Regulation of output from the plant circadian clock

Plants, like many other organisms, have endogenous biological clocks that enable them to organize their physiological, metabolic and developmental processes so that they occur at optimal times. The best studied of these biological clocks are the circadian systems that regulate daily (approximately 24 h) rhythms. At the core of the circadian system in every organism are oscillators responsible for generating circadian rhythms. These oscillators can be entrained (set) by cues from the environment, such as daily changes in light and temperature. Completing the circadian clock model are the output pathways that provide a link between the oscillator and the various biological processes whose rhythms it controls. Over the past few years there has been a tremendous increase in our understanding of the mechanisms of the oscillator and entrainment pathways in plants and many useful reviews on the subject. In this review we focus on the output pathways by which the oscillator regulates rhythmic plant processes. In the first part of the review we describe the role of the circadian system in regulation at all stages of a plant's development, from germination and growth to reproductive development as well as in multiple cellular processes. Indeed, the importance of a circadian clock for plants can be gauged by the fact that so many facets of plant development are under its control. In the second part of the review we describe what is known about the mechanisms by which the circadian system regulates these output processes.     

Input signals to the plant circadian clock

Eukaryotes and some prokaryotes have adapted to the 24 h day/night cycle by evolving circadian clocks, which now control very many aspects of metabolism, physiology and behaviour. Circadian clocks in plants are entrained by light and temperature signals from the environment. The relative timing of internal and external events depends upon a complex interplay of interacting rhythmic controls and environmental signals, including changes in the period of the clock. Several of the phytochrome and cryptochrome photoreceptors responsible have been identified. This review concentrates on the resulting patterns of entrainment and on the multiple proposed mechanisms of light input to the circadian oscillator components.     

Mechanisms of clock output in the Drosophila circadian pacemaker system

Molecular oscillations that underlie the circadian clock are coupled to different output signals by which daily rhythms in downstream events are evoked and/or synchronized. Here the authors review the literature that describes circadian output mechanisms in Drosophila. They begin at the most proximal level, within oscillator cells themselves, by surveying studies of rhythmic gene expression within Drosophila heads. Next the authors describe the several neuron groups that compose the circadian pacemaker network underlying rhythmic locomotor activity, and they detail current models of how that network is organized and coordinated. The authors outline the body of evidence that describes a role for the neuropeptide pigment dispersing factor (PDF) as a circadian transmitter in the fly brain. Finally, in the context of PDF, they consider studies that address mechanisms of signaling from the circadian pacemaker network to downstream neurons and nonneuronal cells that directly control rhythmic outputs.     

Spatially specific mechanisms and functions of the plant circadian clock

Like many organisms, plants have evolved a genetic network, the circadian clock, to coordinate processes with day/night cycles. In plants, the clock is a pervasive regulator of development and modulates many aspects of physiology. Clock-regulated processes range from the correct timing of growth and cell division to interactions with the root microbiome. Recently developed techniques, such as single-cell time-lapse microscopy and single-cell RNA-seq, are beginning to revolutionize our understanding of this clock regulation, revealing a surprising degree of organ, tissue, and cell-type specificity. In this review, we highlight recent advances in our spatial view of the clock across the plant, both in terms of how it is regulated and how it regulates a diversity of output processes. We outline how understanding these spatially specific functions will help reveal the range of ways that the clock provides a fitness benefit for the plant.

Emerging tools and techniques provide insights into how the behavior and outputs of the circadian clock vary across the plant.     

A suite of photoreceptors entrains the plant circadian clock

Circadian rhythms in plants are relatively robust, as they are maintained both in constant light of high fluence rates and in darkness. Plant circadian clocks exhibit the expected modes of photoentrainment, including period modulation by ambient light and phase resetting by brief light pulses. Several of the phytochrome and cryptochrome photoreceptors responsible have been studied in detail. This review concentrates on the resulting patterns of entrainment and on the multiple proposed mechanisms of light input to the circadian oscillator components.     

Regulatory mechanisms across networks of the circadian clock and senescence pathways

Journal of Plant Biochemistry and Biotechnology - The circadian clock serves the fitness of higher plants by controlling various aspects of plant growth and development ranging from photosynthesis...     

The regulation of plant growth by the circadian clock

Circadian regulated changes in growth rates have been observed in numerous plants as well as in unicellular and multicellular algae. The circadian clock regulates a multitude of factors that affect growth in plants, such as water and carbon availability and light and hormone signalling pathways. The combination of high-resolution growth rate analyses with mutant and biochemical analysis is helping us elucidate the time-dependent interactions between these factors and discover the molecular mechanisms involved. At the molecular level, growth in plants is modulated through a complex regulatory network, in which the circadian clock acts at multiple levels.     

Spike firing pattern of output neurons of the Limulus circadian clock

The lateral eyes of the horseshoe crab (Limulus polyphemus) show a daily rhythm in visual sensitivity that is mediated by efferent nerve signals from a circadian clock in the crab's brain. How these signals communicate circadian messages is not known for this or other animals. Here the authors describe in quantitative detail the spike firing pattern of clock output neurons in living horseshoe crabs and discuss its possible significance to clock organization and function. Efferent fiber spike trains were recorded extracellularly for several hours to days, and in some cases, the electroretinogram was simultaneously acquired to monitor eye sensitivity. Statistical features of single- and multifiber recordings were characterized via interval distribution, serial correlation, and power spectral analysis. The authors report that efferent feedback to the eyes has several scales of temporal structure, consisting of multicellular bursts of spikes that group into clusters and packets of clusters that repeat throughout the night and disappear during the day. Except near dusk and dawn, the bursts occur every 1 to 2 sec in clusters of 10 to 30 bursts separated by a minute or two of silence. Within a burst, each output neuron typically fires a single spike with a preferred order, and intervals between bursts and clusters are positively correlated in length. The authors also report that efferent activity is strongly modulated by light at night and that just a brief flash has lasting impact on clock output. The multilayered firing pattern is likely important for driving circadian rhythms in the eye and other target organs.     

The rhythms of life: circadian output pathways in Neurospora

Research in Neurospora crassa pioneered the isolation of clock-controlled genes (ccgs), and more than 180 ccgs have been identified that function in various aspects of the fungal life cycle. Many clock-controlled genes are associated with damage repair, stress responses, intermediary metabolism, protein synthesis, and development. The expression of most of these genes peaks just before dawn and appears to prepare the cells for the desiccation, mutagenesis, and stress caused by sunlight. Progress on characterization of the output signaling pathways from the circadian oscillator mechanism to the ccgs is discussed. The authors also review evidence suggesting that, similar to other clock model organisms, a connection exists between the redox state of the cell and the Neurospora clock. The authors speculate that the clock system may sense not only light but also the redox potential of the cell through one of the PAS domains of the core clock components WC-1 or WC-2.     

Cocaine modulates pathways for photic and nonphotic entrainment of the mammalian SCN circadian clock

Cocaine abuse is highly disruptive to circadian physiological and behavioral rhythms. The present study was undertaken to determine whether such effects are manifest through actions on critical photic and nonphotic regulatory pathways in the master circadian clock of the mouse suprachiasmatic nucleus (SCN). Impairment of SCN photic signaling by systemic (intraperitoneal) cocaine injection was evidenced by strong (60%) attenuation of light-induced phase-delay shifts of circadian locomotor activity during the early night. A nonphotic action of cocaine was apparent from its induction of 1-h circadian phase-advance shifts at midday. The serotonin receptor antagonist, metergoline, blocked shifting by 80%, implicating a serotonergic mechanism. Reverse microdialysis perfusion of the SCN with cocaine at midday induced 3.7 h phase-advance shifts. Control perfusions with lidocaine and artificial cerebrospinal fluid had little shifting effect. In complementary in vitro experiments, photic-like phase-delay shifts of the SCN circadian neuronal activity rhythm induced by glutamate application to the SCN were completely blocked by cocaine. Cocaine treatment of SCN slices alone at subjective midday, but not the subjective night, induced 3-h phase-advance shifts. Lidocaine had no shifting effect. Cocaine-induced phase shifts were completely blocked by metergoline, but not by the dopamine receptor antagonist, fluphenazine. Finally, pretreatment of SCN slices for 2 h with a low concentration of serotonin agonist (to block subsequent serotonergic phase resetting) abolished cocaine-induced phase shifts at subjective midday. These results reveal multiple effects of cocaine on adult circadian clock regulation that are registered within the SCN and involve enhanced serotonergic transmission.     

Beyond Arabidopsis: The circadian clock in non-model plant species

Circadian clocks allow plants to temporally coordinate many aspects of their biology with the diurnal cycle derived from the rotation of Earth on its axis. Although there is a rich history of the study of clocks in many plant species, in recent years much progress in elucidating the architecture and function of the plant clock has emerged from studies of the model plant, Arabidopsis thaliana. There is considerable interest in extending this knowledge of the circadian clock into diverse plant species in order to address its role in topics as varied as agricultural productivity and the responses of individual species and plant communities to global climate change and environmental degradation. The analysis of circadian clocks in the green lineage provides insight into evolutionary processes in plants and throughout the eukaryotes.