You will be presented with the abstract, introduction, and discussion section from a biomedical research article. Your task is to create a summary that a layperson can understand, capturing the essence of the research article. Keep essential scientific terms, but ensure that the language remains clear and the concepts are explained in an uncomplicated manner.

Title: Switching of metabolic programs in response to light availability is an essential function of the cyanobacterial circadian output pathway}
Article:
Abstract:
The transcription factor RpaA is the master regulator of circadian transcription in cyanobacteria, driving genome-wide oscillations in mRNA abundance. Deletion of rpaA has no effect on viability in constant light conditions, but renders cells inviable in cycling conditions when light and dark periods alternate. We investigated the mechanisms underlying this viability defect, and demonstrate that the rpaA- strain cannot maintain appropriate energy status at night, does not accumulate carbon reserves during the day, and is defective in transcription of genes crucial for utilization of carbohydrate stores at night. Reconstruction of carbon utilization pathways combined with provision of an external carbon source restores energy charge and viability of the rpaA- strain in light/dark cycling conditions. Our observations highlight how a circadian output pathway controls and temporally coordinates essential pathways in carbon metabolism to maximize fitness of cells facing periodic energy limitations.
Introduction:
Organisms across kingdoms of life have evolved circadian clocks to temporally align biological activities with the diurnal changes in the environment. In the cyanobacterium Synechococcus elongatus PCC7942, the core circadian oscillator is comprised of the KaiA, KaiB and KaiC proteins( Nishiwaki et al., 2007; Rust et al., 2007) that generate oscillations in the phosphorylation state of KaiC. Time information encoded in the phosphorylation state of KaiC is transmitted to the transcription factor RpaA( Takai et al., 2006; Taniguchi et al., 2010; Markson et al., 2013) to generate circadian changes in gene expression( Markson et al., 2013). In continuous light, the expression of more than 60% of protein-coding genes in S. elongatus is regulated in a circadian manner( Vijayan et al., 2009) with two main phases of gene expression: genes peaking at subjective dawn or subjective dusk, where the term ‘subjective’ refers to an internal estimate of time in the absence of external cues. Deletion of rpaA disrupts these rhythms in mRNA abundance and arrests cells in a subjective dawn-like transcriptional state, rendering them unable to switch to a subjective dusk-like expression program( Markson et al., 2013). While it is clear that the circadian transcriptional program schedules timing of gene expression when the clock is free-running in the absence of changes in external light, it is unclear how circadian control of gene expression is used under more physiologically relevant conditions when light and dark periods alternate. Exposure to darkness restricts energy availability, creating unique metabolic demands in cyanobacteria which depend on sunlight for energy production through photosynthesis. Strikingly, the rpaA- strain exhibits defects in cell growth and viability in cyclic, but not in constant light environments( Takai et al., 2006), suggesting an important role for circadian regulation of gene expression in alternating light/dark cycles. We find that both accumulation and utilization of the carbon reserves required for energy production during periods of darkness are defective in the rpaA- strain, and that correction of these defects restores viability. Our results provide insight into the role of the circadian output pathway in enhancing fitness of cyanobacteria through coordination of central carbon metabolism with the metabolic demands imposed by periodic changes in the external environment.
Discussion:
Daily environmental changes in light availability give rise to periodic demand for metabolism of alternate energy sources in photosynthetic organisms( Doolittle, 1979). To maximize fitness, photosynthetic organisms need to accurately allocate resources by carrying out carbon assimilation during the day and utilizing stored carbohydrate reserves at night( Smith, 1983). Here we show that the phosphorylated form of the transcription factor RpaA, regulated by the circadian clock, is critical for the coordination of carbon anabolism and catabolism and thus cell viability in light/dark cycles. Deletion of rpaA prevents glycogen accumulation in light and renders cells unable to utilize existing glycogen at dusk( Figure 5E) – this leads to alterations in cellular energy charge and, as previously observed, to a severe reduction in fitness. It is yet to be determined whether RpaA is rewiring carbon metabolism solely through transcriptional control or through other mechanisms. The mechanism underlying perturbed carbon accumulation in the rpaA- strain is unclear. The activities of glycogen synthesizing enzymes in the rpaA- strain are high in vitro, however they could be affected in vivo by the redox state of the cell or by metabolite levels. It is also possible that an RpaA-dependent transcript expressed in the afternoon is required to funnel assimilated carbon into glycogen synthesis. Alternatively, additional metabolic flux changes may occur in the rpaA- strain that prevent formation of glycogen stores. Finally, it is formally possible that the rpaA- cells perform a futile cycle, simultaneously synthesizing and breaking glycogen down. However, since the activity of the glycogen phosphorylase involved in glycogen degradation is low in the rpaA- strain, we find this scenario less likely. Our data support a model in which anticipation of periodic dark-induced resource limitation is one essential role of the cyanobacterial circadian system. The output of the core oscillator, through regulation of RpaA activity, temporally coordinates metabolism to prepare cells for the metabolic demands of periods of darkness. Correct scheduling of central carbon metabolic activities allows cells to survive the night. Recently, Lambert et al. observed that the circadian clock orchestrates a trade-off between rapid cell growth in the morning and robustness to starvation in the afternoon, suggesting preparation for the night as a plausible role for the circadian clock( Lambert et al., 2016). Our findings are consistent with this model and provide novel mechanistic insight into circadian regulation of cyanobacterial energy metabolism. It remains to be investigated whether the circadian-driven preparation for darkness is a shared strategy employed by other photosynthetic organisms. Further, our results suggest a molecular explanation for the observed selective advantage of circadian resonance. When the periods of the endogenous circadian system and periods of the environmental fluctuations are equal, organisms show a fitness advantage and outcompete mutants whose clocks have an altered periodicity in the same environment( Ouyang et al., 1998; Woelfle et al., 2004). The mechanistic basis for this observation has been lacking. Based on our findings, we expect that the fitness defects in the strains with core oscillator periods unequal to the period of environmental variation result from mistiming of RpaA activation. The resultant mistiming of accumulation and mobilization of glycogen stores with the onset of the nightfall would lead to a carbon deficit at night, and impact growth as in the rpaA- mutant during dark periods. One role of the KaiABC clock in our model, therefore, is to correctly phase the activity of RpaA and downstream carbon metabolism with the external environment, maximizing fitness and growth. Though we show that RpaA activity is crucial for regulation of key aspects of carbohydrate metabolism, we identify ~90 genes whose expression is abrogated at dusk and throughout darkness in the rpaA- strain and it is possible that additional physiological processes are defective in the absence of rpaA. Moreover, although our results indicate that the KaiABC clock is the main regulator of diurnal RpaA phosphorylation, other factors may influence the activity of RpaA or its regulon under fluctuating environmental conditions. RpaA is known to cooperate with RpaB( Espinosa et al., 2015), a transcription factor crucial for responses to high light conditions. CikA, the clock-controlled regulator of RpaA phosphorylation, has been proposed to directly sense redox state of the cell( Ivleva et al., 2006). Finally, additional RpaA regulators, LabA and CikB, have been proposed( Taniguchi et al., 2010; Boyd et al., 2016). Hence, it is possible that in a rapidly changing environment RpaA integrates circadian cues with environmental inputs important for viability. It will be interesting to analyze how deletion of rpaA affects the ability of cells to respond to other environmental challenges that cyanobacteria routinely face. Finally, our data together with a recent study by Diamond and colleagues( Diamond et al., 2015) emphasize the role of the circadian output pathway in driving oscillations in metabolism. On the other hand, it has been demonstrated that metabolic processes provide feedback to the circadian clock by regulating its resetting, indicating an important role of the fluctuating metabolic status of a cell in driving circadian oscillations( Rust et al., 2011; Pattanayak et al., 2014, 2015). Together, a complex bidirectional relationship between the circadian program and metabolism emerges in which the circadian system both controls and is controlled by the metabolic rhythms to set and tune cell physiology with the environmental cycles. This tight coupling between circadian machinery and metabolism is coming to light as a universal feature across kingdoms of life( Green et al., 2008; Dodd et al., 2015).
The cycle of day and night is one of the most recurrent and predictable environmental changes on our planet . Consequently , organisms have evolved mechanisms that allow them to measure time over 24 hours and prepare for the periodic changes between light and dark . These mechanisms , known as circadian clocks , alter the activity of some of the organism’s genes in a rhythmic way across the course of a day . This in turn causes certain behaviors and biological activities of the organism to follow a daily cycle . The bacterium Synechococcus elongatus needs to be able to track the daily cycle of light and dark because it performs photosynthesis and depends on sunlight to form sugars , which can later be broken down to release energy . The time information encoded in the circadian clock of S . elongatus is transmitted to the protein RpaA , which drives the regular circadian changes in gene activity in the cell . If RpaA is removed from the cell or prevented from working , S . elongatus can no longer control rhythmic gene activity and is unable to survive the night . To better understand how the circadian system schedules biological tasks to help an organism to survive , Puszynska and O'Shea studied S . elongatus cells . This revealed that the bacteria normally prepare for darkness by storing sugars during the day and activating several genes at dusk to make enzymes that are required to break down stored sugars . This provides the cells with energy that they need to survive the night . But mutant cells that lack the gene that produces RpaA do not prepare for darkness; they do not accumulate a store of sugars during the day or activate the vital genes at dusk . They have low internal energy levels in the dark and they cannot survive long periods of darkness . Providing the mutant cells with sugar and restoring the activity of the genes responsible for breaking down sugar enabled the cells to maintain energy in darkness and survive the night . It therefore appears that one role of the circadian system of S . elongatus is to coordinate building up sugar reserves during the day with breaking down sugar stores to generate energy during the night . Puszynska and O'Shea also found many other genes that are not activated at dusk in the mutant cells . It will therefore be important to study whether other pathways that help cells to survive and grow are defective in these mutant cells .