The regulation of circadian period by phototransduction pathways in Arabidopsis

Genetics and molecular analysis of circadian rhythms

The first part of this review summarizes the two best understood aspects of the two best understood circadian systems, the feedback oscillators of Neurospora and Drosophila, concentrating on what we know about the frequency (frq), period (per) and timeless (tim) genes. In the second part, the general circadian genetic and molecular literature is surveyed, with an eye to describing what is known from a variety of systems about input to the oscillator (entrainment), and how the oscillator might work and be temperature compensated, in emerging systems including Synechococcus, Gonyaulax, Arabidopsis, hamsters, and mice. Finally, the conversation of the molecular components of clocks is analyzed: both frq and per are widely conserved in their respective phylogenetic classes. Pharmacological data suggests that most other organisms use a day-phased oscillator of the type seen in Neurospora rather than a night-phased oscillator such as in Drosophila.

A role for transcriptional repression during light control of plant development

Light mediates plant development partly by orchestrating changes in gene expression, a process which involves a complex combination of positive and negative signaling cascades. Genetic investigations using the small crucifer Arabidopsis thaliana have demonstrated a fundamental role for the down-regulation of light-inducible genes in response to darkness, thus offering a suitable model system for investigating how plants repress gene expression in a developmental context. Rapid progress in eukaryotic gene repression mechanisms in general, and light control of plant gene expression in particular, sheds new light on how a class of ten pleiotropic COP/DET/FUS genes might function to down-regulate light-inducible genes in plants.

From seed germination to flowering, light controls plant development via the pigment phytochrome

Plant growth and development are regulated by interactions between the environment and endogenous developmental programs. Of the various environmental factors controlling plant development, light plays an especially important role, in photosynthesis, in seasonal and diurnal time sensing, and as a cue for altering developmental pattern. Recently, several laboratories have devised a variety of genetic screens using Arabidopsis thaliana to dissect the signal transduction pathways of the various photoreceptor systems. Genetic analysis demonstrates that light responses are not simply endpoints of linear signal transduction pathways but are the result of the integration of information from a variety of photoreceptors through a complex network of interacting signaling components. These signaling components include the red/far-red light receptors, phytochromes, at least one blue light receptor, and negative regulatory genes (DET, COP, and FUS) that act downstream from the photoreceptors in the nucleus. In addition, a steroid hormone, brassinolide, also plays a role in light-regulated development and gene expression in Arabidopsis. These molecular and genetic data are allowing us to construct models of the mechanisms by which light controls development and gene expression in Arabidopsis. In the future, this knowledge can be used as a framework for understanding how all land plants respond to changes in their environment.

A role for brassinosteroids in light-dependent development of Arabidopsis

Although steroid hormones are important for animal development, the physiological role of plant steroids is unknown. The Arabidopsis DET2 gene encodes a protein that shares significant sequence identity with mammalian steroid 5 alpha-reductases. A mutation of glutamate 204, which is absolutely required for the activity of human steroid reductase, abolishes the in vivo activity of DET2 and leads to defects in light-regulated development that can be ameliorated by application of a plant steroid, brassinolide. Thus, DET2 may encode a reductase in the brassinolide biosynthetic pathway, and brassinosteroids may constitute a distinct class of phytohormones with an important role in light-regulated development of higher plants.

Isolation and characterization of a Tritordeum cDNA encoding S-adenosylmethionine decarboxylase that is circadian-clock-regulated

Sequence analysis of the two cDNA clones 47/11 and 50A which were isolated by differential screening of an explant cDNA library obtained from the monocot Tritordeum (hexaploid hybrid of diploid wild barley and tetraploid wheat lines) reveals that both clones include the same open reading frame (ORF). The sequence of this ORF shows a high degree of similarity with dicot S-adenosylmethionine decarboxylase (SAMDC) gene sequences and contains regions highly conserved in all known SAMDC sequences. It is further shown that the sequence represented by the cDNA clones 47/11 and 50A is derived from the wild barley (Hordeum chilense) genome, where it is present as a single-copy gene. Northern analyses indicate the corresponding transcript to accumulate in response to wounding and the transcript level changes with a circadian rhythm, having a beak in the middle of the light period. The periodicity continues in constant light, but is changed in constant darkness.

The genetic and molecular dissection of a prototypic circadian system

A great deal is known about this archetypal circadian system, and it is likely that Neurospora will represent the first circadian system in which it will be possible to provide a complete description of the flow of information from the photoreceptor, through the components of oscillator, out to a terminal aspect of regulation. In Neurospora the strongest case has been made for there being a state variable of clock identified (Hall, 1995), it has now been shown that light resetting of the clock is mediated by the rapid light induction of the gene encoding this state variable, and a number of defined clock-regulated output genes have been identified, in two of which the clock-specific parts of the promoters have been localized. In addition to the importance of these factoids themselves, our efforts towards understanding of this system has allowed the development of tools and paradigms (e.g. Loros et al., 1989; Loros and Dunlap, 1991; Aronson et al., 1994a) that will help to pave the way for proving the identity of clock components in more complex systems, for understanding how clocks are regulated by entraining factors, and for showing how time information eventually is used to regulate the behaviors of clock cells, and of whole organisms.

Signal-transduction pathways controlling light-regulated development in Arabidopsis

All metazoan cells are able to make decisions about cell division or cellular differentiation based, in part, on environmental cues. Accordingly, cells express receptor systems that allow them to detect the presence of hormones, growth factors and other signals that manipulate the regulatory processes of the cell. In plants, an unusual signal-light-is required for the induction and regulation of many developmental processes. Past physiological and molecular studies have revealed the variety and complexity of plant responses to light but until recently very little was known about the mechanisms of those responses. Two major breakthroughs have allowed the identification of some photoreceptor signalling intermediates: the identification of photoreceptor and signal transduction mutants in Arabidopsis, and the development of single-cell microinjection assays in which outcomes of photoreceptor signalling can be visualized. Here, we review recent genetic advances which support the notion that light responses are not simply endpoints of linear signal transduction pathways, but are the result of the integration of a variety of input signals through a complex network of interacting signalling components.

Genes that control a temperature-compensated ultradian clock in Caenorhabditis elegans

Substantial progress has been made in understanding the genetic basis of temperature-compensated circadian clocks. Ultradian rhythms, with a period shorter than 24 h, are at least as widespread as circadian rhythms. We have initiated genetic analysis of defecation behavior, which is controlled by an ultradian clock in Caenorhabditis elegans. The defecation motor program is activated every 45 sec, and this rhythm is temperature compensated. We describe mutations in 12 genes that either shorten or lengthen the cycle period. We find that most of these mutations also disrupt temperature compensation, suggesting that this process is an integral part of the clock. These genes open the way for molecular genetic dissection of this ultradian clock.

Molecular control of circadian rhythms

Circadian rhythms are virtually ubiquitous in eukaryotes and have been shown to exist even in some prokaryotes. The generally accepted view is that these rhythms are generated by an endogenous clock. Recent progress, especially in the Drosophila, Neurospora and mouse systems, has revealed new clock components and mechanisms. These include the mouse clock gene, the Drosophila timeless gene, and the role of light in Neurospora.

Circadian oscillations of cytosolic and chloroplastic free calcium in plants

Tobacco and Arabidopsis plants, expressing a transgene for the calcium-sensitive luminescent protein apoaequorin, revealed circadian oscillations in free cytosolic calcium that can be phase-shifted by light-dark signals. When apoaequorin was targeted to the chloroplast, circadian chloroplast calcium rhythms were likewise observed after transfer of the seedlings to constant darkness. Circadian oscillations in free calcium concentrations can be expected to control many calcium-dependent enzymes and processes accounting for circadian outputs. Regulation of calcium flux is therefore fundamental to the organization of circadian systems.

Light-induced resetting of a circadian clock is mediated by a rapid increase in frequency transcript

To understand how light entrains circadian clocks, we examined the effects of light on a gene known to encode a state variable of a circadian oscillator, the frequency (frq) gene. frq is rapidly induced by short pulses of visible light; clock resetting is correlated with frq induction and is blocked by drugs that block the synthesis of protein or translatable RNA. The speed and magnitude of frq induction suggest that this may be the initial clock-specific event in light resetting. Light induction overcomes frq negative autoregulation so that frq expression can remain high in constant light. These data explain how a simple unidirectional signal (light and the induction of frq) may be turned into a bidirectional clock response (time of day-specific advances and delays). This light entrainment model is easily generalized and may be the common mechanism by which the intracellular feedback cycles that comprise circadian clocks are brought into synchrony with external cycles in the real world.

Tripping along the trail to the molecular mechanisms of biological clocks

Solving the mechanism of circadian clocks has become an important goal, in part because daily rhythms are running in such a wide variety of organisms, and contribute to many aspects of their well being. Systematic genetic approaches to studying 'the clock' were initiated in fruitflies more than 20 years ago as a novel means by which neural-pacemaking mysteries might be solved. Such chronogenetic investigations gained momentum when they spread to other species, and became molecular. However, the molecular studies were misleading, that is, until some elementary neuro-anatomical observations, involving the expression of a 'clock gene' in Drosophila, gave the experiments in this molecular-neurogenetic area of chronobiology a new direction. The initially neuro-descriptive studies led to the current investigations that involve negatively acting transcription factors and other clock molecules that are presumed to interact with them. In addition, new mutants and clones have been isolated in a timely manner. These mutations and molecules should permit chronogeneticists, working on a wide variety of organisms, to unravel further details of how the clock works, how environmental information finds its way to it, and how it sends information out into the organism's physiology, biochemistry and behavior.

Circadian clock mutants in Arabidopsis identified by luciferase imaging

The cycling bioluminescence of Arabidopsis plants carrying a firefly luciferase fusion construct was used to identify mutant individuals with aberrant cycling patterns. Both long- and short-period mutants were recovered. A semidominant short-period mutation, timing of CAB expression (toc1), was mapped to chromosome 5. The toc1 mutation shortens the period of two distinct circadian rhythms, the expression of chlorophyll a/b-binding protein (CAB) genes and the movements of primary leaves, although toc1 mutants do not show extensive pleiotropy for other phenotypes.