UC San Diego

The circadian clock is an internal timing mechanism that allows organisms to anticipate and respond to predictable changes in their environment throughout the day and across the year. Circadian processes are particularly important for plants because they are sessile organisms that must adjust their physiology to accommodate the changing world around them. This requires precise coordination of rhythmic gene expression across cells, tissues, and organs of the plant. However, more research is needed to understand the complexity of spatial clock regulation in plants. Here, we present a survey of the circadian transcriptomes of two major organs of the Arabidopsis shoot system: the shoot apex and the leaves (Chapter 2). Our comparative analysis revealed that there are unique rhythmic gene sets in each organ, and that rhythmic genes tend to reach their peak expression earlier in the shoot apex. The notion of organ-specific phase regulation was bolstered by the identification of a shoot apex-enriched transcription factor that regulates the timing of expression of the core clock component CCA1. Ultimately, we formulated a model of the circadian clock architecture in which organ-specific mechanisms modulate the phase of rhythmic genes through upstream regulation of the core clock, while the amplitude of rhythmic expression is controlled independently in each organ downstream of the core clock. Our model was further supported by the results of an organ-level transcriptome survey of the shoot system following a single leaf bacterial infection (Chapter 3). We found that the phase of clock components and of rhythmic gene expression more broadly was altered by the distal infection. This, combined with the observation that infection alters the makeup of organ-specific rhythmic gene sets, reinforces our assertion that phase is controlled upstream of the clock, and amplitude is controlled downstream of the clock, in an organ-specific manner. Organ-specific control of rhythmic gene expression may allow for precision tuning of clock-regulated processes in response to intra- and inter-organ signals, integrating microenvironmental information with internal rhythms in order to balance the needs of growth and reproduction with responses to stressors like pathogen attacks.