and neurodegenerative diseases (ND) such as Alzheimer’s Disease (AD) and Parkinson’s Disease (PD). The elevated ND risk arising from neurotrauma poses significant burdens on healthcare systems and affect life quality of affected individuals, emphasizing the critical need for research aimed at understanding the underlying mechanisms conferring ND risk from the lesion center to CNS. The goal of my thesis is to understand persistent molecular changes post SCI associated with ND using a combination of a rat animal model and neuronal cultures derived from human induced pluripotent stem cells.</p><p dir="ltr">I started with Sprague-Dawley rats with T10 spinal cord contusive injury; and assessed immediate and persistent changes in transcriptomic and epigenetic markers via next generation sequencing (NGS) at primary lesion site and distal spinal cord tissue. Along with global changes in chromatin arrangements and DNA methylation, we observed significant transcriptomic changes enriched for pathways of inflammatory responses, and synaptogenesis. These changes were further verified using immunohistochemistry and super resolution microscopy. To further understand the long-term brain abnormality linked to SCI, we investigated persistent alterations in the composition and molecular profiles of both the male and female motor cortex 30 days after injury. Immunohistochemistry revealed that SCI leads to neuronal loss and changes in synaptic density and morphology; and significant alterations in the neuron-astrocyte ratio and astrocyte morphology, in male motor cortex supporting our hypothesis that SCI may increase the risk of neurodegeneration by affecting the motor cortex. Comparison of transcriptomic data collected at a sub-acute stage in male rats, namely 7 days post injury, with 30 days post injury, identified persistent and de novo changes that occur primarily after recovery of spinal cord injury, which are enriched for neuronal and synaptic function related pathways. Interestingly, neuroendocrine-related pathways were prominently implicated at the chronic stage of SCI, with Esr1 identified as a major upstream regulator offering protective effects in females that did not exhibit significant alterations in cellular composition or morphology after SCI. Collectively, our study paved the way towards understanding sexual dimorphism in brains after spinal cord injury and provides a plausible connection between spinal cord injury and neurodegeneration later in life that were further investigated using a humanized culture model.</p><p dir="ltr">We established the feasibility of using hiPSC derived neurons to examine long term neurotoxic mechanism using lead (Pb) as a model chemical with strong associations with elevated AD risks later in life. A similar culture system was then used to assess persistent neurotoxicity of acrolein, a chemical that is known to emerge in brains post traumatic injury. We found that acrolein induced alterations in neuronal network morphology, synaptic density, and excitability. Furthermore, acrolein exposure negatively impacted mitochondrial function and persistently altered neuronal resilience towards a secondary stressor of mitochondria, namely MPP+. Acrolein exposure also alters the expression of tau and tau phosphorylation which collectively result in increased cellular vulnerability toward paired helical filament (PHF-tau) seeding, a known neurotoxin associated with ND. These findings collectively provide molecular insights as to how acrolein can partake alterations in neural function and resilience to stressors; and relay ND risks in neurotrauma patients later in life.</p><p dir="ltr">In conclusion, our comprehensive investigation employing both rat and hiPSC models uncovers plausible molecular pathways connecting SCI to neurodegenerative diseases, providing insights into the enduring consequences of these injuries on affected patients.</p>

BACKGROUND:The rhizome, the original stem of land plants, enables species to invade new territory and is a critical component of perenniality, especially in grasses. Red rice (Oryza longistaminata) is a perennial wild rice species with many valuable traits that could be used to improve cultivated rice cultivars, including rhizomatousness, disease resistance and drought tolerance. Despite these features, little is known about the molecular mechanisms that contribute to rhizome growth, development and function in this plant.RESULTS:We used an integrated approach to compare the transcriptome, proteome and metabolome of the rhizome to other tissues of red rice. 116 Gb of transcriptome sequence was obtained from various tissues and used to identify rhizome-specific and preferentially expressed genes, including transcription factors and hormone metabolism and stress response-related genes. Proteomics and metabolomics approaches identified 41 proteins and more than 100 primary metabolites and plant hormones with rhizome preferential accumulation. Of particular interest was the identification of a large number of gene transcripts from Magnaportha oryzae, the fungus that causes rice blast disease in cultivated rice, even though the red rice plants showed no sign of disease.CONCLUSIONS:A significant set of genes, proteins and metabolites appear to be specifically or preferentially expressed in the rhizome of O. longistaminata. The presence of M. oryzae gene transcripts at a high level in apparently healthy plants suggests that red rice is resistant to this pathogen, and may be able to provide genes to cultivated rice that will enable resistance to rice blast disease.

The C₄ photosynthetic cycle acts to concentrate CO₂ around the enzyme Rubisco. By doing so, C₄ photosynthesis leads to increased radiation, water and nitrogen use efficiencies. As such, C₄ photosynthesis is the most productive form of photosynthesis known. Because it enables such high levels of productivity there are large international efforts to introduce C₄ photosynthesis into non-C₄ crop species such as rice. Kranz anatomy is a characteristic leaf cellular arrangement of concentric rings of bundle sheath and mesophyll cells around closely spaced veins and is crucial to C₄ photosynthesis in almost all known examples. Despite the fact that Kranz has evolved on over 60 times independently little is known about the genetic regulation of Kranz development, as attempts to elucidate Kranz regulators using conventional mutagenesis screens have provided few insights. However, the advent of next generation DNA sequencing technologies has enabled the interrogation of genetic networks at a previously unprecedented scale. The work in this thesis describes a genome-wide transcriptomic analysis of leaf development in maize, a C₄ species, that develops both Kranz-type and non-Kranz-type leaves. Detailed bioinformatics analyses identified candidate regulators of both Kranz development and additional aspects of maize leaf development. Three of the identified Kranz candidates were functionally characterised in both C₄ and non-C₄ species. Furthermore, expression and phylogenetic analyses of GOLDEN2-LIKE (GLK) genes, a small transcription factor family previously implicated in C₄ development in maize, were extended to determine the generality of GLK function in C₄ evolution.

Thesis (PhD(Agric) Viticulture and Oenology. Wine Biotechnology))--University of Stellenbosch, 2009. / The main goal of this project was to elucidate the underlying genetic factors responsible for the different fermentation phenotypes and physiological adaptations of industrial wine yeast strains. To address this problem an ‘omic’ approach was pursued: Five industrial wine yeast strains, namely VIN13, EC1118, BM45, 285 and DV10, were subjected to transcriptional, proteomic and exometabolomic profiling during alcoholic fermentation in simulated wine-making conditions. The aim was to evaluate and integrate the various layers of data in order to obtain a clearer picture of the genetic regulation and metabolism of wine yeast strains under anaerobic fermentative conditions. The five strains were also characterized in terms of their adhesion/flocculation phenotypes, tolerance to various stresses and survival under conditions of nutrient starvation. Transcriptional profiles for the entire yeast genome were obtained for three crucial stages during fermentation, namely the exponential growth phase (day 2), early stationary phase (day 5) and late stationary phase (day 14). Analysis of changes in gene expression profiles during the course of fermentation provided valuable insights into the genetic changes that occur as the yeast adapt to changing conditions during fermentation. Comparison of differentially expressed transcripts between strains also enabled the identification of genetic factors responsible for differences in the metabolism of these strains, and paved the way for genetic engineering of strains with directed modifications in key areas. In particular, the integration of exo-metabolite profiles and gene expression data for the strains enabled the construction of statistical models with a strong predictive capability which was validated experimentally. Proteomic analysis enabled correlations to be made between relative transcript abundance and protein levels for approximately 450 gene and protein pairs per analysis. The alignment of transcriptome and proteome data was very accurate for interstrain comparisons. For intrastrain comparisons, there was almost no correlation between trends in protein and transcript levels, except in certain functional categories such as metabolism. The data also provide interesting insights into molecular evolutionary mechanisms that underlie the phenotypic diversity of wine yeast strains. Overall, the systems biology approach to the study of yeast metabolism during alcoholic fermentation opened up new avenues for hypothesis-driven research and targeted engineering strategies for the genetic enhancement/ modification of wine yeast for commercial applications.

La surface des vignobles mondiaux représente environ 7,9 millions ha, ce qui correspond à une production annuelle de 67 millions de tonnes de baies. La production mondiale annuelle de vins est de l’ordre de 300 millions hl/an. La surface du vignoble français est de 843 000 ha. La viticulture moderne doit affronter trois défis majeurs interdépendants : réduire l’utilisation des produits phytosanitaires, s'adapter au changement climatique, maîtriser la qualité et la typicité pour garder ou conquérir de nouveaux marchés.En 2007, la vigne est devenue la première espèce fruitière pérenne dont le génome a été séquencé. Cette avancée scientifique ouvre de nombreuses perspectives en termes de génomique fonctionnelle (ensemble de méthodes permettant de caractériser la fonction des gènes) et de biologie intégrative (ensemble de méthodes visant à appréhender le fonctionnement global de la plante et ses réponses à l’environnement). Ces perspectives dépendent pour une bonne part de la maîtrise de quantités importantes de données qu’il convient d’organiser et de corréler grâce à des outils informatiques adaptés.Des approches fonctionnelles concernant des gènes candidats et des approches transcriptomiques à haut débit ont permis d’identifier certains gènes ou certaines familles de gènes impliqués dans le développement et la maturation de la baie de raisin, mais au moment où cette thèse a débuté, aucun travail de biologie intégrative n’avait été entrepris.Le travail présenté ici, qui décrit l’obtention et l’analyse de métadonnées transcriptomiques et biochimiques portant sur la réponse de la baie à l’environnement radiatif, s’inscrit dans ce contexte. En procédant à un effeuillage partiel après la véraison, nous avons modulé l’exposition des baies au rayonnement solaire. Ceci a permis d’étudier l’influence du rayonnement (baie exposée, non exposée), de la position de la grappe (est, ouest) et de la position de la baie (à l’extérieur ou à l’intérieur de la grappe). Des baies ont été récoltées à 5 moments différents après l’effeuillage et utilisées pour des analyses métabolomiques et transcriptomiques. Leur contenu en sucres, acides organiques, acides aminés, anthocyanes et flavonols a été analysé par des dosages enzymatiques et par chromatographie liquide à haute performance). L’expression des gènes a été étudiée avec des microarrays représentatifs de l’ensemble du génome de la vigne (29600 gènes) pour les conditions présentant les différences métaboliques les plus marquées (baies exposées, situées à l’ouest et à l’extérieur de la grappe vs baies non exposées, situées à l’est et à l’intérieur de la grappe). Des analyses statistiques et corrélatives ont été conduites pour (a) déterminer les métabolites qui répondent au traitement et les facteurs qui les influencent (b) déterminer les gènes qui répondent aux traitements et ceux qui semblent co-régulés (c) préciser les réseaux de gènes et de métabolites qui semblent reliés. L’effeuillage n’affecte pas la teneur en sucres ou en acide tartrique des baies, il affecte peu les acides aminés, mais il augmente la teneur en flavonols et diminue la teneur en acide malique. Il affecte plus particulièrement les gènes associés au stress abiotique, au métabolisme secondaire, au transport et au métabolisme hormonal. Des expériences complémentaires ont permis d’identifier divers gènes spécifiquement associés à la composante thermique de l’exposition au soleil, parmi lequels des gènes codant pour des HSP, des transporteurs ABC, et des enzymes du métabolisme flavonoïdique. Des réseaux reliant des gènes et des métabolites ont pu être construits, qui associent des métabolites secondaires à des gènes de fonctions connues, ou à de nouveaux gènes candidats dont il conviendra d’étudier la fonction précise. / The total surface of vineyards worldwide is about 7.9 millions ha, which corresponds to an annual production of 67 millions tons berries. The annual world production of wines is about 300 millions hl/year. The French wineyard occupies 843 000 ha, among which 481 000 ha are dedicated to high quality wines (VQPRD) and 362 000 ha to table wines. Modern viticulture must deal with three major and related challenges : reduce the use of organic and inorganic phytochemicals, adapt the vineyard to climatic change and control the quality and the typicity in order to keep or gain new markets.In 2007, the grapevine became the first perennial fruit species whose genome was sequenced. This scientific breakthrough opens new pespectives in terms of functional genomics (set of methods allowing to characterize the function of genes) and integrative biology (set of methods allowing to study the global functioning of the plant and its response to the environment). These perspectives mainly depend on our ability to analyze large sets of data with adequate informatic tools.Functional approaches on candidate genes, and high throughput transcriptomic approaches have allowed to identify some genes or some gene families involved in the development and ripening of the grape berry, but when this Ph. D work started, no paper based on integrative biology was published on grapevine. The present work, which describes the collection and analysis of transcriptomic and metabolomic metadata related to the response of the berry to sun exposure. The exposure of the berries to the sun was controlled through a partial defoliation after veraison. This allowed to study the effects of sun exposure (exposed or shaded berries), of the position of the cluster (east, west) and of the anatomical position of the berry (outside or inside the berry). Berries were collected at 5 different time points after defoliation and used for metabolomic and transcriptomic analysis. Their content in sugars, amino acids, organic acids, anthocyanins and flavonols was analyzed by enzymatic assays and high performance liquid chromatography. For the berries whose metabolic content differed the most (exposed, west and outside berries vs shaded, east and inside berries), gene expression was studied with microarrays bearing a set of probes covering the whole genome of grapevine (29600 genes). Correlative and statistical analysis were conducted in order to (a) determine the metabolites that are the most responsive to the treatment, and the most important factors that control them (b) determine the genes that respond to the treatment and seem to be co-regulated (c) to precise the networks of genes and metabolites which seem related. Defoliation does not affect the sugar and tartaric acid contents, hardly affects amino acids, but it increases flavonol content and decreases malic acid content. It affects more specifically genes associated with abiotic stress, secondary metabolism, transport and hormonal metabolism. Additional experiments allowed us to identify genes that are specifically associated with the thermal component of sun exposure, among which genes encoding HSP, ABC transporters, and enzymes of flavonoid metabolism. Networks relating genes and metabolites could be constructed. These networks associate secondary metabolites with genes of known function and new candidate genes for which the function will have to be precised.

Xanthomonas oryzae pv. oryae (Xoo) est l'agent causal de la bactériose vasculaire du riz (BLB), maladie entraînant des pertes de rendement importantes dans la plupart des régions rizicoles, notamment en Afrique. La virulence des souches Asiatiques de Xoo dépend des effecteurs de la famille AvrBs3/PthA ou TAL (pour Transcription Activator-Like). Des études appro fondies sur le mode d'action des effecteurs TAL ont montré que l'activité de virulence ou d'avirulence que les TAL confèrent à la bactérie dépend essentiellement de leur interaction avec les gènes de sensibilité et/ou de résistance correspondants chez le riz. Les souches de Xoo originaires d'Afrique isolées récemment ne présentent que huit effecteurs de type TAL dans leur génome et leur rôle dans la virulence est jusqu'à présent inconnu. Les travaux de cette thèse ont porté sur la caractérisation des effecteurs de type TAL dans la souche africaine de Xoo BAI3. Une mutagenèse systématique par recombinaison homologue sur l'ensemble des huit gènes tal de la souche BAI3 a été effectuée et a conduit à l'identification et à la caractérisation du gène talC. TalC se caractérise par 21.5 répétitions et est phylogénétiquement proche des TAL de Xanthomonas oryzae pv. oryzicola (Xoc). Le mutant BAI3ΔtalC est incapable de développer les symptômes de la maladie sur plante sensible. Toutefois, les bactéries se multiplient très bien au niveau de l'apex foliaire proche du site d'inoculation, laissant supposer que TalC est requis pour la colonisation du système vasculaire. Parmi les cibles directes potentielles identifiées via l'analyse du transcriptome de feuilles de riz sensible (BAI3 versus BAI3ΔtalC), Os11N3 code une protéine de la famille des noduline-3 MtN3 et est fortement induit durant l'infection par la souche sauvage BAI3. Nous avons identifié dans la région promotrice de Os11N3 une séquence nucléotidique ciblée par TalC et démontré qu'elle était fonctionnelle via des expériences d'expression en trans dans N. benthamiana. Les travaux de cette thèse montrent pour la première fois que les effecteurs de type TAL contribuent de manière importante à la virulence de la souche africaine Xoo BAI3. Ces travaux contribueront à l'amélioration génétique des lignées de riz pour la résistance à la bactériose vasculaire du riz en Afrique. / Xanthomonas oryzae pv. oryzae (Xoo) is the causal agent of Bacterial Leaf Blight (BLB) on rice, a serious disease causing important yield losses in the main rice growing regions including Africa. The virulence of Asian Xoo strains mainly depends on the type III effectors of avrBs3/pthA gene family, namely TAL (for Transcription Activator Like) effectors. In depth studies on the function of TAL effectors revealed that the virulence and/or the avirulence activities conferred by these effectors requires the binding and the induction of the corresponding S and/or R genes. African Xoo strains was shown to harbor 8 TAL effectors in their genomes. However, the contribution of these TAL effectors to Xoo virulence is still unknown. This work reports on the identification and characterization of TAL effectors in the African Xoo strain BAI3R. A random mutagenesis based on homologous recombination in the genes encoding TAL effector was conducted in Xoo str ain BAI3R and led to the identification of talC. TalC harbors 21.5 repeats in its central domain and is phylogenetically more related to TAL effectors of Xanthomonas oryzae pv. oryzicola (Xoc). The BAI3RΔtalC mutant is seriously impaired in its virulence on susceptible rice varieties. Interestingly, bacteria are still able to grow at wild-type levels in the apex of the leaf, suggesting a requirement of talc for vascular colonization. Potential direct host targets were identified by conducting a transcriptomic analysis of rice leaves challenged with Xoo strain BAI3R vs. BAI3RΔtalC. Among the identified targets, the rice gene Os11N3 was found to be highly induced upon infection by the wild type strain but not the mutant one. A DNA target box for TalC was located in the Os11N3 upstream region and proved to be functional using GUS assays. We also show that the Os11N3 341-bp upstream region is transcriptionnally activated by TalC. Our results demonstrated for the first time that TAL effectors play an important role in the virulence of Xoo strain BAI3R. Our work will contribute to better improve rice for resistance to bacterial leaf blight.