Plants have molecular mechanisms for nutrient-related stress responses; however, their exact regulation remains unclear. For example, the integral myo-inositol (inositol) signal transduction pathway allows Arabidopsis thaliana to sense and respond to changes in environmental stimuli, such as water, light availability, and nutrient stress. The inositol signaling pathway relies on dynamic changes in second messenger levels of inositol(1,4,5)P3 (InsP3) and is regulated by myo-inositol polyphosphate 5-phosphatases (5PTases). The 5PTses keep balance between InsP3 signal transduction and termination. Previous work has identified the Sucrose non-fermenting (Snf) 1-related kinase (SnRK1.1) as a binding partner to 5PTase13, a potential InsP3 regulator, and a novel protein called P80, a predicted component of the Cullin4 (CUL4) E3 Ubiquitin ligase complex. In plants, SnRK1.1 is a central integrator of metabolism, stress responses, and developmental signals. Moreover, SnRK1.1 is conserved with the eukaryotic AMP-activated protein (AMPK) and Snf1 kinases—enzymes fundamental to transcriptional regulation and metabolic balance. Studying SnRK1.1 regulation may reveal mechanisms for agricultural sustainability and may offer valuable links to understanding metabolic diseases and lifespan in humans. Therefore, the research presented here centered on characterizing the regulation of SnRK1 gene expression and steady-state protein levels in plants. I show developmental and nutrient-related regulation of spatial expression patterns of SnRK1 genes and SnRK1.1 protein. Further, I present a model for regulation of SnRK1.1 protein stability in vivo based on SnRK1.1 steady-state protein levels in p80 and cul4 co-suppressed (cs) mutants. My results indicate SnRK1.1 regulation is dynamic, and dependent on the timing of particular cues from development and the environment. / Master of Science

Polyclonal antibodies against the first two enzymes of the Arabidopsis thaliana flavonoid biosynthetic pathway were developed using conventional and phage antibody technology. cDNAs from Arabidopsis coding regions of chalcone synthase (CHS) and chalcone isomerase (CHI) were sub-cloned in frame into a bacterial expression vector as fusions with glutathione Stransferase (GST) using standard directional cloning techniques. Analysis of crude extracts of Escherichia coli containing GST .. CHS or GST .. CHI fusion protein indicated that the cells expressed equivalent amounts per volume of culture. CHS and CHI were purified to near homogeneity, yielding approximately 100 micrograms of GST .. CHS and 1 milligram of GST-CHI per liter of culture. The purified fusion proteins were injected into chickens and polyclonal lgY·s were purified from egg yolk Accumulation of CHS and CHI, as well as products of the pathway, were compared during the first eight days of Arabidopsis development. CHS and CHI are sequentially induced and reach maximal accumulation levels by day 5. Anthocyanidin levels are offset by one reaching maximal levels at day 6. The fusion proteins were also used to screen a phage-display library for Fabl fragments that recognize CHS and CHI epitopes. Preliminary data indicated that enrichment of phage displaying antibodies against CHS and CHI was successful. Phage-derived antibodies against CHS and CHI provide valuable tools for future experiments addressing Western blot analysis, immunolocalization experiments, and disruption of the flavonoid biosynthetic pathway by introduction of the corresponding genes into transgenic Arabidopsis plants. / Master of Science

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.

Eukaryotic organisms require the ability to respond to their environments. They do so by utilizing signal transduction pathways that allow for signals to effect final biological responses. Many times, these final responses require new gene expression events that have been stimulated or repressed within the nucleus. Thus, much of the understanding of signal transduction pathways converges on the understanding of how signaling affects gene expression alterations (Kumar et al., 2004). The regulation of gene expression involves the modification of chromatin between condensed (closed, silent) and expanded (open, active) states. Histone modifications, such as acetylation, can determine the open versus closed status of chromatin. The PHD (Plant HomeoDomain) finger is a structural domain primarily found in nuclear proteins across eukaryotes. This domain specifically recognizes the epigenetic marks H3K4me2 and H3K4me3, which are di- and tri-methylated lysine 4 residues of Histone H3 (Loewith et al., 2000; Kuzmichev et al., 2002; Vieyra et al. 2002; Shiseki et al., 2003; Pedeux et al., 2005, Doyon et al., 2006). It is estimated that there are ~150 proteins that contain the PHD finger in humans (Solimon and Riabowol, 2007). The PHD finger is conserved in yeast and plants, however an analysis of this domain has only been performed done in Arabidopsis thaliana (Lee et al., 2009). The work presented in this report aims to extend the analysis of this domain in plants by identifying the PHD fingers of the crop species Oryza sativa (rice). In addition, a phylogenetic analysis of all PHD fingers in Arabidopsis and rice was undertaken. From these analyses, it was determined that there are 78 PHD fingers in Arabidopsis and 70 in rice. In addition, these domains can be categorized into classes and groups by defining features within the conserved motif. In a separate study, I investigated the function of two of the PHD finger proteins from Arabidopsis, ING1 (INhibitor of Growth1) and ING2. In humans, these proteins can be found in complexes associated with both open and closed chromatin. They facilitate chromatin remodeling by recruiting histone acetyltransferases and histone deacetylases to chromatin (Doyon et al., 2006, Pena et al., 2006). In addition, these proteins recognize H3K4me2/3 marks and are believed to be "interpreters" of the histone code (Pena et al., 2006, Shi et al., 2006). To understand the function of ING proteins in plants, I took a reverse genetics approach and characterized ing1 and ing2 mutants. My analysis revealed that these mutants are altered in time of flowering, as well as their response to nutrient and stress conditions. Lastly, I was able to show that ING2 protein interacts in vitro with SnRK1.1, a nutrient/stress sensor (Baena-Gonzalez et al., 2007). These results indicate a novel function for PHD proteins in plant growth, development and stress response. / Master of Science

We are using the yeast two-hybrid (Y2H) system to identify novel protein-protein interactions (PPI) relevant to wood formation. Bait proteins for Y2H binary assays and screening against a xylem cDNA prey library were selected from approximately 400 Populus trichocarpa genes that are at least 8-fold more highly expressed in differentiating secondary xylem versus phloem-cambium, and designated here as poplar biomass (PB) genes. Here we report some of the interactions involving selected PB proteins and efforts to characterize their functions in Populus and Arabidopsis. Members of the ROP GTPase family, PB15 in poplar and ROP11 in Arabidopsis, interact with the domain of unknown function (DUF) 620 (DUF620) proteins (e.g., PB129 in poplar). Ectopic co-expression of PB15 and PB129 in Arabidopsis caused outgrowths at the base of flower pedicels and altered leaf morphology. Interestingly, the co-expression phenotype could not be observed in transgenic plants that are only expressing either one of the interacting partners separately. Transgenics altered in expression of PB15 and/or PB129 were prepared in Populus and characterization of transgenic trees will be performed in greenhouse and field. In addition to DUF620 family proteins, ROP11 also interacts with the COP9 subunit CSN5A in Arabidopsis. We confirmed the interaction of ROP11 and CSN5A in Y2H and employed available mutants for ROP11 and CSN5A in Arabidopsis to genetically characterize this interaction. Surprisingly, loss of ROP11 was found to rescue the csn5a-2 pleiotropic phenotype. Ectopic expression of a ROP11 dominant negative mutant in the csn5a-2 background also complemented the stunted growth phenotype. Transcript analysis and gel blot assays showed that CSN5A transcript levels remained unchanged in all rescue lines, whereas CSN5A protein levels increased relative to WT. Taken together, we concluded that ROP11 negatively regulate CSN5A protein level in plant by some as yet unknown mechanism. / Ph. D.

Computational biology enabled us to manage vast amount of experimental data and make inferences on observations that we had not made. Among the many methods, predicting metabolic functions with genome-scale models had shown promising results in the recent years. Using sophisticated algorithms, such as flux balance analysis, OptKnock, and OptForce, we can predict flux distributions and design metabolic engineering strategies at a greater efficiency. The caveat of these current methods is the accuracy of the predictions. We proposed using flux balance analysis with flux ratios as a possible solution to improving the accuracy of the conventional methods. To examine the accuracy of our approach, we implemented flux balance analyses with flux ratios in five publicly available genome-scale models of five different organisms, including Arabidopsis thaliana, yeast, cyanobacteria, Escherichia coli, and Clostridium acetobutylicum, using published metabolic engineering strategies for improving product yields in these organisms. We examined the limitations of the published strategies, searched for possible improvements, and evaluated the impact of these strategies on growth and product yields. The flux balance analysis with flux ratio method requires a prior knowledge on the critical regions of the metabolic network where altering flux ratios can have significant impact on flux redistribution. Thus, we further developed the reverse flux balance analysis with flux ratio algorithm as a possible solution to automatically identify these critical regions and suggest metabolic engineering strategies. We examined the accuracy of this algorithm using an Arabidopsis genome-scale model and found consistency in the prediction with our experimental data. / Master of Science

Advances in bioinformatics and computational biology have enabled integration of an enormous amount of known biological interactions. This has enabled researchers to use models and data to design experiments and guide new discovery as well as test for consistency. One such computational method is constraint-based metabolic flux modeling. This is performed using genome-scale metabolic models (GEMs) that are a collection of biochemical reactions, derived from a genome's annotation. This type of flux modeling enables prediction of net metabolite conversion rates (metabolic fluxes) to help understand metabolic activities under specific environmental conditions. It can also be used to derive metabolic engineering strategies that involve genetic manipulations. Over the past decade, GEMs have been constructed for several different microbes, plants, and animal species. Researchers have also developed advanced algorithms to use GEMs to predict genetic modifications for the overproduction of biofuel and valuable commodity chemicals. Many of the predictive algorithms for microbes were validated with experimental results and some have been applied industrially. However, there is much room for improvement. For example, many algorithms lack straight-forward predictions that truly help non-computationally oriented researchers understand the predicted necessary metabolic modifications. Other algorithms are limited to simple genetic manipulations due to computational demands. Utilization of GEMs and flux-based modeling to predict in vivo characteristics of multicellular organisms has also proven to be challenging. Many researchers have created unique frameworks to use plant GEMs to hypothesize complex cellular interactions, such as metabolic adjustments in rice under variable light intensity and in developing tomato fruit. However, few quantitative predictions have been validated experimentally in plants. This research demonstrates the utility of GEMs and flux-based modeling in both metabolic engineering and analysis by tackling the challenges addressed previously with alternative approaches. Here, a novel predictive algorithm, Node-Reward Optimization (NR-Opt) toolbox, was developed. It delivers concise and accurate metabolic engineering designs (i.e. genetic modifications) that can truly improve the efficiency of strain development. As a proof-of-concept, the algorithm was deployed on GEMs of E. coli and Arabidopsis thaliana, and the predicted metabolic engineering strategies were compared with results of well-accepted algorithms and validated with published experimental data. To demonstrate the utility of GEMs and flux-based modeling in analyzing plant metabolism, specifically its response to changes in the signaling pathway, a novel modeling framework and analytical pipeline were developed to simulate changes of growth and starch metabolism in Arabidopsis over multiple stages of development. This novel framework was validated through simulation of growth and starch metabolism of Arabidopsis plants overexpressing sucrose non-fermenting related kinase 1.1 (SnRK1.1). Previous studies suggest that SnRK1.1 may play a critical signaling role in plant development and starch level (a critical carbon source for plant night growth). It has been shown that overexpressing of SnRK1.1 in Arabidopsis can delay vegetative-to-reproductive transition. Many studies on plant development have correlated the delay in developmental transition to reduction in starch turnover at night. To determine whether starch played a role in the delayed developmental transition in SnRK1.1 overexpressor plants, starch turnover was simulated at multiple developmental stages. Simulations predicted no reduction in starch turnover prior to developmental transition. Predicted results were experimentally validated, and the predictions were in close agreement with experimental data. This result further supports previous data that SnRK1.1 may regulate developmental transition in Arabidopsis. This study further validates the utility of GEMs and flux-based modeling in guiding future metabolic research. / Ph. D.

Secondary xylem, commonly known as wood, is a valuable commercial commodity. Among the major components of wood are the elongated, thick-walled water-conducting cells known as tracheary elements. Understanding tracheary element differentiation and maturation is of scientific and commercial importance as it may lead to broad understanding of cellular differentiation processes as well as ways to increase both the quality and quantity of wood produced by economically important tree species. One way to begin to understand the regulation of tracheary element differentiation is to identify elements that control expression of genes associated with tracheary elements. In Arabidopsis thaliana, Xylem Cysteine Protease 1 (XCP1) is specifically expressed in tracheary elements where it catalyzes microautolysis. Thus XCP1 can serve as a useful model for identifying factors that regulate tracheary element-specific gene expression. A deletion analysis of the XCP1 promoter was conducted to identify promoter elements that are necessary and sufficient for tracheary element-restricted gene expression. Two regions required for tracheary element-specific gene expression were identified. One of these was assembled as a multimeric bait construct and used in yeast one-hybrid assays to identify candidate transcription factors that bind to the XCP1 promoter region. Subsequently, a southwestern blot analysis was used to identify transcription factors displaying specific binding to a previously reported cis-element, CTTCAAAGCCA, found in the XCP1 promoter and other tracheary element-associated genes from multiple species. / Master of Science

Cysteine proteases are associated with xylem tracheary element differentiation. XCP1 was recently identified as a xylem-specific cysteine protease in Arabidopsis (Zhao, et al., 2000). For this study a recombinant polyhistidine-tagged XCP1 (XCP1H6) was expressed and purified from an E. coli expression system. A polyclonal anti-XCP1 antibody was produced using purified XCP1H6. Immunoblot analysis of a developmental time course of xylem and bark protein extracted from root-hypocotyl segments demonstrated that XCP1 was expressed in xylem only. Further analysis under optimized immunoblot conditions, however, revealed that anti-XCP1 antibody reacted with protein present in both xylem and bark. The vast majority of immunoreactivity, however, was restricted to xylem. Cell-type localization of GUS expression under the control of a putative XCP1 promoter indicated that the XCP1 promoter specifies expression of XCP1 in tracheary elements in leaves, stems, roots and flowers. XCP1 promoter-driven GUS activity was not associated with senescing tissues. / Master of Science

Yes / The coexistence of hermaphrodites and female-sterile individuals, or androdioecy, has been documented in only a handful of plants and animals. This study reports its existence in the plant species Cardamine amara (Brassicaceae), in which female-sterile individuals have shorter pistils than seed-producing hermaphrodites. Morphological analysis, in situ manual pollination, microsatellite genotyping and differential gene expression analysis using Arabidopsis microarrays were used to delimit variation between female-sterile individuals and hermaphrodites. Female sterility in C. amara appears to be caused by disrupted ovule development. It was associated with a 2.4- to 2.9-fold increase in clonal propagation. This made the pollen number of female-sterile genets more than double that of hermaphrodite genets, which fulfils a condition of co-existence predicted by simple androdioecy theories. When female-sterile individuals were observed in wild androdioecious populations, their ramet frequencies ranged from 5 to 54 %; however, their genet frequencies ranged from 11 to 29 %, which is consistent with the theoretically predicted upper limit of 50 %. The results suggest that a combination of sexual reproduction and increased asexual proliferation by female-sterile individuals probably explains the invasion and maintenance of female sterility in otherwise hermaphroditic populations. To our knowledge, this is the first report of the coexistence of female sterility and hermaphrodites in the Brassicaceae.