flexible-measurement-bioluminescent-reporters-using-an-automated

Flexible Measurement of Bioluminescent Reporters Using an Automated Longitudinal Luciferase Imaging Gas- and Temperature-optimized Recorder (ALLIGATOR)

Luciferase-based reporters of cellular gene expression are in widespread use for both longitudinal and end-point assays of biological activity. In ...

MRC Laboratory of Molecular Biology

Circadian timekeeping in mammals is driven by transcriptional/posttranslational feedback loops that are active within both peripheral tissues and the circadian pacemaker of the suprachiasmatic nuclei (SCN). Spontaneous synchronization of these molecular loops between SCN neurons is a primary requirement of its pacemaker role and distinguishes it from peripheral tissues, which require extrinsic, SCN-dependent cues to impose cellular synchrony. Vasoactive intestinal polypeptide (VIP) is an intrinsic SCN factor implicated in acute activation and electrical synchronization of SCN neurons and coordination of behavioral rhythms. Using real-time imaging of cellular circadian gene expression across entire SCN slice cultures, we show for the first time that the Vipr2 gene encoding the VPAC2 receptor for VIP is necessary both to maintain molecular timekeeping within individual SCN neurons and to synchronize molecular timekeeping between SCN neurons embedded within intact, organotypical circuits. Moreover, we demonstrate that both depolarization and a second SCN neuropeptide, gastrin-releasing peptide (GRP), can acutely enhance and synchronize molecular timekeeping in Vipr2-/- SCN neurons. Nevertheless, transiently activated and synchronized Vipr2-/- cells cannot sustain synchrony in the absence of VIP-ergic signaling. Hence, neuropeptidergic interneuronal signaling confers a canonical property upon the SCN: spontaneous synchronization of the intracellular molecular clockworks of individual neurons.

Synchronization and maintenance of timekeeping in suprachiasmatic circadian clock cells by neuropeptidergic signaling.

Transcriptional/post-translational feedback loops have dominated ideas about how circadian clocks are able to keep time. An entirely new level of feedback regulation -- post-transcriptional regulatory microRNAs -- has now been added to the circadian mix.

Circadian clocks: timely interference by microRNAs.

Daily and seasonal rhythms in the endocrine system are co-ordinated by a hypothalamic pacemaker, the suprachiasmatic nuclei (SCN) that is synchronised to solar time by direct retinal afferents. Individual SCN neurons are circadian clocks, their intrinsic oscillator consisting of a series of interlinked autoregulatory transcriptional/post-translational feedback loops incorporating Period (Per) and Cryptochrome (Cry) genes. Mutations that alter the rate of transcription of Per and Cry genes or the stability of Per and Cry proteins affect clock speed. Molecular timekeeping in SCN neurons is synchronised and sustained by interneuronal neuropeptidergic signals. A molecular clock mechanism comparable to that of the SCN is present in most major organ systems. These tissue clocks are synchronised by endocrine, autonomic and behavioural cues that are dependent on the SCN, and in turn they drive the circadian expression of local transcriptomes, thereby co-ordinating circadian metabolism and physiology. Rhythmic glucocorticoid signalling is a prominent mediator of SCN output and internal synchroniser. The role of local SCN-synchronised clocks in controlling vital processes, including xenobiotic detoxification, cell division and nutrient metabolism, is essential to health, and disturbances to circadian timing arising from modern working schedules are becoming recognised as an increasingly relevant factor in major systemic illness. Moreover, the newly identified molecular components of circadian control systems provide novel avenues for therapeutic intervention.

Circadian clocks: regulators of endocrine and metabolic rhythms.

The daily rhythms that adapt organisms to the solar cycle are driven by internal circadian clocks. The hypothesis that the core pacemakers of these clocks consist of auto-regulatory transcriptional/post-translational feedback loops (TTFLs) was first developed in flies and fungi and has now been extended successfully to describe circadian timing mechanisms in mammals and plants. TTFL models revolve around the protein products of 'clock' genes that feedback periodically to regulate their own expression. From this simple beginning, the models have been expanded to encompass multiple, interlinked loops. However, experimental data now highlight the limitations of the TTFL model. Until recently, the focus on transcription caused rhythms in cytosolic signalling pathways to be viewed as outputs of the 'core' transcriptional clockwork, or else as a mechanism for its entrainment by extra-cellular stimuli. Recent work in Arabidopsis thaliana, Drosophila melanogaster and mammals now reveals that cytosolic rhythms in small signalling molecules have a central role within the circadian pacemaker. The logic is consistent across taxa: oscillatory cytoplasmic elements integrate with transcriptional feedback loops to sustain them and determine their rhythmic properties. Thus, clock outputs can constitute inputs to subsequent cycles and so become indistinguishable from a core mechanism. This emphasises the interdependence of nuclear and cytoplasmic processes in circadian pacemaking, such that the pacemakers of some species might encompass the entire cell and its intercellular environment.

Cellular circadian pacemaking and the role of cytosolic rhythms.

A substantial proportion of mammalian physiology is organized around the day/night cycle, being regulated by the co-ordinated action of numerous cell-autonomous circadian oscillators throughout the body. Disruption of internal timekeeping, by genetic or environmental perturbation, leads to metabolic dysregulation, whereas changes in metabolism affect timekeeping.

Circadian redox and metabolic oscillations in mammalian systems.

Using basic research to advance a practical application, a recent study demonstrates that the circadian clock in cyanobacteria can be 'reprogrammed' to improve yields of heterologous protein production - a green future surely beckons.

Circadian rhythms: hijacking the cyanobacterial clock.

The evolution of tight coupling between the circadian system and redox homeostasis of the cell has been proposed to coincide roughly with the appearance of the first aerobic organisms, around 3 billion years ago. The rhythmic production of oxygen and its effect on core metabolism are thought to have exerted selective pressure for the temporal segregation of numerous metabolic pathways. Until recently, the only evidence for such coupling came from studies showing circadian cycles in the abundance of various redox metabolites, with many arguing that these oscillations are simply an output from the transcription-translation feedback loop. The recent discovery that the peroxiredoxin (PRX) proteins exhibit circadian cycles in their oxidation status, even in the absence of transcription, demonstrated the existence of autonomous oscillations in the redox status of the cell. The PRXs are a family of cellular thiol peroxidases, whose abundance and high reaction rate make them the major cellular sink for cellular peroxides. Interestingly, as part of the normal catalytic cycle, PRXs become inactivated by their own substrate via overoxidation of the catalytic residue, with the inactivated form of the enzyme displaying circadian accumulation. Here, we describe the biochemical properties of the PRX system, with particular emphasis on the features important for the experimental analysis of these enzymes. We will also present a detailed protocol for measuring PRX overoxidation across circadian time in adherent cell cultures, red blood cells, and fruit flies (Drosophila melanogaster), providing practical suggestions for ensuring consistency and reproducibility of the results.

Analysis of the redox oscillations in the circadian clockwork.

Cell-autonomous circadian rhythms allow organisms to temporally orchestrate their internal state to anticipate and/or resonate with the external environment. Although ∼24-hr periodicity is observed across aerobic eukaryotes, the central mechanism has been hard to dissect because few simple models exist, and known clock proteins are not conserved across phylogenetic kingdoms. In contrast, contributions to circadian rhythmicity made by a handful of post-translational mechanisms, such as phosphorylation of clock proteins by casein kinase 1 (CK1) and glycogen synthase kinase 3 (GSK3), appear conserved among phyla. These kinases have many other essential cellular functions and are better conserved in their contribution to timekeeping than any of the clock proteins they phosphorylate. Rhythmic oscillations in cellular redox state are another universal feature of circadian timekeeping, e.g., over-oxidation cycles of abundant peroxiredoxin proteins. Here, we use comparative chronobiology to distinguish fundamental clock mechanisms from species and/or tissue-specific adaptations and thereby identify features shared between circadian rhythms in mammalian cells and non-circadian temperature-compensated respiratory oscillations in budding yeast. We find that both types of oscillations are coupled with the cell division cycle, exhibit period determination by CK1 and GSK3, and have peroxiredoxin over-oxidation cycles. We also explore how peroxiredoxins contribute to YROs. Our data point to common mechanisms underlying both YROs and circadian rhythms and suggest two interpretations: either certain biochemical systems are simply permissive for cellular oscillations (with frequencies from hours to days) or this commonality arose via divergence from an ancestral cellular clock.

Metabolic Cycles in Yeast Share Features Conserved among Circadian Rhythms.

Caffeine's wakefulness-promoting and sleep-disrupting effects are well established, yet whether caffeine affects human circadian timing is unknown. We show that evening caffeine consumption delays the human circadian melatonin rhythm in vivo and that chronic application of caffeine lengthens the circadian period of molecular oscillations in vitro, primarily with an adenosine receptor/cyclic adenosine monophosphate (AMP)-dependent mechanism. In a double-blind, placebo-controlled, ~49-day long, within-subject study, we found that consumption of a caffeine dose equivalent to that in a double espresso 3 hours before habitual bedtime induced a ~40-min phase delay of the circadian melatonin rhythm in humans. This magnitude of delay was nearly half of the magnitude of the phase-delaying response induced by exposure to 3 hours of evening bright light (~3000 lux, ~7 W/m(2)) that began at habitual bedtime. Furthermore, using human osteosarcoma U2OS cells expressing clock gene luciferase reporters, we found a dose-dependent lengthening of the circadian period by caffeine. By pharmacological dissection and small interfering RNA knockdown, we established that perturbation of adenosine receptor signaling, but not ryanodine receptor or phosphodiesterase activity, was sufficient to account for caffeine's effects on cellular timekeeping. We also used a cyclic AMP biosensor to show that caffeine increased cyclic AMP levels, indicating that caffeine influenced a core component of the cellular circadian clock. Together, our findings demonstrate that caffeine influences human circadian timing, showing one way that the world's most widely consumed psychoactive drug affects human physiology.

Effects of caffeine on the human circadian clock in vivo and in vitro.

Circadian rhythms are essential for health and are frequently disturbed in disease. A full understanding of the causal relationships between behavioural and molecular circadian rhythms requires simultaneous longitudinal observations over time in individual organisms. Current experimental paradigms require the measurement of each rhythm separately across distinct populations of experimental organisms, rendering the comparability of the resulting datasets uncertain. We therefore developed FLYGLOW, an assay using clock gene controlled luciferase expression detected by exquisitely sensitive EM-CCD imaging, to enable simultaneous quantification of parameters including locomotor, sleep consolidation and molecular rhythms in single flies over days/weeks. FLYGLOW combines all the strengths of existing techniques, and also allows powerful multiparametric paired statistics. We found the age-related transition from rhythmicity to arrhythmicity for each parameter occurs unpredictably, with some flies showing loss of one or more rhythms during middle-age. Using single-fly correlation analysis of rhythm robustness and period we demonstrated the independence of the peripheral clock from circadian behaviours in wild type flies as well as in an Alzheimer's model. FLYGLOW is a useful tool for investigating the deterioration of behavioural and molecular rhythms in ageing and neurodegeneration. This approach may be applied more broadly within behavioural neurogenetics research.

Flyglow: Single-fly observations of simultaneous molecular and behavioural circadian oscillations in controls and an Alzheimer's model.

Firefly luciferase (Fluc) is frequently used to report circadian gene expression rhythms in mammalian cells and tissues. During longitudinal assays it is generally assumed that enzymatic substrates are in saturating excess, such that total bioluminescence is directly proportional to Fluc protein level. To test this assumption, we compared the enzyme kinetics of purified luciferase with its activity in mammalian cells. We found that Fluc activity in solution has a lower Michaelis constant (Km) for luciferin, lower temperature dependence, and lower catalytic half-life than Fluc in cells. In consequence, extracellular luciferin concentration significantly affects the apparent circadian amplitude and phase of the widely used PER2::LUC reporter in cultured fibroblasts, but not in SCN, and we suggest that this arises from differences in plasma membrane luciferin transporter activity. We found that at very high concentrations (>1 mM), luciferin lengthens circadian period, in both fibroblasts and organotypic SCN slices. We conclude that the amplitude and phase of circadian gene expression inferred from bioluminescence recordings should be treated with some caution, and we suggest that optimal luciferin concentration should be determined empirically for each luciferase reporter and cell type.

In-depth Characterization of Firefly Luciferase as a Reporter of Circadian Gene Expression in Mammalian Cells.

Fibroblasts are primary cellular protagonists of wound healing. They also exhibit circadian timekeeping, which imparts an approximately 24-hour rhythm to their biological function. We interrogated the functional consequences of the cell-autonomous clockwork in fibroblasts using a proteome-wide screen for rhythmically expressed proteins. We observed temporal coordination of actin regulators that drives cell-intrinsic rhythms in actin dynamics. In consequence, the cellular clock modulates the efficiency of actin-dependent processes such as cell migration and adhesion, which ultimately affect the efficacy of wound healing. Accordingly, skin wounds incurred during a mouse's active phase exhibited increased fibroblast invasion in vivo and ex vivo, as well as in cultured fibroblasts and keratinocytes. Our experimental results correlate with the observation that the time of injury significantly affects healing after burns in humans, with daytime wounds healing ~60% faster than nighttime wounds. We suggest that circadian regulation of the cytoskeleton influences wound-healing efficacy from the cellular to the organismal scale.

Article	Year
Synchronization and maintenance of timekeeping in suprachiasmatic circadian clock cells by neuropeptidergic signaling. Current biology : CB\| PubMed ID: 16546085	2006
Circadian clocks: timely interference by microRNAs. Current biology : CB\| PubMed ID: 17803925	2007
Circadian clocks: regulators of endocrine and metabolic rhythms. The Journal of endocrinology\| PubMed ID: 17951531	2007
Cellular circadian pacemaking and the role of cytosolic rhythms. Current biology : CB\| PubMed ID: 18786386	2008
Circadian redox and metabolic oscillations in mammalian systems. Antioxidants & redox signaling\| PubMed ID: 24063592	2014
Circadian rhythms: hijacking the cyanobacterial clock. Current biology : CB\| PubMed ID: 24309283	2013
Analysis of the redox oscillations in the circadian clockwork. Methods in enzymology\| PubMed ID: 25707278	2015
Metabolic Cycles in Yeast Share Features Conserved among Circadian Rhythms. Current biology : CB\| PubMed ID: 25866393	2015
Effects of caffeine on the human circadian clock in vivo and in vitro. Science translational medicine\| PubMed ID: 26378246	2015
Flyglow: Single-fly observations of simultaneous molecular and behavioural circadian oscillations in controls and an Alzheimer's model. Scientific reports\| PubMed ID: 27658441	2016
In-depth Characterization of Firefly Luciferase as a Reporter of Circadian Gene Expression in Mammalian Cells. Journal of biological rhythms\| PubMed ID: 28112045	2016
Circadian actin dynamics drive rhythmic fibroblast mobilization during wound healing. Science translational medicine\| PubMed ID: 29118260	2017

John S. O'Neill

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