Metabolism is a collection of enzymatic reactions that transform obtained energy and nutrients into metabolites necessary for cellular functions. This process is fundamental to all organisms and regulation of metabolism is crucial to the survival of an organism. Regulatory mechanisms underlying metabolism exist at every level of the central dogma from DNA to protein. While previous studies have focused mostly on post-translational regulation of metabolism, much remains unknown about transcriptional regulation of metabolism, particularly in multicellular plants. This dissertation focuses on the transcriptional regulatory networks that determine plant primary and a subset of specialized metabolism, specifically on the tricarboxylic acid (TCA) cycle and the regulation of aliphatic glucosinolate (GSL) biosynthesis in Arabidopsis, respectively.
The introduction chapter reviews current literature describing transcriptional regulatory networks that coordinate various metabolic processes. My co-authors and I provided many examples in which transcription factor (TF) networks coordinate metabolism with development and the environment. I also updated the review by including recent publications on transcriptional regulation of phenylpropanoid biosynthesis and nitrogen metabolism.
Chapters 1 and 2 build upon a previous study that identified 29 novel aliphatic GSL TFs clustered into 8 phenotypic groups. We tested the extent of genetic interactions, or epistasis, of TFs and thus tested epistasis within double and triple mutants of 20 TFs for genetic interactions of TFs between and within phenotypic groups. Chapter 1 evaluates the metabolic consequences of this epistasis to test the hypothesis that TFs from different phenotypic groups display more epistasis than TFs within the same phenotypic group. Chapter 2 explores the phenotypic outcomes of the epistasis including flowering and growth rate of the higher order mutants and the correlation between defense traits and growth and developmental traits. Given that the TFs were identified in the context of defense metabolism, we examined the relationship between growth and defense in these higher order TF mutants to determine if i) we would observe a negative correlation between growth and defense, indicating there was trade-offs between growth and defense driven by energy costs or ii) if there was a dynamic and intricate model of coordination between growth and defense. We found extensive between-group and within-group TF x TF epistasis that is conditional on the traits measured and the tissue and the environment sampled. Additionally, these 20 GSL TFs significantly influence the growth, but we did not find any correlation between defense and growth effects of the TF mutants. Instead, the effects of the TFs varied across growth and defense phenotypes based on environmental conditions and the age of the plant, supporting the second model of complex TF coordination between defense and growth. These studies revealed that TFs can integrate internal and external signals to coordinate multiple phenotypes, demonstrating their potential utility to optimize plant growth and defense in various environments.
The final chapter investigates the transcriptional regulation of the TCA cycle. Enhanced high-throughput yeast one-hybrid (eY1H) assays were used to show that over 40% of Arabidopsis TFs can bind to the promoters of TCA cycle genes. Correlation analysis indicated that the majority of these interactions likely occur in a condition-specific manner due to low percentages of highly correlated interactions shared between abiotic stress and developmental datasets. Based on the results from the correlation analysis, seventeen TFs were selected for subsequent functional analyses to determine (i) if these TFs contribute to growth, as would be predicted for a regulator of central carbon metabolism; and (ii) if our hypothesis regarding condition-specific transcriptional regulation of the TCA cycle was indeed valid. We tested mutant alleles of the 17 TFs in conditions in which the TCA cycle is critical for growth. Functional analyses revealed that perturbation of TFs involved in the TCA cycle affects respiration-dependent growth, abiotic stress responses, and the expression of genes in the TCA cycle and broader central carbon metabolism. In Arabidopsis, TF effects on the TCA cycle are conditional on organ development and the environment, indicating transcription regulation of metabolism is specific to various tissues and/or organs, age and environmental conditions. Comparisons with other multicellular organisms will determine if this regulatory principle is unique to plants or common to all multicellular organisms.
|Advisor:||Kliebenstein, Daniel J.|
|Commitee:||Callis, Judy, Maloof, Julin N., Brady, Siobhan M.|
|School:||University of California, Davis|
|School Location:||United States -- California|
|Source:||DAI-B 82/2(E), Dissertation Abstracts International|
|Subjects:||Plant sciences, Systematic biology, Molecular biology|
|Keywords:||Glucosinolates, Networks, Primary metabolism, Secondary metabolism, Transcriptional regulation|
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