[ES] La Biología Sintética de Plantas tiene como objetivo rediseñar las plantas para que adquieran características y funcionalidades novedosas a través de circuitos reguladores ortogonales. Para lograr este objetivo, se deben desarrollar nuevas herramientas moleculares con la capacidad de interactuar con factores endógenos de manera potente y específica. CRISPR/Cas9 surgió como una herramienta prometedora que combina la capacidad personalizable de unión al DNA, a través de la versión catalíticamente inactivada de la proteína Cas9 (dCas9), con la posibilidad de anclar dominios autónomos de activación transcripcional (TADs) a su estructura para lograr una regulación específica de la expresión génica. Los activadores transcripcionales programables (PTAs) pueden actuar como procesadores específicos, ortogonales y versátiles para el desarrollo de nuevos circuitos genéticos en las plantas. En busca de dCas9-PTA optimizados, se llevó a cabo una evaluación combinatoria de diferentes arquitecturas dCas9 con un catálogo de varios TAD. La mejor herramienta resultante de esta comparación, denominada dCasEV2.1, se basa en la estrategia scRNA y la combinación de los dominios de activación EDLL y VPR con un bucle multiplexable gRNA2.1, que es una versión mutada del gRNA2.0 descrito previamente. En este trabajo, el activador programable dCasEV2.1 demostró ser una herramienta potente y específica, logrando tasas de activación más altas que otras estrategias dCas9 disponibles en plantas. Se observaron tasas de activación sin precedentes dirigidas a genes endógenos en N. benthamiana, acompañadas de una estricta especificidad en todo el genoma, lo que hace que esta herramienta sea adecuada para la regulación estricta de redes reguladoras complejas. Como prueba de concepto, se diseñaron cuatro programas de activación para distintas ramas de la ruta de los flavonoides, buscando obtener enriquecimientos metabólicos específicos en hojas de N. benthamiana. El análisis metabólico de las hojas metabólicamente reprogramadas mediante dCasEV2.1 reveló un enriquecimiento selectivo de los metabolitos diana y sus derivados glicosilados, que se correlacionaron con el programa de activación empleado. Estos resultados demuestran que dCasEV2.1 es una herramienta eficaz para la ingeniería metabólica y un componente clave en los circuitos genéticos destinados a reprogramar los flujos metabólicos. Finalmente, basándonos en dCasEV2.1, desarrollamos un sistema optimizado de regulación de genes inducidos por virus (VIGR) que utiliza un vector Potato Virus X (PVX) para el suministro de los programas de activación CRISPR codificados con gRNA. Este enfoque permite controlar el transcriptoma de la planta a través de una aplicación sistémica basada en aerosol de componentes CRISPR a plantas adultas. El nuevo sistema PVX-VIGR produjo una fuerte activación transcripcional en varios genes diana endógenos, incluidos tres factores de transcripción MYB-like seleccionados. Las activaciones específicas de MYB condujeron a perfiles metabólicos distintivos, demostrando que las aplicaciones potenciales de la herramienta dCasEV2.1 en plantas incluyen la obtención de perfiles metabólicos personalizados utilizando un suministro basado en aerosol de instrucciones de reprogramación transcripcional codificadas por gRNA. En resumen, esta tesis proporciona herramientas novedosas para la activación transcripcional fuerte, ortogonal y programable en plantas, con una caja de herramientas ampliada para el suministro de los programas de activación. / [CA] La Biologia Sintètica de Plantes té com objectiu redissenyar les plantes per que obtinguen característiques i funcionalitats innovadores mitjançant circuits reguladors ortogonals. Per arribar a aquest objectiu, s'han de desenvolupar noves ferramentes moleculars amb la capacitat d'interactuar amb factor endògens d'una manera potent i específica. CRISPR/Cas9 va sorgir com una ferramenta prometedora que combina la capacitat personalitzable d'unió al DNA, mitjançant la versió catalíticament inactivada de la proteïna Cas9 (dCas9), amb la possibilitat de fixar dominis autònoms de activació transcripcional (TADs) a la seua estructura per aconseguir una regulació específica de la expressió gènica. Els activadors transcripcionals programables (PTAs) poden actuar com a processadors específics, ortogonals i versàtils per al desenvolupament de nous circuits genètics a les plantes. Buscant dCas9-PTA optimitzats, es va realitzar una avaluació combinatòria de distintes arquitectures dCas9 amb un catàleg de diversos TAD. La millor ferramenta segons aquesta comparació, anomenada dCasEV2.1, es basa en la estratègia scRNA i la combinació del dominis d'activació EDLL i VPR amb un bucle multiplexable gRNA2.1, que es una versió mutada del gRNA2.0 descrit prèviament. En aquest treball, el activador programable dCasEV2.1 es va mostrar com una ferramenta potent i específica, aconseguint nivells d'activació majors que altes estratègies dCas9 disponibles en plantes. Es van observar taxes d'activació sense precedents dirigides a gens endògens en N. benthamiana, junt a una estricta especificitat en tot el genoma, indicant que aquesta ferramenta és adequada per a la regulació estricta de xarxes reguladores complexes. Como proba de concepte, se van dissenyar quatre programes d'activació per a diferent branques de la ruta dels flavonoides, cercant obtenir enriquiments metabòlics específics en fulles de N. benthamiana. L'anàlisi metabòlic de les fulles metabòlicament reprogramades mitjançant dCasEV2.1 va revelar un enriquiment selectiu del metabòlits diana i els seus derivats glicosilats que es correlacionen amb el programa d'activació emprat. Aquests resultats demostren que dCasEV2.1 és una ferramenta eficaç per a l'enginyeria metabòlica i un component clau als circuits genètics destinats a reprogramar els fluxos metabòlics. Finalment, en base a dCasEV2.1, desenvoluparem un sistema optimitzat de regulació de gens induïts per virus (VIGR) que utilitza un vector Potato Virus X (PVX) per al subministrament dels programes d'activació CRISPR codificats amb gRNA. Aquesta aproximació permet controlar el transcriptoma de la planta mitjançant l'aplicació sistèmica basada en aerosol de components CRISPR a plantes adultes. El nou sistema PVX-VIGR va produir una gran activació transcripcional en diversos gens diana endògens, inclosos tres factors de transcripció MYB-like seleccionats prèviament. Les activacions específiques de MYB conduïren a perfils metabòlics distintius, demostrant que les aplicacions potencials de la ferramenta dCasEV2.1 en plantes inclouen la obtenció de perfils metabòlics personalitzats emprant un subministrament basat en aerosol de instruccions de reprogramació transcripcional codificades per gRNA. En resum, aquesta tesis proporciona noves ferramentes per a l'activació transcripcional forta, ortogonal i programable en plantes, amb una caixa de ferramentes eixamplada per al subministraments dels programes d'activació. / [EN] Plant Synthetic Biology aims to redesign plants to acquire novel traits and functionalities through orthogonal regulatory circuits. To achieve this goal, new molecular tools with the capacity of interacting with endogenous factors in a potent and specific manner must be developed. CRISPR/Cas9 emerged as promising tools which combine a customizable DNA-binding activity through the catalytically inactivated version of Cas9 protein (dCas9) with the possibility to anchor autonomous transcriptional activation domains (TADs) to its structure to achieve a specific regulation of the gene expression. The Programmable Transcriptional Activators (PTAs) could act as specific, orthogonal and versatile processor components in the development of new genetic circuits in plants. In search for optimized dCas9-PTAs, a combinatorial evaluation of different dCas9 architectures with a catalogue of various TADs was performed. The best resulting tool of this comparison, named dCasEV2.1, is based on the scRNA strategy and the combination of EDLL and VPR activation domains with a multiplexable gRNA2.1 loop, which is a mutated version of the previously described gRNA2.0. In this work, the dCasEV2.1 programable activator was proved to be a strong and specific tool, achieving higher activation rates than other available dCas9 strategies in plants. Unprecedented activation rates were observed targeting endogenous genes in N. benthamiana, accompanied by strict genome-wide specificity that makes this tool suitable to perform a tight regulation of complex regulatory networks. As a proof of concept, a design of four activation programs to activate different branches of the flavonoid pathway and obtain specific metabolic enrichments in N. benthamiana leaves was performed. The metabolic analysis on the dCasEV2.1 metabolically reprogrammed leaves revealed a selective enrichment of the targeted metabolites and their glycosylated derivatives that correlated with the activation program employed. These results demonstrate that dCasEV2.1 is a powerful tool for metabolic engineering and a key component in genetic circuits aimed at reprogramming metabolic fluxes. Finally, based on dCasEV2.1, we developed an optimized Viral Induced Gene Regulation (VIGR) system that makes use of a Potato Virus X (PVX) vector for the delivery of the gRNA-encoded CRISPR activation programs. This approach offers a way to control the plant transcriptome through a spray-based systemic delivery of CRISPR components to adult plants. The new PVX-VIGR system led to strong transcriptional activation in several endogenous target genes, including three selected MYB-like transcription factors. Specific MYB activations lead to distinctive metabolic profiles, showing that the potential applications of the dCasEV2.1 tool in plants include the obtention of custom metabolic profiles using a spray-based delivery of gRNA-encoded transcriptional reprogramming instructions. In sum, this thesis provides novel tools for strong, orthogonal and programmable transcriptional activation in plants, with an expanded toolbox for the delivery of the activation programs. / Selma García, S. (2022). Development of CRISPR-based programmable transcriptional regulators and their applications in plants [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/185046 / TESIS

La moléculture végétale est une alternative abordable et sécuritaire pour la production de protéines recombinantes d’intérêt clinique. Cependant, ces protéines sont souvent sujettes à la dégradation par les protéases endogènes dans les cellules végétales. Plusieurs stratégies ont été mises en place pour contrer ce phénomène, incluant notamment la co-expression d’inhibiteurs de protéases compagnons. Peu de données ont décrit toutefois comment la physiologie de la plante hôte, associée en particulier à son développement, a un impact sur l’expression et la protection d’une protéine d’intérêt. Dans ce projet, nous avons évalué les activités de protéases de types cystéine et aspartate dans des feuilles agroinfiltrées de la plante hôte Nicotiana benthamiana, en fonction de leur stade de développement. Nous démontrons que l’expression de l’inhibiteur SlCYS8 de tomate, actif contre les protéases de type cystéine, permet d’augmenter d’environ 40% le rendement en anticorps monoclonal C5-1, notre protéine modèle, dans les feuilles jeunes et matures où les activités protéolytiques sont moindres. Ces résultats prometteurs sur le plan appliqué font ressortir, en revanche, la complexité des processus biochimiques en cause et la pertinence de développer des stratégies complémentaires pour augmenter les teneurs en protéine recombinante. Dans cette optique, une nouvelle approche basée sur une diversion dirigée du métabolisme de défense de la plante hôte a été explorée. Nous démontrons qu’une activation du sentier de l’acide jasmonique induit dans les feuilles la production de protéines de stress, incluant des inhibiteurs de protéases de classes fonctionnelles variées; et une diminution de la teneur en RuBisCO, un contaminant majeur pendant la purification des protéines recombinantes. Sur cette base, nous avons adjoint à notre procédure de transfection un prétraitement des plantes au jasmonate de méthyle, une forme volatile de l’acide jasmonique. Ce prétraitement a permis d’une part de réduire considérablement les teneurs en RuBisCO dans les feuilles, et de doubler d’autre part le taux d’expression et le rendement en anticorps C5-1. Nos données appuient l’utilité éventuelle d’une manipulation du métabolisme de défense sur les rendements en protéine recombinante, complémentaire aux approches basées sur la co-expression d’inhibiteurs de protéases recombinants. / Plant molecular farming is an affordable and safe alternative to conventional expression animal and microbial systems for the production of clinically-useful recombinant proteins. However, these proteins are often susceptible to degradation by endogenous proteases of the host plant cells. Several strategies have been described to counter degradation processes including the co-expression of companion protease inhibitors. Few data, however, were available describing how the host plant’s physiology, especially its developmental stage, could impact the expression and protection of a clinically useful heterologous protein. In this study, we assessed changes in the activity of cysteine and aspartate proteases in the widely adopted expression host Nicotiana benthamiana, as a function of leaf age. We demonstrate that the expression of a tomato cysteine protease inhibitor, SlCYS8, allows to increase by nearly 40% the total yield of a model protein, the blood-typing C5-1 monoclonal antibody, in young and mature leaves where proteolytic activities are lower. Our results, while promising in practice, highlighted on the other hand the complexity of biochemical processes involved and the relevance of developing additional strategies to boost recombinant protein accumulation in planta. Towards this end, a new approach based on a deliberate diversion of the host plant defense metabolism was explored. We show that an activation of the jasmonic acid pathway in leaves induces the production of stress-related proteins, including protease inhibitors of various functional classes; and a significant decrease in the content of RuBisCO, a major contaminant during the purification of recombinant proteins. Based on this we included in our transfection procedure a pretreatment of plants with methyl jasmonate, a volatile form of jasmonic acid. This pretreatment significantly reduced RuBisCO levels in leaves, concomitant with a more than twofold increase of C5-1 yield in mature leaves. Our data highlight, overall, the potential of manipulating the host plant’s defense metabolism to increase heterologous protein yields, in complement to current protein protection strategies involving the co-expression of recombinant protease inhibitors.

Les systèmes d’expression végétaux sont utilisés couramment pour la production hétérologue de protéines recombinantes complexes. Des contraintes biochimiques dans le système de sécrétion cellulaire, comme l’abondance de protéases peu spécifiques ou des variations de pH d’un organite à l’autre, compromettent toutefois l’expression de plusieurs protéines d’intérêt. Des approches ont été développées pour améliorer l’environnement intracellulaire dans la plante hôte de manière à accroître la qualité et le rendement des protéines sécrétées. Dans ce projet, nous avons évalué l’impact de l’homéostasie du pH dans le système de sécrétion cellulaire des feuilles du Nicotiana benthamiana sur l’expression et la stabilité des protéines recombinantes. Nous démontrons le potentiel du canal ionique M2 du virus de l’Influenza comme nouvel outil pour augmenter le pH des compartiments acides du système de sécrétion cellulaire, une approche éventuellement utile pour la stabilisation des protéines sensibles aux milieux acides. En lien avec l’influence bien documentée du pH sur l’activité des protéases cellulaires, nous montrons ensuite qu’une modification du pH induite par l’expression du canal M2 influence les profils de dégradation de protéines de fusion sensibles à la protéolyse, des observations qui confirment l’impact du pH sur l’activité protéolytique des cellules végétales et qui suggèrent le potentiel du canal ionique M2 comme protéine accessoire pour augmenter la stabilité et le rendement des protéines recombinantes in planta. Finalement, nous abordons l’impact du canal ionique M2 sur l’expression des protéines endogènes à l’échelle de la cellule. Nous démontrons qu’une altération du pH dans le système de sécrétion en réponse à l’expression du canal ionique a des effets étendus sur le protéome foliaire, affectant la teneur de protéines retrouvées dans plusieurs compartiments cellulaires incluant les chloroplastes, le cytosol et la vacuole. Nous rapportons aussi l’établissement d’un ‘protéome hybride’ dans les plantes exprimant M2, composé de protéines caractéristiques aussi bien de plantes témoins non infectées que de plantes agroinfectées exprimant activement des protéines de défense. En résumé, nos données mettent en évidence le rôle de l’homéostasie du pH sur le protéome des cellules végétales et l’impact significatif du gradient de pH dans le système de sécrétion cellulaire sur la stabilité et le rendement des protéines recombinantes sensibles à l’acidité ou à la protéolyse. / Plant expression systems are commonly used for the heterologous production of complex recombinant proteins. However, biochemical conditions in the plant cell secretory pathway, such as the presence of poorly-specific proteases or pH variations from one organelle to another, impair the expression of several potentially useful proteins. Approaches have been developed to improve the cellular environment of the host plant in such a way as to increase the quality and yield of secreted recombinant proteins. In this project, we assessed the impact of pH homoeostasis in the leaf cell secretory pathway of wild tobacco Nicotiana benthamiana on the expression and stability of recombinant proteins. We demonstrate the potential of Influenza virus proton channel M2 as a new tool to increase pH in acidic compartments of the cell secretory pathway, eventually useful to stabilize acid-labile recombinant proteins. In line with the well-established influence of pH on cell protease activities, we then show that pH modification induced by the expression of the M2 channel influences the degradation profile of fusion proteins susceptible to proteolysis, thus confirming the impact of pH on protease activities in plant cells and highlighting the potential of M2 as an accessory protein to increase the stability and yield of recombinant proteins in planta. Finally, we describe the impact of the M2 proton channel on the expression of endogenous proteins at the cellular scale. We show that pH alteration in the secretion system upon M2 expression has cell-wide effects on the leaf proteome, affecting the content of proteins found in various cell compartments including the chloroplast, the cytosol and the vacuole. We report the establishment of a ‘hybrid proteome’ in leaf cells expressing the proton channel, composed of protein clusters characteristic of both control, non-infected plants and agroinfected plants actively expressing defense-related proteins. Overall, our data highlight the central role of pH homeostasis on the proteome of plant cells and the strong impact of pH gradient in the cell secretory pathway on the stability and yield of acidic pH-labile and protease-susceptible recombinant proteins.

Pheromone lures and trap crops are appealing pest management tools that use insect and/or plant volatiles to reduce pest populations on crops of interest. Generating pheromone-emitting trap plants may allow for a continuing and highly-specific attraction of insect pests without repeated and costly application of synthetic pheromones. These trap plants may also be used to develop area-wide pest management strategies. As a proof-of-principle study we tested the possibility of producing the pheromone of the crucifer flea beetle Phyllotreta cruciferae in transgenic plants. P. cruciferae is an important pest of Brassica crops. In the presence of a host plant, males emit an aggregation pheromone, which attracts both males and females. Himachaladiene, a sesquiterpene, has been identified as a key component of the aggregation pheromone of P. cruciferae. In a close relative, Phyllotreta striolata, the compound is synthesized by a two-step pathway with an isoprenyl diphosphate synthase (PsIDS3) making (Z,E)-farnesyl diphosphate (FPP), which is converted by a terpene synthase (PsTPS1) to himachaladiene. Transient transformation of N. benthamiana with PsIDS3-TPS1 co-localized to the plastid resulted in the emission of himachaladiene and other known PsTPS1 products. Daily emissions of himachaladiene were approximately 1 µg per plant, which is six-fold higher than emissions from individual male flea beetles. Stable transformation of Arabidopsis thaliana with the same vector construct resulted in transgenic plants that expressed PsTPS1 and PsIDS3 transcripts, but no himachaladiene or other PsTPS1 products were present in volatile collections or leaf extracts of these plants. Moreover, no PsTPS1 enzyme activity was observed, indicating that post-transcriptional/translational effects prevent proper expression or targeting of functional PsIDS3 and/or PsTPS1 proteins in A. thaliana. Overall, this study demonstrates that the key component of the P. cruciferae aggregation pheromone, himachaladiene, can be transiently produced and emitted in a plant system at rates that are biologically relevant for insect attraction. However, further work is required for the stable production of the pheromone in plants. In addition, preliminary results are presented for the development of simple two-choice arenas that may allow for assessment of the movement of beetles toward host plant leaf tissue. This work can inform future efforts in developing methods for the economic production of himachaladiene in a plant system or the establishment of transgenic plants for the production and deployment of himachaladiene in a field setting. / Master of Science / The crucifer flea beetle is an important pest of vegetable and oilseed Brassica crops such as broccoli, cabbage and canola. Feeding by beetles has its greatest impact on crop health and yield in the early spring, when adult beetles emerge from overwintering sites and feed on newly- emerging Brassica seedlings. Currently these insects are controlled using broad spectrum insecticides. A general awareness of the negative aspects of insecticides drives the search for alternative pest management strategies that could diversify our management strategies and reduce reliance on insecticides. Previous work has found that the crucifer flea beetle navigates to its host plants, in part, through plant-emitted volatiles. After locating the plant host, males emit a volatile aggregation pheromone that when blended with host plant volatiles increases attraction. Here work towards the development of a specialized trap crop is presented. Plants were engineered to emit a key component of the crucifer flea beetle aggregation pheromone. In an engineered non-host plant, Nicotiana benthamiana, transient production of the aggregation pheromone was established. However, in an engineered Brassica plant, Arabidopsis thaliana, no aggregation pheromone was detected despite evidence of the presence and expression of the required biosynthetic genes for its production. A discussion on alternative engineering strategies for A. thaliana is presented. In addition, preliminary results are presented for the development of a simple behavior assay to assess the attraction of beetles toward different smells. This work can inform future efforts aimed at developing methods for the economic production of the aggregation pheromone in a plant system or the establishment of plants for the production and deployment of the aggregation pheromone in a field setting.

Pepper and tomato, as two common, popular, and important vegetables grown worldwide, provide human beings with high quality fruit of flavor and aroma, and a high concentration of vitamins and antioxidants. Pepper and tomato production is frequently affected by various pathogens, including nematodes, fungi, and bacteria. Among those phytopathogens, Xanthomonas euvesicatoria (Xe) causes a severe bacterial spot (BS) disease on pepper and tomato. The BS disease could cause a loss of approximately 10% of the total crop yield in the world. Breeding tomato and pepper cultivars with improved BS disease resistance is one of the most important breeding goals. A better understanding of the virulence mechanism of Xe could help breeders design new strategies for resistance breeding. In this dissertation, we characterized the virulence and avirulence functions of four Xe Type Three Secretion Effectors (T3Es): Xe-XopQ, Xe-XopX, Xe-XopN, and Xe-avrRxo1. Xe-XopQ is a Xe T3E that functions as a determinant of host specificity. Here, we further explored the virulent and avirulent functions of Xe-XopQ. We identified another T3E Xe-XopX that could interact with XopQ and subsequently elicit the hypersensitive response in N. benthamiana in the Agrobacterium-mediated transient assay and Xe-mediated disease assay. The interaction is confirmed by bimolecular fluorescence complementation, co-immunoprecipitation and split luciferase assay. Intriguingly, we also revealed that XopX also interacts with multiple Xe T3Es including AvrBS2, XopN, XopB, and XopD in the co-IP assay. The virulent and avirulent functions of XopQ and AvrBS2 are compromised in the absence of Xe-XopX. Since XopX is conserved in diverse Xanthomonas spp., we speculate that Xe-XopX may have a general role required for the pathogenesis of Xe. Xe-XopN has been reported to be a T3E with virulence function via targeting host defense-related proteins, including atypical receptor-like kinase named TARK1 and a 14-3-3 protein to suppress the PAMPs (pathogen-associated molecular patterns) triggered immunity upon Xe colonization of tomato. In this study, we revealed additional virulence mechanisms of Xe-XopN, where Xe-XopN, is required for triggering the water-soaking symptom on Nicotiana benthamiana and pepper plants infected with Xe. In addition, we identified that XopN interacts with a transcription factor, NbVOZ, and represses the expression of NPR1, a key component of the basal defense. Therefore, XopN has a role in maintaining a water-affluent environment for better replication of Xe, and it can also interact with NbVOZ1/2 to regulate plant immunity. AvrRxo1, a T3E of Xanthomonas oryzae pv. oryzicola (Xoc), was previously identified to function as a NAD kinase. Here, we characterized a Xe T3E, Xe avrRxo1, that is a functional homologue of AvrRxo1, which is required for the full virulence of Xe to colonize the pepper and N. benthamiana plants. Overexpression of AvrRxo1 in bacterial or plant cells is toxic. Our group previously demonstrated AvrRxo1-ORF2 functions as an antitoxin that binds to AvrRxo1 to suppress its toxicity. In this study, we identified Xe4429 as the homologue of AvrRxo1-ORF2, which could interact with Xe-avrRxo1 to suppress its toxicity. We also revealed that Xe4429 could bind to the promoter of Xe-avrRxo1 and suppress its transcription. Therefore, we found Xe4429 encodes protein functions as an antitoxin and a transcription repressor in Xe bacterial cells. / Doctor of Philosophy / Peppers and tomatoes are two of the most important vegetables grown worldwide, providing humans with high quality of flavor and aroma, vitamins, and antioxidants. The pepper and tomato production is frequently threatened by various pathogens, including nematodes, fungi, and bacteria. Among those phytopathogens, Xanthomonas euvesicatoria (Xe) causes a severe bacterial spot (BS) disease on peppers and tomatoes. The BS disease can be easily identified due to the appearance of the dark, irregular, water-soaked areas on the leaf, which can cause approximately 10% loss of the total yield of peppers and tomatoes. Breeding tomato and pepper cultivars with improved BS disease resistance is one of the most critical breeding goals. A better understanding of the virulence mechanism of Xe could help breeders to design new strategies for resistance breeding. In my seminar, I will discuss the virulence and avirulence functions of Xe type three secretion (T3S) effectors: Xe XopN, Xe XopQ, and Xe XopX. In my study, I identified Xe XopN is a key factor that regulates the development of the water-soaking symptom on pepper plants infected with Xe. In addition, we revealed Xe XopN interacts with a transcription factor NbVOZ to regulate the expression of NbNPR1 and PR1 genes expression, which may also contribute to the development of water-soaking phenotype. In addition, I identified that Xe XopN could interact with a transcription factor, NbVOZ, and represses the expression of NbNPR1, a key component of the basal defense, and the pathogenesis-related gene PR1. Therefore, Xe XopN has a role in regulating a water-affluent environment to promote bacterial proliferation in the infected plant tissue. Xe XopQ is a Xe T3S effector that functions as a determinant of host specificity. In my study, I identified another T3S effector Xe XopX that could interact with Xe XopQ to trigger the defense response in Nicotiana benthamiana. I also confirmed Xe XopQ physically interacts with Xe XopX inside of plant cells by using bimolecular fluorescence complementation, co-immunoprecipitation and split luciferase assay. Intriguingly, Xe XopX could also interact with multiple Xe T3Es including AvrBS2 in a co-IP assay. The virulence and avirulent functions of Xe XopQ and AvrBS2 are compromised in the absence of Xe XopX.

Bacterial fruit blotch (BFB) of cucurbits is caused by Acidovorax citrulli, a Gram-negative seedborne bacterium that can cause up to 100% fruit yield losses in the field. Currently, BFB is a major problem for the cucurbits industry worldwide. Thus far, attempts to identify resistance in cucurbit germplasm for controlling BFB have been unsuccessful. Despite the importance of the disease, little is known about the molecular mechanisms of A. citrulli pathogenicity, due to a lack of molecular tools for studying the A. citrulli/cucurbit interaction. The genomic sequence of A. citrulli strain AAC00-1 has been determined, and the components of type III secretion system have been identified. The goal of this research was to develop molecular tools for studying the BFB disease. Nineteen putative type III effector genes were cloned from two representative A. citrulli strains (AAC00-1 and M6). The distribution of 19 type III effectors among A. citrulli strains, collected worldwide, was studied. A novel Gateway-compatible binary vector was developed for transient expression of A. citrulli type III effectors genes in planta. A set of modified vectors for marker-exchange mutagenesis in A. citrulli were constructed. The model plant species Nicotiana benthamiana was found to be susceptible to A. citrulli, while Nicotiana tabacum was resistance to A. citrulli, so therefore could carry nonhost resistance genes. Two T3S effectors, Aave1548 and Aave2166, triggered water soaking-like cell death in N. benthamiana, but HR-like cell death in N. tabacum. Bacterial mutagenesis and in planta disease assay confirmed that both Aave1548 and Aave2166 have significant virulence contributions to A. citrulli in N. benthamiana plant and melon seeds. Aave2166 encodes a putative acetyltransferase that belongs to the YopJ super family, which is conserved in both animal and plant pathogenic bacteria. Wild type but not the putative catalytic mutant (C232A) of Aave2166 can trigger cell death phenotype in N. benthamiana and N. tabacum. N. benthamiana yeast two-hybrid cDNA library screening using Aave2166 identified six N. benthamiana proteins/peptides which specifically interacted with Aave2166. Further characterization of these Aave2166 interactors may allow us to understand the virulence mechanism provided by Aave2166. The identification of nonhost resistance genes that can recognize Aave2166 and other type III effectors may help to develop novel strategies to control BFB disease of cucurbit. / Ph. D.

Soil and root microbial communities have been studied for decades, and the incorporation of high-throughput techniques and analysis has allowed the identification of endophytic/non-culturable organisms. This has helped characterize and establish the core microbiome of many model plant species which include underground and aboveground organs. Unfortunately, the information obtained from some of these model plants is not always transferable to other agronomic species. In this project, we decided to study the microbiome of the Nicotiana genus because of its importance in plant physiological and plant-microbe interactions studies. The data obtained was used as baseline information that allowed us to better understand the effect of microbial inoculums on the assembly of the microbiome of the plant. We analyzed 16s rRNA amplicons to survey the microbiome in different plant organs and rhizosphere from four different species. Bacterial strains evaluated were screened for a consistent reduction or improvement in plant growth. Four bacterial strains were tested and used as seed inoculum (Lf-Lysinobacillus fusisormis, Ms –Micrococcus sp., Bs–Bacillus sp., Bc–Bacillus cereus). Bs and Bc inoculants caused plant growth promotion, and in contrast Ms caused retarded growth, while Lf acted as a neutral or non-inducing phenotype strain. Data supported that microbial inoculum used as seed treatment caused systemic changes in the host plant microbiome. Functionality of the inoculum was studied and the response in plant growth was linked to hormonal changes (evaluated in the plant and in the bacterial strains). Gene expression analysis using a genome-scale approach revealed that genes that could possibly be involved in stress response are down-regulated for Bc and Bs treatments and up-regulated for Ms. Flexibility variability of the inoculum was also evaluated to have a better understanding of the main factors involved in the promotion or suppression of growth, and possibly its effect in following generations. In summary, the findings of this project support that the plant functional microbiome responds to exogenous stimulation from abiotic and biotic factors by adapting endogenous hormone responses.

ARGONAUTE proteins (AGOs) are generally accepted as key components of the post transcriptional gene silencing mechanism, also involved in plant antiviral defense. Except for reports on the antiviral roles of AGO1, AGO2 and AGO7 in Arabidopsis, the exact roles played by the individual AGOs in other plant species are largely unknown. This research focused on the identification and characterization of AGOs involved in antiviral RNAi response to various viruses in N. benthamiana. Based on the temporal and spatial distribution of AGO transcripts in 3 and 8-week old plant root, stem and leaf tissues, expressions of NbAGO mRNAs were found to vary with age and tissue specificity. Plant endogenous AGO mRNAs were knocked down through virus induced gene silencing techniques using the Tobacco rattle virus vector system and posteriorly challenged with a GFP-chimeric virus construct deficient of a silencing suppressor. Unlike in control non-silenced plants, the Tomato bushy stunt virus construct deficient of its P19 silencing suppressor was consistently seen to exhibit a strong fluorescence on N. benthamiana plants silenced for NbAGOs 2 and X. Similar results were also obtained upon silencing of NbAGO2 using hairpin vector techniques. Comparable observations were also made when Tobacco mosaic virus GFP constructs were agroinfiltrated on NbAGO2 silenced plants further hinting the antiviral defense roles played by these AGOs. Agroinfiltration of Foxtailmosaic virus, Sunnhemp mosaic virus, and Turnip crinkle virus GFP chimeric constructs on NbAGO2 silenced N. benthamiana plants, however did not result in accumulation of GFP indicating the AGO antiviral defense specificity to TBSV and TMV. The results also hinted at a role for AGO7. Collectively my findings suggest that the expression of AGOs in N. benthamiana is tissue and age dependent, and that unlike in the model plant Arabidopsis where the main antiviral AGO is thought to be AtAGO1; in N. benthamiana, NbAGOs 2 and X seem to be involved in an antiviral defense role against TBSV and TMV with other AGOs perhaps contributing.

Thesis (MSc)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: Almost all processes during the life of a plant are affected by the environment. Changes in phytohormone, metabolite and protein levels follow in response to changes in the environment. Plant growth promoting substances can stimulate changes at these levels to facilitate increased plant growth and yields above what the plant would normally establish. In this study, the effects of two growth promoting substances, smoke water (SW) derived from bubbling smoke from the burning of plant material through water, and a synthetic strigolactone analogue, GR24, on plant growth and architecture, as well as the proteome and metabalome of salt stressed Nicotiana benthamiana seedlings were investigated. Physiological studies were conducted to identify the effects of the growth substances on salt stressed seedlings in a tissue culture system. Under non-stress conditions, SW treatment increased seedling fresh mass, root length and leaf area. Under salt stress conditions (100 mM and 150 mM NaCl), SW increased fresh mass, root length, leaf number and lateral root number significantly. Under non-stress conditions, GR24-treated seedlings showed increased fresh mass, leaf number and area and root length. When GR24-treated seedlings were placed under salt stress, the seedlings showed significant increases in fresh mass, leaf number and lateral root number, but only marginal increases in root length and leaf area. Despite these similarities, slight differences were observed in the metabolomes and proteomes of smoke water and GR24-treated seedlings, both with and without the addition of salt stress. Relatively few of the differentially expressed proteins could be identified with the instruments available. Changes in the metabolome indicated that photoassimilation and photosynthesis could be affected in response to smoke water and GR24 treatment. Our results suggest that smoke water and GR24 both promote growth under salt stress conditions in seedlings and we furthermore conclude that, although there are distinct overlaps between treatments, this is accomplished via slightly different mechanisms. / AFRIKAANSE OPSOMMING: Gedurende ‘n plant se lewe word omtrent alle prosesse deur die omgewing geaffekteer. Veranderinge in die omgewing word gevolg deur veranderinge in hormoon, metaboliet en protein vlakke. Plant groei stimulante affekteer hierdie vlakke om plant groei en -opbrengs na bo normalle vlakke te verhoog. In hierdie studie word die effek van twee groei stimulante, rook water verkry deur rook van plant materiaal deur water te borrel en ‘n sintetiese strigolaktoon, GR24, ondersoek op ‘n morfologiese, metaboliese en ‘n proteomiese vlak in Nicotiana benthamiana saailinge. ’n Studie is onderneem om die veranderinge as gevolg van die onderskeie groei stimulante te ondersoek in ‘n weefsel kultuur sisteem. Rook water het onder normale groei omstandighede vars en droeë massa, blaar aantal asook wortel en blaar lengte verhoog. Rook water het na sout behandeling (100 en 150 mM NaCl) steeds vars massa, wortel lengte, blaai aantal en laterale wortel aantal beduidend verhoog in vergelyking met die sout stres kontrole. Behandeling met GR24 het ook vars massa, wortel lengte, blaar aantal en grootte verhoog en onder sout stres met GR24 is ‘n beduidende vergroting opgemerk in vars massa, blaar grootte en laterale wortel aantal. Ongeag van die veranderinge in groei is klein verskille opgemerk in die metaboliet en protein studies. Net ‘n paar proteine kon positief geidentifiseer word met die apparaat beskikbaar. Verandering in die metaboloom wys na veranderinge in fotoassimilasie en fotosintese in reaksie tot rook water en GR24. Hierdie resultate lei tot die gevolgtrekking dat rook water en GR24 beide groei verbeter in saailing behandel met sout en ook dat alhoewel daar sekere ooreenkomste is tussen die reaksies as gevolg van die plant groei stimulante, dit wel geskiet deur geringe verskillende meganismes.

Orientador: Tatiane Maria Rodrigues / Resumo: A morfologia, histoquímica e ultraestrutura dos tricomas glandulares têm sido estudadas em muitas espécies vegetais. Entretanto, alguns aspectos têm sido pouco abordados, como o envolvimento do citoesqueleto na morfologia e funcionamento glandular. Estudo recente demonstrou a relação entre a predominância de filamentos de actina e microtúbulos em células secretoras e a composição da secreção em tricomas glandulares. Além disso, pesquisas têm comprovado o envolvimento dos elementos do citoesqueleto na origem e manutenção dos tricomas tectores em plantas, sem informações para os tricomas glandulares. Sabe-se que o funcionamento do citoesqueleto está relacionado com a disponibilidade do cálcio, sendo que baixas concentrações desse íon podem prejudicar processos modulados por microtúbulos e actina. Apesar da presença de tricomas glandulares representar um caráter constitutivo em diversas espécies vegetais, fatores exógenos podem influenciar o desenvolvimento e o funcionamento glandular. Estudos têm mostrado que o ataque de herbívoros induz a formação de tricomas glandulares, levando a produção de substâncias com potencial repelente ou inseticida. Os objetivos desse trabalho foram investigar o papel do citoesqueleto na morfogênese e funcionamento de tricomas glandulares e no transporte lipídico em células secretoras de óleo, além de investigar a influência da herbivoria no desenvolvimento e funcionamento de tricomas glandulares. Foram estudadas duas espécies de Lamiaceae (Hyptis v... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The morphology, histochemistry and ultrastructure of glandular trichomes have been studied in many plant species. However, some aspects have been poorly approached, such as the involvement of the cytoskeleton on the gland morphology and functioning. Recent study demonstrated a relation between the predominance of actin filaments and microtubules in secretory cells and the secretion composition in glandular trichomes. In addition, researches have proven the involvement of the cytoskeletal elements in the origin and maintenance of non-glandular trichomes in plants, with no information for glandular trichomes. It is known that the cytoskeleton functioning is related with calcium availability and that low concentration of this ion can harm process modulated by actin filaments and microtubules. Despite the presence of glandular trichomes is a constitutive character in several plant species, exogenous factors can influence their development and functioning. Studies have showed that herbivore attacks induce the glandular trichomes formation, leading to the production of substances with repellent and insecticide potential. This work aimed to investigate the role of cytoskeleton in the glandular trichome morphogenesis and functioning, and in the lipid transport in oil secretory cells, in addition to investigate the influence of herbivory in the glandular trichomes formation and functioning. We studied two Lamiaceae species (Hyptis villosa and Ocimum gratissimum) and the model species ... (Complete abstract click electronic access below) / Doutor