Successful bacterial pathogens manipulate crucial intracellular host processes as a virulence strategy. One particular potent mechanism utilized by bacterial phytopathogens is to inject virulence factors (effectors) directly into the host cell. While many effectors have been identified and shown to suppress plant immune responses, very few have well-characterized enzymatic activities or host targets. To overcome the challenges of functional analysis of effectors, I designed two heterologous screens to characterize effector proteins of the bacterial phytopathogen Pseudomonas syringae. Specifically, my objective was to identify those P. syringae effectors that target evolutionarily conserved host proteins or processes and to subsequently elucidate the molecular mechanisms of these effectors. The first heterologous screen that I performed was to utilize tandem-affinity-purification (TAP)-tagged effectors in human cells to identify potential interacting host proteins. The second heterologous screen iii utilized a high-throughput genomics approach in yeast, known as the pathogenic genetic array (PGA), to characterize P. syringae effectors. Using the first heterologous approach, I have identified HopZ1a as the first bacterial phytopathogen effector that binds tubulin. I have shown that HopZ1a is an acetyltransferase activated by the eukaryotic co-factor, phytic acid. In vitro, activated HopZ1a acetylates itself and tubulin. In Arabidopsis thaliana, activated HopZ1a causes microtubule destruction, disrupts the secretory pathway and suppresses cell wall-mediated defense. The acetyltransferase activity of HopZ1a is dependent on the conserved catalytic cysteine residue (C216) and a conserved lysine residue (K289). Using the second heterologous screen in yeast, I have shown that HopZ1a may target the mitogen-activated protein kinase (MAPK) signaling cascades. Together, my work has identified novel eukaryotic targets and elucidated the virulence functions of HopZ1a.

Successful bacterial pathogens manipulate crucial intracellular host processes as a virulence strategy. One particular potent mechanism utilized by bacterial phytopathogens is to inject virulence factors (effectors) directly into the host cell. While many effectors have been identified and shown to suppress plant immune responses, very few have well-characterized enzymatic activities or host targets. To overcome the challenges of functional analysis of effectors, I designed two heterologous screens to characterize effector proteins of the bacterial phytopathogen Pseudomonas syringae. Specifically, my objective was to identify those P. syringae effectors that target evolutionarily conserved host proteins or processes and to subsequently elucidate the molecular mechanisms of these effectors. The first heterologous screen that I performed was to utilize tandem-affinity-purification (TAP)-tagged effectors in human cells to identify potential interacting host proteins. The second heterologous screen iii utilized a high-throughput genomics approach in yeast, known as the pathogenic genetic array (PGA), to characterize P. syringae effectors. Using the first heterologous approach, I have identified HopZ1a as the first bacterial phytopathogen effector that binds tubulin. I have shown that HopZ1a is an acetyltransferase activated by the eukaryotic co-factor, phytic acid. In vitro, activated HopZ1a acetylates itself and tubulin. In Arabidopsis thaliana, activated HopZ1a causes microtubule destruction, disrupts the secretory pathway and suppresses cell wall-mediated defense. The acetyltransferase activity of HopZ1a is dependent on the conserved catalytic cysteine residue (C216) and a conserved lysine residue (K289). Using the second heterologous screen in yeast, I have shown that HopZ1a may target the mitogen-activated protein kinase (MAPK) signaling cascades. Together, my work has identified novel eukaryotic targets and elucidated the virulence functions of HopZ1a.

Le système de sécrétion de type III est un des déterminants majeurs de la pathogénicité de Ralstonia pseudosolanacearum qui lui permet d’injecter des effecteurs de type III (les « Rip », « Ralstonia Injected Protein ») directement dans les cellules des plantes hôtes. Les effecteurs RipH1, RipH2 et RipH3 sont des effecteurs de type III conservés dans la plupart des souches séquencées. Au cours de ma thèse, le rôle de ces effecteurs RipH lors de l’infection de différentes plantes a été étudié en prenant comme point d’entrée les protéines de tomates avec lesquelles ces effecteurs interagissent. Un criblage par double hybride dans la levure a permis d’identifier 19 de ces protéines « cibles » de tomate. Des méthodes de génétique inverse ont ensuite été utilisées pour chercher le rôle des orthologues de ces protéines dans différentes plantes modèles lors de l’infection par Ralstonia pseudosolanacearum. Du VIGS chez Nicotiana benthamiana a permis de mettre en évidence l’implication des orthologues de la protéine TOM3 : la multiplication bactérienne est moins importante dans les feuilles lorsque l’expression de ces gènes est diminuée. Dans Arabidopsis thaliana, des mutants d’un gène orthologue de la cible TOM9, décrit comme jouant entre autres un rôle dans la remodélisation de la chromatine, est plus résistant à l’infection par R. pseudosolanacearum. Dans un deuxième chapitre correspondant à un article publié, le rôle de l’effecteur RipAX2 a été étudié dans la résistance des aubergines AG91-25. La présence de cet effecteur dans la souche GMI1000 est nécessaire à l’établissement de la résistance de cette variété dans laquelle le locus de résistance EBWR9 a été mis en évidence. L’ajout de RipAX2 dans la souche PSS4, une souche pathogène de AG91-25 qui ne possède pas cet effecteur naturellement, la rend non pathogène. De plus, le motif protéique putatif « zincbinding » qui est décrit comme nécessaire pour l’induction de réponses de défense chez l’espèce proche de l’aubergine Solanum torvum n’est pas nécessaire pour la résistance de AG91-25. Enfin, la conservation de l’effecteur RipAX2 dans les différentes souches du complexe d’espèces de Ralstonia solanacearum a été étudiée pour évaluer l’efficacité potentielle de cette source de résistance contre différentes souches. / One of the major virulence determinants of plant pathogenic Ralstonia species is the type III secretion system that enables it to inject proteins (also called “Ralstonia Injected Proteins” or Rip) into the host cells. The RipH1,2,3 type III effectors are conserved in different strains of the Ralstonia solanacearum species complex. The role of these effectors during infection has been studied, taking as an entry point the tomato proteins they interact with. Using yeast-two-hybrid screenings we have identified 19 tomato targets of these three RipH. Reverse genetics methods have then been used to study the role of orthologous genes of these targets in other model plants. Virus induced gene silencing in Nicotiana benthamiana showed that the orthologous genes of TOM3 were involved in plant response to Ralstonia pseudosolanacearum, as the bacterial multiplication was diminished in plants silenced for these genes. In Arabidopsis thaliana, mutants of the TOM9 orthologous gene which is described as involved in chromatin remodelisation were more tolerant to infection. In a second chapter corresponding to a published article, the role of RipAX2 has been studied. This effector triggers specific resistance in AG9125 eggplant which carry the major resistance locus EBWR9. This eggplant accession AG9125 is resistant to the wild type R. pseudosolanacearum strain GMI1000, while a ripAX2 defective mutant of this strain can cause wilt. The addition of ripAX2 from GMI1000 to the naturally pathogenic strain PSS4 suppresses its pathogenicity, demonstrating that RipAX2 causes AG9125 resistance. Moreover, a zinc binding motif described as necessary to induce defenses on the eggplant wild relative Solanum torvum upon RipAX2 recognition is not necessary for AG91-25 resistance. The conservation of RipAX2 has been studied in the different strains of the bacteria in order to determine the potential of this resistance source against various strains for breeding

Symbiosis is the close and protracted interaction between organisms. The molecular interactions that occur during symbiosis are complex with multiple barriers that must be overcome. Many Gram-negative, host-associated bacteria use a type III secretion system to mediate associations with their eukaryotic hosts. This secretion system is a specialized apparatus for the injection of type III effector proteins directly into host cells, which in the case of plant pathogens, are collectively necessary to modulate host defense. The type III secretion system is not a mechanism exclusive to pathogens, however, as many strains of commensal Pseudomonas fluorescens and mutualistic rhizobia demonstrably require a type III secretion system to interact with their host plants. The work presented in this thesis describes genome-enabled approaches for characterizing type III effector genes across the range of plant symbiosis. Using high-throughput sequencing technology, draft genome sequences were generated for the plant pathogen, Xanthomonas hortorum pv. carotae M081, the plant commensal, Pseudomonas fluorescens WH6, and six strains from the plant mutualists Sinorhizobium fredii and Bradyrhizobium japonicum. Analyses of the draft genome sequences and publicly available finished sequences contributed insights into mechanisms of host-association and to increasing the inventory of type III effector sequences as well as developing methods directly applicable for agriculture. Finally, characterization of the genetic diversity of type III effectors from rhizobia shows that collections of type III effectors of mutualists are static, with little diversity in content and sequence variation. This represents the first comprehensive cataloging of type III effector from species of mutualistic bacteria and the first to provide evidence for purifying selection of this important class of genes. / Graduation date: 2012

<p> The plant cytoskeleton is commonly considered a vital component of cell growth and development; however, it also plays a critical role in plant immunity. During plant immunity, the cytoskeleton orchestrates rapid and precise immune-associated processes. For instance, the cytoskeleton mobilizes and orients the movement of organelles, proteins, and chemical signaling. To counter plant immunity, bacterial pathogens deliver virulence proteins, known as T3Es (type III effectors), into plant cells through a needle-like apparatus called the type III secretion system (T3SS). A novel T3E, called RipU, interacts with the cytoskeleton. Data has shown that RipU co-localizes with cytoskeletal markers in tobacco leaves. Ectopic expression of RipU can suppress PTI responses like ROS bursts or seedling growth inhibition. Tomato plants inoculated with <em>Rs</em> K60 lacking RipU showed less wilting and root colonization, suggesting that RipU plays a role in pathogenesis and virulence. Furthermore, inducible expression of RipU in Arabidopsis dramatically alters plant development. These plants have wavy roots, branching root hairs, and underdeveloped true leaves. Our results suggest that by targeting the cytoskeleton, RipU contributes to <em>Rs</em> K60s pathogenicity and virulence. </p>