IDENTIFYING, CHARACTERIZING, AND REPROGRAMMING CEP SIGNALING IN TOMATO
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Nitrogen (N) is a critical macronutrient and a major limiting factor in global agriculture. To cope with variable nutrient availability in heterogeneous soils, plants have evolved long-distance signaling systems to coordinate resource allocation. One such system is the C-terminally Encoded Peptide (CEP) signaling pathway, which mediates root-to-shoot and shoot-to-root communication in response to nitrogen deprivation. This dissertation investigates the CEP signaling network in tomato (Solanum lycopersicum) and applies synthetic biology strategies to re-engineer this system as a programmable platform for environmental sensing.Chapter 1 reviews the CEP signaling mechanism, its role in systemic nitrogen signaling, and its potential to be used in synthetic biology. We propose that rewiring this pathway could enable plants to function as self-reporting biosensors for environmental stress. In Chapter 2, we used bioinformatic analyses to identify 21 putative tomato CEP (SlCEP) genes and prioritized six (SlCEP1–6) based on root-enriched expression. Peptide assays reveal that tomato CEPs can trigger shoot-localized transcriptional responses, supporting their conserved role in nitrogen-responsive signaling and providing a foundation for synthetic manipulation. Chapter 3 describes transgenic tomato lines expressing pigment- and fluorescence-based reporters driven by CEP Downstream (CEPD) promoters. Using hydroponic culture systems, we show that reporter activation corresponds with nitrogen availability, demonstrating that CEPD promoter activity can serve as a visible, non-invasive proxy for internal nitrogen status. These lines represent a new tool for monitoring systemic signaling in vivo. In Chapter 4, we reprogram CEP1 expression to respond to drought-induced hormonal cues using synthetic and ABA-inducible promoters. Transgenic lines exhibit CEP1 and DsRed expression in response to ABA, with variability among events. To discover endogenous drought-inducible promoters, we conducted transcriptomic analysis during a 72-hour drought time course, identifying two strong, root-specific candidates (Solyc03g034130 and Solyc12g019630) for future synthetic circuit development. Overall, this work provides a framework for understanding and engineering CEP signaling in tomato. By integrating molecular genetics, transcriptomics, and synthetic biology, we advance the development of programmable, plant-based biosensors capable of reporting real-time environmental conditions—tools with broad potential for precision agriculture and climate-resilient crop systems.