<p>Like other eukaryotic cells, plant cells contain an endomembrane system composed of compartmentalized organelles with specialized functions. Vesicle trafficking mediates the transport of materials between different organelles and between cells and the environment. The vesicle trafficking process is highly dynamic and plays essential roles in maintaining cellular homeostasis and environmental adaptation. Because of the essential roles of vesicle trafficking in plant growth and development, genes that are involved in vesicle trafficking often have redundant function when they exist as a large family or cause embryonic lethality when they exist as a signal gene or small gene family. Chemical genetics uses small molecule inhibitors to affect protein function without interfering with plant’s genome. Bioactive small molecules can generate a temporary perturbation of a biological system in a reversible and dose-dependent fashion, which allow us to observe dynamic cellular processes and discover new components in trafficking machineries. We recently discovered two small molecules named Endosidin2 (ES2) and Endosidin20 (ES20) that disrupt vesicle trafficking in plants. ES2 inhibits exocytosis by targeting the EXO70A1 subunit of the exocyst complex in plant cells. ES20 targets cellulose synthase (CESA) at the catalytic site and inhibits the delivery of Cellulose Synthase Complex (CSC) to the plasma membrane. This research thesis aims to characterize the specificity of ES2 on EXO70 homologs and identify new genes that mediate CSC trafficking. Drug Affinity Responsive Target Stability (DARTS) assay was used to test the specificity of ES2 in targeting different EXO70s in Arabidopsis. Chemical genetic screen for mutants that have increased sensitivity was conducted to identify novel genes related to CSC trafficking. This project provides new insights in the specificity of ES2 in targeting different EXO70s in plants and the regulatory mechanisms of CSC trafficking that control plant cellulose synthesis.</p><p><br></p>

<p>Here, we seek to address the importance of biodiversity in plant ecosystems. We examined the productivity-diversity relationship through the lens of the modern coexistence theory, using a combination of both experimentation and mathematical simulation. We did this by tracking and comparing the productivity of mixed and monoculture plots, analyzing the growth responses of individual trees at forest plots (Chapter 1), confirming the productivity-diversity relationship in a greenhouse experiment using local herbaceous plants (Chapter 2), and finally simulating the productivity response of monoculture vs polyculture plantations to specialist enemy attack (Chapter 3).</p><p>It is no surprise that biodiversity has been decreasing at an exponential rate on the global scale because of effects such as habitat fragmentation, invasive species, spreading pathogens, and anthropogenic influences. Ecologists often found that plants in more species rich locations often exhibited higher productivity and stability in the face of stress. One such phenomenon is known as the productivity diversity relationship that implies biodiversity is key to sustaining ecosystems. Notably, while efforts are being put forth to address ecosystem destruction, much of the current tree planting strategy in the USA is based on timber profit rather than forest productivity and species coexistence with tree biology often being a secondary consideration. These thought processes are in opposition with historical experiments that indicate polyculture communities create more biomass making them significantly more productive than monocultures. However, we also acknowledge that it is not simply biodiversity that must be taken into consideration for a productive ecosystem but also species interaction through coexistence indicate whether or not a community will persevere. These interactions can be addressed using the modern coexistence theory which depends on these complementarity and fitness similarities for species to coexist through time. Here, we seek to address the importance of biodiversity in plant ecosystems. We examined the productivity-diversity relationship through the lens of the modern coexistence theory, using a combination of both experimentation and mathematical simulation. We did this by tracking and comparing the productivity of mixed and monoculture plots, analyzing the growth responses of individual trees at forest plots (Chapter 1), confirming the productivity-diversity relationship in a greenhouse experiment using local herbaceous plants (Chapter 2), and finally simulating the productivity response of monoculture vs polyculture plantations to specialist enemy attack (Chapter 3). Our research across the combination of approaches used found that species with overlapping niches and very different finesses will exclude one another due to high competition. Further, the productivity diversity correlation is necessary for ecosystem growth, but it is not sufficient for species coexistence. However, species can maintain this positive relationship despite a lack of coexistence if they maintain niche complementarity. Lastly, using a theoretic game model we were able to identify the impacts of a specialist pest on polyculture and monoculture forest. These results showed that a polyculture forest was more productive than that of a monoculture forest regardless of the presence of a specialist enemy. The results of the multiple threads of evidence found from these combined experiments indicate that while the productivity diversity correlation is important to ecosystems it is likely due to the impacts of niche complementarity that determine whether or not species will be productive within an ecosystem.</p>

Nitrogen (N), an essential plant macronutrient, is among the most limiting factors of crop yield. To sustain modern agriculture, N is often amended in soil in the form of chemical N fertilizer, a major anthropogenic contributor to nutrient pollution that affects climate, biodiversity and human health. To achieve agricultural sustainability, a comprehensive understanding of the regulation of N response in plants is required, in order to engineer crops with higher N use efficiency. Recently, epigenetic mechanisms, such as histone modifications, have gained increasing importance as a new layer of regulation of biological processes. However, our understanding of how epigenetic processes regulate N uptake and assimilation is still in its infancy. To fill this knowledge gap, we first performed a meta-analysis that combined functional genomics and network inference approaches to identify a set of N-responsive epigenetic regulators and predict their effects in regulating epigenome and transcriptome during plant N response. Our analysis suggested that histone modifications could serve as a regulatory mechanism underlying the global transcriptomic reprogramming during plant N response. To test this hypothesis, I applied chromatin immunoprecipitation-sequencing (ChIP-Seq) to monitor the genome-wide changes of four histone marks (H3K27ac, H3K4me3, H3K36me3 and H3K27me3) in response to N supply in tomato plants, followed by RNA-Seq to profile the transcriptomic changes. To investigate the organ specificity of histone modifications, I assayed shoots and roots separately. My results suggest that up to two-thirds of differentially expressed genes (DEGs) are modified in at least one of the four histone marks, supporting an integral role of histone modification in regulating N response. I observed a synergistic modification of active histone marks (H3K27ac, H3K4me3 and H3K36me3) at gene loci functionally relevant to N uptake and assimilation. Surprisingly, I uncovered a non-canonical role of H3K27me3, which is conventionally associated with repressed genes, in modulating active gene expression. Interestingly, such regulatory role of H3K27me3 is specifically associated with highly expressed genes or low expressed genes, depending on the organ context. Overall, I revealed the multi-faceted role of histone marks in mediating the plant N response, which will guide breeding and engineering of better crops with higher N use efficiency