Harmer Lab:Research

Room 2123 Department of Plant Biology 1002 Life Sciences, One Shields Ave. University of California Davis Davis, CA 95616 Contact: slharmer at ucdavis.edu

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Background As one adage has it, the only constant is change. A striking example of such constant change is the regular alterations in the environment caused by the daily rotation of the earth on its axis. Along with the obvious diurnal changes in light and temperature, other important environmental variables such as humidity also change on a daily basis. This periodicity in the geophysical world is mirrored by daily periodicity in the behavior and physiology of most organisms. Examples include sleep/wake cycles in animals, developmental transitions in filamentous fungi, the incidence of heart attacks in humans, and changes in organ position in plants. Many of these daily biological rhythms are controlled by the circadian clock, an internal timer or oscillator that keeps approximately 24-hour time. Less obviously, the circadian clock is also important for processes that occur seasonally, including flowering in plants, hibernation in mammals, and long-distance migration in butterflies. In fact, circadian clocks have been found in most organisms that have been appropriately investigated, ranging from photosynthetic bacteria to trees [1]. Figure 1. Figure 1. Model of the plant clock. Three feedback loops (loops A - C) form a transcriptional network that regulates clock function. Also essential to clock function are post-transcriptional regulatory mechanisms (loop D). See [1] for further details. Many additional genes implicated in clock function have been omitted for clarity. Circadian rhythms have been studied for hundreds of years, with plants used as the first model system (see [2] for an excellent summary of the history of clock research in plants). Recent experimental and mathematical studies have suggested that the plant circadian clock consists of three interlocked transcriptional feedback loops (see Figure 1 for a simplified model). In addition to regulated transcription, post-transcriptional regulation is also clearly essential for proper clock function. Our lab is interested in understanding the molecular nature of the plant circadian clock and how the clock influences plant physiology. Identification of a novel clock-associated gene We use firefly luciferase driven by a clock-regulated promoter to monitor circadian rhythms in transgenic plants (Figure 2). This system has the advantage of being relatively high throughput, non-destructive, and automated. After inducing mutations in plants carrying such a luciferase reporter gene, we isolated many mutants with altered circadian rhythms [3]. One such mutant has an alteration in a gene of unknown function. When this gene, XAP5 CIRCADIAN TIMEKEEPER (XCT), is mutated, plants show altered clock function and light responses (Figure 3). Intriguingly, the C. elegans XCT homolog is essential for viability [4] and there this gene is highly conserved across eukaryotes (Figure 4). Despite this high degree of conservation, the molecular function of XCT or its homologs is currently unknown. We are using genetic and biochemical approaches in Arabidopsis and S. pombe to better understand the molecular function of XCT in plant clock and light signaling pathways and its fundamental biochemical role in eukaryotes. In addition, we have carried out an enhancer screen to identify mutations that exacerbate the short-period phenotype of gi-200 plants [3]. One such enhancer of gi (egi) mutant has been mapped to a region of the genome with no known clock genes, suggesting it represents a new locus involved in clock function. We are currently using positional cloning to molecularly identify this gene. Clock regulation of plant physiology We are interested in how the clock influences plant physiology at both the mechanistic and descriptive levels. What processes are influenced by the clock? How does the clock regulate its many outputs so that each occurs at the most appropriate time of day? We have taken a genomic approach to address both kinds of questions. Using DNA microarrays, we have found that in young seedlings grown in constant light and temperature, at least 30% of expressed genes show circadian variation in steady-state mRNA levels [5, 6]. Peak expression of these genes occurs at a wide range of times, just as clock regulated physiological pathways show peak activity at diverse times of day. We have taken advantage of the large number of gene expression profiling experiments carried out in Arabidopsis to identify pathways that might be clock regulated. We found that clock-regulated genes are over-represented among all of the classical plant hormone and multiple stress response pathways, suggesting that all of these pathways are influenced by the circadian clock [6] (Figure 5). Indeed, physiological studies revealed that endogenous auxin signaling is clock regulated and that plant responses to exogenous auxin are gated by the clock (that is, auxin sensitivity varies with the time of day) (Figure 6). In recent studies, we have identified a transcription factor that acts a node between the clock and auxin signaling networks. Further exploration of the links between the clock and diverse signaling pathways will lead to a better understanding of how the circadian clock affects plant growth and leads to improved fitness. Bibliography <biblio> McClung-2006 pmid=16595397 Martin-Tryon-2007 pmid=17098855 Martin-Tryon-2008 pmid=18515502 Harmer-2009 pmid=19133818 Harmer-2000 pmid=11118138 Covington-2008 pmid=18710561 Covington-2007 pmid=17683202 Piano-2002 pmid=12445391