Circadian rhythms in rapidly dividing cyanobacteria

Dynamics of the Synechococcus elongatus cytoskeletal GTPase FtsZ yields mechanistic and evolutionary insight into cyanobacterial and chloroplast FtsZs

The division of cyanobacteria and their chloroplast descendants is orchestrated by filamenting temperature-sensitive Z (FtsZ), a cytoskeletal GTPase that polymerizes into protofilaments that form a "Z ring" at the division site. The Z ring has both a scaffolding function for division-complex assembly and a GTPase-dependent contractile function that drives cell or organelle constriction. A single FtsZ performs these functions in bacteria, whereas in chloroplasts, they are performed by two copolymerizing FtsZs, called AtFtsZ2 and AtFtsZ1 in Arabidopsis thaliana, which promote protofilament stability and dynamics, respectively. To probe the differences between cyanobacterial and chloroplast FtsZs, we used light scattering to characterize the in vitro protofilament dynamics of FtsZ from the cyanobacterium Synechococcus elongatus PCC 7942 (SeFtsZ) and investigate how coassembly of AtFtsZ2 or AtFtsZ1 with SeFtsZ influences overall dynamics. SeFtsZ protofilaments assembled rapidly and began disassembling before GTP depletion, whereas AtFtsZ2 protofilaments were far more stable, persisting beyond GTP depletion. Coassembled SeFtsZ-AtFtsZ2 protofilaments began disassembling before GTP depletion, similar to SeFtsZ. In contrast, AtFtsZ1 did not alter disassembly onset when coassembled with SeFtsZ, but fluorescence recovery after photobleaching analysis showed it increased the turnover of SeFtsZ subunits from SeFtsZ-AtFtsZ1 protofilaments, mirroring its effect upon coassembly with AtFtsZ2. Comparisons of our findings with previous work revealed consistent differences between cyanobacterial and chloroplast FtsZ dynamics and suggest that the scaffolding and dynamics-promoting functions were partially separated during evolution of two chloroplast FtsZs from their cyanobacterial predecessor. They also suggest that chloroplasts may have evolved a mechanism distinct from that in cyanobacteria for promoting FtsZ protofilament dynamics.

Genomic analysis and biochemical profiling of an unaxenic strain of Synechococcus sp. isolated from the Peruvian Amazon Basin region

Cyanobacteria are diverse photosynthetic microorganisms able to produce a myriad of bioactive chemicals. To make possible the rational exploitation of these microorganisms, it is fundamental to know their metabolic capabilities and to have genomic resources. In this context, the main objective of this research was to determine the genome features and the biochemical profile of Synechococcus sp. UCP002. The cyanobacterium was isolated from the Peruvian Amazon Basin region and cultured in BG-11 medium. Growth parameters, genome features, and the biochemical profile of the cyanobacterium were determined using standardized methods. Synechococcus sp. UCP002 had a specific growth rate of 0.086 ± 0.008 μ and a doubling time of 8.08 ± 0.78 h. The complete genome of Synechococcus sp. UCP002 had a size of ∼3.53 Mb with a high coverage (∼200x), and its quality parameters were acceptable (completeness = 99.29%, complete and single-copy genes = 97.5%, and contamination = 0.35%). Additionally, the cyanobacterium had six plasmids ranging from 24 to 200 kbp. The annotated genome revealed ∼3,422 genes, ∼ 3,374 protein-coding genes (with ∼41.31% hypothetical protein-coding genes), two CRISPR Cas systems, and 61 non-coding RNAs. Both the genome and plasmids had the genes for prokaryotic defense systems. Additionally, the genome had genes coding the transcription factors of the metalloregulator ArsR/SmtB family, involved in sensing heavy metal pollution. The biochemical profile showed primary nutrients, essential amino acids, some essential fatty acids, pigments (e.g., all-trans-β-carotene, chlorophyll a, and phycocyanin), and phenolic compounds. In conclusion, Synechococcus sp. UCP002 shows biotechnological potential to produce human and animal nutrients and raw materials for biofuels and could be a new source of genes for synthetic biological applications.

A novel photosynthetic biologic topical gel for enhanced localized hyperoxygenation augments wound healing in peripheral artery disease

Peripheral artery disease and the associated ischemic wounds are substantial causes of global morbidity and mortality, affecting over 200 million people worldwide. Although advancements have been made in preventive, pharmacologic, and surgical strategies to treat this disease, ischemic wounds, a consequence of end-stage peripheral artery disease, remain a significant clinical and economic challenge. Synechococcus elongatus is a cyanobacterium that grows photoautotrophically and converts carbon dioxide and water into oxygen. We present a novel topical biologic gel containing S. elongatus that provides oxygen via photosynthesis to augment wound healing by rescuing ischemic tissues caused by peripheral artery disease. By using light rather than blood as a source of energy, our novel topical therapy significantly accelerated wound healing in two rodent ischemic wound models. This novel topical gel can be directly translated to clinical practice by using a localized, portable light source without interfering with patients' daily activities, demonstrating potential to generate a paradigm shift in treating ischemic wounds from peripheral artery disease. Its novelty, low production cost, and ease of clinical translatability can potentially impact the clinical care for millions of patients suffering from peripheral arterial disease.

Spectres of Clock Evolution: Past, Present, and Yet to Come

Circadian clocks are phylogenetically widespread biological oscillators that allow organisms to entrain to environmental cycles and use their steady-state phase relationship to anticipate predictable daily phenomena – such as the light-dark transitions of a day – and prepare accordingly. Present from cyanobacteria to mammals, circadian clocks are evolutionarily ancient and are thought to increase the fitness of the organisms that possess them by allowing for better resource usage and/or proper internal temporal order. Here, we review literature with respect to the ecology and evolution of circadian clocks, with a special focus on cyanobacteria as model organisms. We first discuss what can be inferred about future clock evolution in response to climate change, based on data from latitudinal clines and domestication. We then address our current understanding of the role that circadian clocks might be contributing to the adaptive fitness of cyanobacteria at the present time. Lastly, we discuss what is currently known about the oldest known circadian clock, and the early Earth conditions that could have led to its evolution.

The circadian clock ensures successful DNA replication in cyanobacteria

Disruption of circadian rhythms causes decreased health and fitness, and evidence from multiple organisms links clock disruption to dysregulation of the cell cycle. However, the function of circadian regulation for the essential process of DNA replication remains elusive. Here, we demonstrate that in the cyanobacterium Synechococcus elongatus, a model organism with the simplest known circadian oscillator, the clock generates rhythms in DNA replication to minimize the number of open replication forks near dusk that would have to complete after sunset. Metabolic rhythms generated by the clock ensure that resources are available early at night to support any remaining replication forks. Combining mathematical modeling and experiments, we show that metabolic defects caused by clock-environment misalignment result in premature replisome disassembly and replicative abortion in the dark, leaving cells with incomplete chromosomes that persist through the night. Our study thus demonstrates that a major function of this ancient clock in cyanobacteria is to ensure successful completion of genome replication in a cycling environment.

Evolution of kaiA, a key circadian gene of cyanobacteria

The circadian system of cyanobacteria is built upon a central oscillator consisting of three genes, kaiA, kaiB, and kaiC. The KaiA protein plays a key role in phosphorylation/dephosphorylation cycles of KaiC, which occur over the 24-h period. We conducted a comprehensive evolutionary analysis of the kaiA genes across cyanobacteria. The results show that, in contrast to the previous reports, kaiA has an ancient origin and is as old as cyanobacteria. The kaiA homologs are present in nearly all analyzed cyanobacteria, except Gloeobacter, and have varying domain architecture. Some Prochlorococcales, which were previously reported to lack the kaiA gene, possess a drastically truncated homolog. The existence of the diverse kaiA homologs suggests significant variation of the circadian mechanism, which was described for the model cyanobacterium, Synechococcus elongatus PCC7942. The major structural modifications in the kaiA genes (duplications, acquisition and loss of domains) have apparently been induced by global environmental changes in the different geological periods.

Translating around the clock: Multi-level regulation of post-transcriptional processes by the circadian clock

The endogenous circadian clock functions to maintain optimal physiological health through the tissue specific coordination of gene expression and synchronization between tissues of metabolic processes throughout the 24 hour day. Individuals face numerous challenges to circadian function on a daily basis resulting in significant incidences of circadian disorders in the United States and worldwide. Dysfunction of the circadian clock has been implicated in numerous diseases including cancer, diabetes, obesity, cardiovascular and hepatic abnormalities, mood disorders and neurodegenerative diseases. The circadian clock regulates molecular, metabolic and physiological processes through rhythmic gene expression via transcriptional and post-transcriptional processes. Mounting evidence indicates that post-transcriptional regulation by the circadian clock plays a crucial role in maintaining tissue specific biological rhythms. Circadian regulation affecting RNA stability and localization through RNA processing, mRNA degradation, and RNA availability for translation can result in rhythmic protein synthesis, even when the mRNA transcripts themselves do not exhibit rhythms in abundance. The circadian clock also targets the initiation and elongation steps of translation through multiple pathways. In this review, the influence of the circadian clock across the levels of post-transcriptional, translation, and post-translational modifications are examined using examples from humans to cyanobacteria demonstrating the phylogenetic conservation of circadian regulation. Lastly, we briefly discuss chronotherapies and pharmacological treatments that target circadian function. Understanding the complexity and levels through which the circadian clock regulates molecular and physiological processes is important for future advancement of therapeutic outcomes.

The malaria parasite has an intrinsic clock

Malarial rhythmic fevers are the consequence of the synchronous bursting of red blood cells (RBCs) on completion of the malaria parasite asexual cell cycle. Here, we hypothesized that an intrinsic clock in the parasite Plasmodium chabaudi underlies the 24-hour-based rhythms of RBC bursting in mice. We show that parasite rhythms are flexible and lengthen to match the rhythms of hosts with long circadian periods. We also show that malaria rhythms persist even when host food intake is evenly spread across 24 hours, suggesting that host feeding cues are not required for synchrony. Moreover, we find that the parasite population remains synchronous and rhythmic even in an arrhythmic clock mutant host. Thus, we propose that parasite rhythms are generated by the parasite, possibly to anticipate its circadian environment.

Dissolved oxygen from microalgae-gel patch promotes chronic wound healing in diabetes

Chronic wounds in diabetes undergo a lifetime risk of developing into diabetic foot ulcers. Oxygen is crucial to wound healing by regulating cell proliferation, migration, and neovascularization. However, current oxygen therapies, including hyperbaric oxygen (HBO) and topical gaseous oxygen (TGO), mainly employ gaseous oxygen delivery, which is much less effective in penetrating the skin. Here, we introduce an oxygen-producing patch, made of living microalgae hydrogel, which can produce dissolved oxygen. The superior performance of the patch that results from its dissolved oxygen delivery is >100-fold much more efficient than TGO penetrating the skin. Further experiments indicate that the patch could promote cell proliferation, migration, and tube formation in vitro, and improve chronic wound healing and the survival of skin grafts in diabetic mice. We believe that the microalgae-gel patch can provide continuous dissolved oxygen to improve chronic wound healing.

Are There Circadian Clocks in Non-Photosynthetic Bacteria?

Circadian clocks in plants, animals, fungi, and in photosynthetic bacteria have been well-described. Observations of circadian rhythms in non-photosynthetic Eubacteria have been sporadic, and the molecular basis for these potential rhythms remains unclear. Here, we present the published experimental and bioinformatical evidence for circadian rhythms in these non-photosynthetic Eubacteria. From this, we suggest that the timekeeping functions of these organisms will be best observed and studied in their appropriate complex environments. Given the rich temporal changes that exist in these environments, it is proposed that microorganisms both adapt to and contribute to these daily dynamics through the process of temporal mutualism. Understanding the timekeeping and temporal interactions within these systems will enable a deeper understanding of circadian clocks and temporal programs and provide valuable insights for medicine and agriculture.

The Kai-Protein Clock-Keeping Track of Cyanobacteria's Daily Life

Life has adapted to Earth's day-night cycle with the evolution of endogenous biological clocks. Whereas these circadian rhythms typically involve extensive transcription-translation feedback in higher organisms, cyanobacteria have a circadian clock, which functions primarily as a protein-based post-translational oscillator. Known as the Kai system, it consists of three proteins KaiA, KaiB, and KaiC. In this chapter, we provide a detailed structural overview of the Kai components and how they interact to produce circadian rhythms of global gene expression in cyanobacterial cells. We discuss how the circadian oscillation is coupled to gene expression, intertwined with transcription-translation feedback mechanisms, and entrained by input from the environment. We discuss the use of mathematical models and summarize insights into the cyanobacterial circadian clock from theoretical studies. The molecular details of the Kai system are well documented for the model cyanobacterium Synechococcus elongatus, but many less understood varieties of the Kai system exist across the highly diverse phylum of Cyanobacteria. Several species contain multiple kai-gene copies, while others like marine Prochlorococcus strains have a reduced kaiBC-only system, lacking kaiA. We highlight recent findings on the genomic distribution of kai genes in Bacteria and Archaea and finally discuss hypotheses on the evolution of the Kai system.

Cellular Timekeeping: It's Redox o'Clock

Mounting evidence in recent years supports the extensive interaction between the circadian and redox systems. The existence of such a relationship is not surprising because most organisms, be they diurnal or nocturnal, display daily oscillations in energy intake, locomotor activity, and exposure to exogenous and internally generated oxidants. The transcriptional clock controls the levels of many antioxidant proteins and redox-active cofactors, and, conversely, the cellular redox poise has been shown to feed back to the transcriptional oscillator via redox-sensitive transcription factors and enzymes. However, the circadian cycles in the S-sulfinylation of the peroxiredoxin (PRDX) proteins constituted the first example of an autonomous circadian redox oscillation, which occurred independently of the transcriptional clock. Importantly, the high phylogenetic conservation of these rhythms suggests that they might predate the evolution of the transcriptional oscillator, and therefore could be a part of a primordial circadian redox/metabolic oscillator. This discovery forced the reappraisal of the dogmatic transcription-centered view of the clockwork and opened a new avenue of research. Indeed, the investigation into the links between the circadian and redox systems is still in its infancy, and many important questions remain to be addressed.

Circadian clock during plant development

Plants have endogenous biological clocks that allow organisms to anticipate and prepare for daily and seasonal environmental changes and increase their fitness in changing environments. The circadian clock in plants, as in animals and insects, mainly consists of multiple interlocking transcriptional/translational feedback loops. The circadian clock can be entrained by environmental cues such as light, temperature and nutrient status to synchronize internal biological rhythms with surrounding environments. Output pathways link the circadian oscillator to various physiological, developmental, and reproductive processes for adjusting the timing of these biological processes to an appropriate time of day or a suitable season. Recent genomic studies have demonstrated that polymorphism in circadian clock genes may contribute to local adaptations over a wide range of latitudes in many plant species. In the present review, we summarize the circadian regulation of biological processes throughout the life cycle of plants, and describe the contribution of the circadian clock to local adaptation.

An innovative biologic system for photon-powered myocardium in the ischemic heart

Coronary artery disease is one of the most common causes of death and disability, afflicting more than 15 million Americans. Although pharmacological advances and revascularization techniques have decreased mortality, many survivors will eventually succumb to heart failure secondary to the residual microvascular perfusion deficit that remains after revascularization. We present a novel system that rescues the myocardium from acute ischemia, using photosynthesis through intramyocardial delivery of the cyanobacterium Synechococcus elongatus. By using light rather than blood flow as a source of energy, photosynthetic therapy increases tissue oxygenation, maintains myocardial metabolism, and yields durable improvements in cardiac function during and after induction of ischemia. By circumventing blood flow entirely to provide tissue with oxygen and nutrients, this system has the potential to create a paradigm shift in the way ischemic heart disease is treated.

Circadian Rhythm and the Gut Microbiome

Circadian rhythms are 24-h patterns regulating behavior, organs, and cells in living organisms. These rhythms align biological functions with regular and predictable environmental patterns to optimize function and health. Disruption of these rhythms can be detrimental resulting in metabolic syndrome, cancer, or cardiovascular disease, just to name a few. It is now becoming clear that the intestinal microbiome is also regulated by circadian rhythms via intrinsic circadian clocks as well as via the host organism. Microbiota rhythms are regulated by diet and time of feeding which can alter both microbial community structure and metabolic activity which can significantly impact host immune and metabolic function. In this review, we will cover how host circadian rhythms are generated and maintained, how host circadian rhythms can be disrupted, as well as the consequences of circadian rhythm disruption. We will further highlight the newly emerging literature indicating the importance of circadian rhythms of the intestinal microbiota.

Circadian Timing Mechanism in the Prokaryotic Clock System of Cyanobacteria

Cyanobacteria are the simplest organisms known to exhibit circadian rhythms and have provided experimental model systems for the dissection of basic properties of circadian organization at the molecular, physiological, and ecological levels. This review focuses on the molecular and genetic mechanisms of circadian rhythm generation in cyanobacteria. Recent analyses have revealed the existence of multiple feedback processes in the prokaryotic circadian system and have led to a novel molecular oscillator model. Here, the authors summarize current understanding of, and open questions about, the cyanobacterial oscillator.

Circadian Rhythms in Cyanobacteria

Life on earth is subject to daily and predictable fluctuations in light intensity, temperature, and humidity created by rotation of the earth. Circadian rhythms, generated by a circadian clock, control temporal programs of cellular physiology to facilitate adaptation to daily environmental changes. Circadian rhythms are nearly ubiquitous and are found in both prokaryotic and eukaryotic organisms. Here we introduce the molecular mechanism of the circadian clock in the model cyanobacterium Synechococcus elongatus PCC 7942. We review the current understanding of the cyanobacterial clock, emphasizing recent work that has generated a more comprehensive understanding of how the circadian oscillator becomes synchronized with the external environment and how information from the oscillator is transmitted to generate rhythms of biological activity. These results have changed how we think about the clock, shifting away from a linear model to one in which the clock is viewed as an interactive network of multifunctional components that are integrated into the context of the cell in order to pace and reset the oscillator. We conclude with a discussion of how this basic timekeeping mechanism differs in other cyanobacterial species and how information gleaned from work in cyanobacteria can be translated to understanding rhythmic phenomena in other prokaryotic systems.

Optimal Prediction by Cellular Signaling Networks

Living cells can enhance their fitness by anticipating environmental change. We study how accurately linear signaling networks in cells can predict future signals. We find that maximal predictive power results from a combination of input-noise suppression, linear extrapolation, and selective readout of correlated past signal values. Single-layer networks generate exponential response kernels, which suffice to predict Markovian signals optimally. Multilayer networks allow oscillatory kernels that can optimally predict non-Markovian signals. At low noise, these kernels exploit the signal derivative for extrapolation, while at high noise, they capitalize on signal values in the past that are strongly correlated with the future signal. We show how the common motifs of negative feedback and incoherent feed-forward can implement these optimal response functions. Simulations reveal that E. coli can reliably predict concentration changes for chemotaxis, and that the integration time of its response kernel arises from a trade-off between rapid response and noise suppression.

Giving Time Purpose: The Synechococcus elongatus Clock in a Broader Network Context

Early research on the cyanobacterial clock focused on characterizing the genes needed to keep, entrain, and convey time within the cell. As the scope of assays used in molecular genetics has expanded to capture systems-level properties (e.g., RNA-seq, ChIP-seq, metabolomics, high-throughput screening of genetic variants), so has our understanding of how the clock fits within and influences a broader cellular context. Here we review the work that has established a global perspective of the clock, with a focus on (a) an emerging network-centric view of clock architecture, (b) mechanistic insights into how temporal and environmental cues are transmitted and integrated within this network,

Integrative analysis of circadian transcriptome and metabolic network reveals the role of de novo purine synthesis in circadian control of cell cycle

Metabolism is the major output of the circadian clock in many organisms. We developed a computational method to integrate both circadian gene expression and metabolic network. Applying this method to zebrafish circadian transcriptome, we have identified large clusters of metabolic genes containing mostly genes in purine and pyrimidine metabolism in the metabolic network showing similar circadian phases. Our metabolomics analysis found that the level of inosine 5'-monophosphate (IMP), an intermediate metabolite in de novo purine synthesis, showed significant circadian oscillation in larval zebrafish. We focused on IMP dehydrogenase (impdh), a rate-limiting enzyme in de novo purine synthesis, with three circadian oscillating gene homologs: impdh1a, impdh1b and impdh2. Functional analysis revealed that impdh2 contributes to the daily rhythm of S phase in the cell cycle while impdh1a contributes to ocular development and pigment synthesis. The three zebrafish homologs of impdh are likely regulated by different circadian transcription factors. We propose that the circadian regulation of de novo purine synthesis that supplies crucial building blocks for DNA replication is an important mechanism conferring circadian rhythmicity on the cell cycle. Our method is widely applicable to study the impact of circadian transcriptome on metabolism in complex organisms.

Metabolic compensation and circadian resilience in prokaryotic cyanobacteria

For a biological oscillator to function as a circadian pacemaker that confers a fitness advantage, its timing functions must be stable in response to environmental and metabolic fluctuations. One such stability enhancer, temperature compensation, has long been a defining characteristic of these timekeepers. However, an accurate biological timekeeper must also resist changes in metabolism, and this review suggests that temperature compensation is actually a subset of a larger phenomenon, namely metabolic compensation, which maintains the frequency of circadian oscillators in response to a host of factors that impinge on metabolism and would otherwise destabilize these clocks. The circadian system of prokaryotic cyanobacteria is an illustrative model because it is composed of transcriptional and nontranscriptional oscillators that are coupled to promote resilience. Moreover, the cyanobacterial circadian program regulates gene activity and metabolic pathways, and it can be manipulated to improve the expression of bioproducts that have practical value.

Improved Free Fatty Acid Production in Cyanobacteria with Synechococcus sp. PCC 7002 as Host

Microbial free fatty acids (FFAs) have been proposed as a potential feedstock for renewable energy. The ability to directly convert carbon dioxide into FFAs makes cyanobacteria ideal hosts for renewable FFA production. Previous metabolic engineering efforts using the cyanobacterial hosts Synechocystis sp. PCC 6803 and Synechococcus elongatus PCC 7942 have demonstrated this direct conversion of carbon dioxide into FFAs; however, FFA yields in these hosts are limited by the negative impact of FFA production on the host cell physiology. This work investigates the use of Synechococcus sp. PCC 7002 as a cyanobacterial host for FFA production. In comparison to S. elongatus PCC 7942, Synechococcus sp. PCC 7002 strains produced and excreted FFAs at similar concentrations but without the detrimental effects on host physiology. The enhanced tolerance to FFA production with Synechococcus sp. PCC 7002 was found to be temperature-dependent, with physiological effects such as reduced photosynthetic yield and decreased photosynthetic pigments observed at higher temperatures. Additional genetic manipulations were targeted for increased FFA production, including thioesterases and ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). Overexpression of non-native RuBisCO subunits (rbcLS) from a psbAI promoter resulted in more than a threefold increase in FFA production, with excreted FFA concentrations reaching >130 mg/L. This work illustrates the importance of host strain selection for cyanobacterial biofuel production and demonstrates that the FFA tolerance of Synechococcus sp. PCC 7002 can allow for high yields of excreted FFA.

Metabolic and nontranscriptional circadian clocks: eukaryotes

Circadian clocks are cellular timekeeping mechanisms that coordinate behavior and physiology around the 24-h day in most living organisms. Misalignment of an organism's clock with its environment is associated with long-term adverse fitness consequences, as exemplified by the link between circadian disruption and various age-related diseases in humans. Current eukaryotic models of the circadian oscillator rely on transcription/translation feedback loop mechanisms, supplemented with accessory cytosolic loops that connect them to cellular physiology. However, mounting evidence is questioning the absolute necessity of transcription-based oscillators for circadian rhythmicity, supported by the recent discovery of oxidation-reduction cycles of peroxiredoxin proteins, which persist even in the absence of transcription. A more fundamental mechanism based on metabolic cycles could thus underlie circadian transcriptional and cytosolic rhythms, thereby promoting circadian oscillations to integral properties of cellular metabolism.

Rhythmic and sustained oscillations in metabolism and gene expression of Cyanothece sp. ATCC 51142 under constant light

Cyanobacteria, a group of photosynthetic prokaryotes, oscillate between day and night time metabolisms with concomitant oscillations in gene expression in response to light/dark cycles (LD). The oscillations in gene expression have been shown to sustain in constant light (LL) with a free running period of 24 h in a model cyanobacterium Synechococcus elongatus PCC 7942. However, equivalent oscillations in metabolism are not reported under LL in this non-nitrogen fixing cyanobacterium. Here we focus on Cyanothece sp. ATCC 51142, a unicellular, nitrogen-fixing cyanobacterium known to temporally separate the processes of oxygenic photosynthesis and oxygen-sensitive nitrogen fixation. In a recent report, metabolism of Cyanothece 51142 has been shown to oscillate between photosynthetic and respiratory phases under LL with free running periods that are temperature dependent but significantly shorter than the circadian period. Further, the oscillations shift to circadian pattern at moderate cell densities that are concomitant with slower growth rates. Here we take this understanding forward and demonstrate that the ultradian rhythm under LL sustains at much higher cell densities when grown under turbulent regimes that simulate flashing light effect. Our results suggest that the ultradian rhythm in metabolism may be needed to support higher carbon and nitrogen requirements of rapidly growing cells under LL. With a comprehensive Real time PCR based gene expression analysis we account for key regulatory interactions and demonstrate the interplay between clock genes and the genes of key metabolic pathways. Further, we observe that several genes that peak at dusk in Synechococcus peak at dawn in Cyanothece and vice versa. The circadian rhythm of this organism appears to be more robust with peaking of genes in anticipation of the ensuing photosynthetic and respiratory metabolic phases.

Growth-rate-dependent dynamics of a bacterial genetic oscillator

Gene networks exhibiting oscillatory dynamics are widespread in biology. The minimal regulatory designs giving rise to oscillations have been implemented synthetically and studied by mathematical modeling. However, most of the available analyses generally neglect the coupling of regulatory circuits with the cellular "chassis" in which the circuits are embedded. For example, the intracellular macromolecular composition of fast-growing bacteria changes with growth rate. As a consequence, important parameters of gene expression, such as ribosome concentration or cell volume, are growth-rate dependent, ultimately coupling the dynamics of genetic circuits with cell physiology. This work addresses the effects of growth rate on the dynamics of a paradigmatic example of genetic oscillator, the repressilator. Making use of empirical growth-rate dependencies of parameters in bacteria, we show that the repressilator dynamics can switch between oscillations and convergence to a fixed point depending on the cellular state of growth, and thus on the nutrients it is fed. The physical support of the circuit (type of plasmid or gene positions on the chromosome) also plays an important role in determining the oscillation stability and the growth-rate dependence of period and amplitude. This analysis has potential application in the field of synthetic biology, and suggests that the coupling between endogenous genetic oscillators and cell physiology can have substantial consequences for their functionality.

Non-transcriptional oscillators in circadian timekeeping

Circadian clocks have evolved as an adaptation to life on a rotating planet, and orchestrate rhythmic changes in physiology to match the time of day. For decades, cellular circadian rhythms were considered to solely result from feedback between the products of rhythmically expressed genes. These transcriptional/translational feedback loops (TTFLs) have been ubiquitously studied, and explain the majority of circadian outputs. In recent years, however, non-transcriptional processes were shown to be major contributors to circadian rhythmicity. These key findings have profound implications on our understanding of the evolution and mechanistic basis of cellular circadian timekeeping. This review summarises and discusses these results and the experimental and theoretical evidence of a possible relation between non-transcriptional oscillator (NTO) mechanisms and TTFL oscillations.

The cyanobacterial circadian system: from biophysics to bioevolution

Recent studies have unveiled the molecular machinery responsible for the biological clock in cyanobacteria and found that it exerts pervasive control over cellular processes including global gene expression. Indeed, the entire chromosome undergoes daily cycles of topology/compaction! The circadian system comprises both a posttranslational oscillator (PTO) and a transcriptional/translational feedback loop (TTFL). The PTO can be reconstituted in vitro with three purified proteins (KaiA, KaiB, and KaiC) and ATP. These are the only circadian proteins for which high-resolution structures are available. Phase in this nanoclockwork has been associated with key phosphorylations of KaiC. Structural considerations illuminate the mechanism by which the KaiABC oscillator ratchets unidirectionally. Models of the complete in vivo system have important implications for our understanding of circadian clocks in higher organisms, including mammals. The conjunction of structural, biophysical, and biochemical approaches to this system has brought our understanding of the molecular mechanisms of biological timekeeping to an unprecedented level.

Identification and modeling of genes with diurnal oscillations from microarray time series data

Behavior of living organisms is strongly modulated by the day and night cycle giving rise to a cyclic pattern of activities. Such a pattern helps the organisms to coordinate their activities and maintain a balance between what could be performed during the "day" and what could be relegated to the "night." This cyclic pattern, called the "Circadian Rhythm," is a biological phenomenon observed in a large number of organisms. In this paper, our goal is to analyze transcriptome data from Cyanothece for the purpose of discovering genes whose expressions are rhythmic. We cluster these genes into groups that are close in terms of their phases and show that genes from a specific metabolic functional category are tightly clustered, indicating perhaps a "preferred time of the day/night" when the organism performs this function. The proposed analysis is applied to two sets of microarray experiments performed under varying incident light patterns. Subsequently, we propose a model with a network of three phase oscillators together with a central master clock and use it to approximate a set of "circadian-controlled genes" that can be approximated closely.

Robust circadian clocks from coupled protein-modification and transcription-translation cycles

The cyanobacterium Synechococcus elongatus uses both a protein phosphorylation cycle and a transcription-translation cycle to generate circadian rhythms that are highly robust against biochemical noise. We use stochastic simulations to analyze how these cycles interact to generate stable rhythms in growing, dividing cells. We find that a protein phosphorylation cycle by itself is robust when protein turnover is low. For high decay or dilution rates (and compensating synthesis rates), however, the phosphorylation-based oscillator loses its integrity. Circadian rhythms thus cannot be generated with a phosphorylation cycle alone when the growth rate, and consequently the rate of protein dilution, is high enough; in practice, a purely posttranslational clock ceases to function well when the cell doubling time drops below the 24-h clock period. At higher growth rates, a transcription-translation cycle becomes essential for generating robust circadian rhythms. Interestingly, although a transcription-translation cycle is necessary to sustain a phosphorylation cycle at high growth rates, a phosphorylation cycle can dramatically enhance the robustness of a transcription-translation cycle at lower protein decay or dilution rates. In fact, the full oscillator built from these two tightly intertwined cycles far outperforms not just each of its two components individually, but also a hypothetical system in which the two parts are coupled as in textbook models of coupled phase oscillators. Our analysis thus predicts that both cycles are required to generate robust circadian rhythms over the full range of growth conditions.

Coupling cellular oscillators--circadian and cell division cycles in cyanobacteria

Understanding how different cellular subsystems are coupled to each other is a fundamental question in the quest for reliably predicting the dynamic state of a cell. Coupling of oscillatory subsystems is especially interesting as dynamic interactions play an important role in cell physiology. Here we review recent efforts that investigate and quantify the coupling between the circadian and cell cycle clocks in cyanobacteria as a model system. We discuss studies that quantify the coupling from a systems point of view in which the oscillators are described in abstract terms. We also emphasize recent developments aimed at uncovering the molecular details underlying the coupling between these systems. Finally we review recent studies that describe a potentially more overarching regulation scheme through global circadian regulation of DNA packing and gene expression.

Circadian clocks and cell division: what's the pacemaker?

Evolution has selected a system of two intertwined cell cycles: the cell division cycle (CDC) and the daily (circadian) biological clock. The circadian clock keeps track of solar time and programs biological processes to occur at environmentally appropriate times. One of these processes is the CDC, which is often gated by the circadian clock. The intermeshing of these two cell cycles is probably responsible for the observation that disruption of the circadian system enhances susceptibility to some kinds of cancer. The core mechanism underlying the circadian clockwork has been thought to be a transcription & translation feedback loop (TTFL), but recent evidence from studies with cyanobacteria, synthetic oscillators and immortalized cell lines suggests that the core circadian pacemaking mechanism that gates cell division in mammalian cells could be a post-translational oscillator (PTO).

Synchronization of circadian oscillation of phosphorylation level of KaiC in vitro

In recent experimental reports, robust circadian oscillation of the phosphorylation level of KaiC has been reconstituted by incubating three cyanobacterial proteins, KaiA, KaiB, and KaiC, with ATP in vitro. This reconstitution indicates that protein-protein interactions and the associated ATP hydrolysis suffice to generate the oscillation, and suggests that the rhythm arising from this protein-based system is the circadian clock pacemaker in cyanobacteria. The mechanism of this reconstituted oscillation, however, remains elusive. In this study, we extend our previous model of oscillation by explicitly taking two phosphorylation sites of KaiC into account and we apply the extended model to the problem of synchrony of two oscillatory samples mixed at different phases. The agreement between the simulated and observed data suggests that the combined mechanism of the allosteric transition of KaiC hexamers and the monomer shuffling between them plays a key role in synchronization among KaiC hexamers and hence underlies the population-level oscillation of the ensemble of Kai proteins. The predicted synchronization patterns in mixtures of unequal amounts of two samples provide further opportunities to experimentally check the validity of the proposed mechanism. This mechanism of synchronization should be important in vivo for the persistent oscillation when Kai proteins are synthesized at random timing in cyanobacterial cells.

Information-optimal transcriptional response to oscillatory driving

Intracellular transmission of information via chemical and transcriptional networks is thwarted by a physical limitation: The finite copy number of the constituent chemical species introduces unavoidable intrinsic noise. Here we solve for the complete probabilistic description of the intrinsically noisy response to an oscillatory driving signal. We derive and numerically verify a number of simple scaling laws. Unlike in the case of measuring a static quantity, response to an oscillatory signal can exhibit a resonant frequency which maximizes information transmission. Furthermore, we show that the optimal regulatory design is dependent on biophysical constraints (i.e., the allowed copy number and response time). The resulting phase diagram illustrates under what conditions threshold regulation outperforms linear regulation.

Ultradian Growth in Prochlorococcus spp

Species of the widespread marine prokaryote Prochlorococcus exhibited ultradian growth (faster than 1 division per day) both in situ and in culture, even though cell division is strictly phased to the light-dark cycle. Under optimal conditions a second DNA replication and cell division closely followed, but did not overlap with, the first division. The timing of cell cycle events was not affected by light intensity or duration, suggesting control by a light-triggered timer or circadian clock rather than by completion of a light-dependent assimilation phase. This mode of ultradian growth has not been observed previously and poses new questions about the regulation of cellular rhythms in prokaryotes. In addition, it implies that conclusions regarding the lack of nutrient limitation of Prochlorococcus in the open ocean, which were based on the appearance that cells were growing at their maximal rate, need to be reconsidered.

The molecular clockwork of a protein-based circadian oscillator

The circadian clock of the cyanobacterium Synechococcus elongatus PCC 7942 is governed by a core oscillator consisting of the proteins KaiA, KaiB, and KaiC. Remarkably, circadian oscillations in the phosphorylation state of KaiC can be reconstituted in a test tube by mixing the three Kai proteins and adenosine triphosphate. The in vitro oscillator provides a well-defined system in which experiments can be combined with mathematical analysis to understand the mechanism of a highly robust biological oscillator. In this Review, we summarize the biochemistry of the Kai proteins and examine models that have been proposed to explain how oscillations emerge from the properties of the oscillator's constituents.

Diel and daily fluctuations in virioplankton production in coastal ecosystems

Viruses saturate the world around us, yet a basic understanding of how viral impacts on microbial host organisms vary over days to hours, which typify the replication cycles of aquatic viruses, remains elusive. Thus, diel patterns of viral production (VP) in Chesapeake Bay surface waters were examined on five sampling dates. Day-to-day variations in VP in the Chesapeake and coastal California surface waters were also investigated. Significant variations in VP were detected over 24 h cycles during four of five studies, but rates did not vary significantly over the course of a few days in either location. Diel patterns of VP displayed seasonality with shorter viral assemblage turnover times and shorter times to maximum viral abundance in summer, implying shorter replication cycles for virus-host systems in warmer months. No correlation was found between VP and time of day, likely due to seasonal changes in the diel patterns of VP. This analysis significantly increases our knowledge of the short-term patterning of in situ VP, and thus viral impacts, and suggests that variations in viral biology in response to changes in host communities or physio-chemical properties affect both diel and seasonal cycles and magnitudes of VP.

Cyanobacterial daily life with Kai-based circadian and diurnal genome-wide transcriptional control in Synechococcus elongatus

In the unicellular cyanobacterium Synechococcus elongatus PCC 7942, essentially all promoter activities are under the control of the circadian clock under continuous light (LL) conditions. Here, we used high-density oligonucleotide arrays to explore comprehensive profiles of genome-wide Synechococcus gene expression in wild-type, kaiABC-null, and kaiC-overexpressor strains under LL and continuous dark (DD) conditions. In the wild-type strains, >30% of transcripts oscillated significantly in a circadian fashion, peaking at subjective dawn and dusk. Such circadian control was severely attenuated in kaiABC-null strains. Although it has been proposed that KaiC globally represses gene expression, our analysis revealed that dawn-expressed genes were up-regulated by kaiC-overexpression so that the clock was arrested at subjective dawn. Transfer of cells to DD conditions from LL immediately suppressed expression of most of the genes, while the clock kept even time in the absence of transcriptional feedback. Thus, the Synechococcus genome seems to be primarily regulated by light/dark cycles and is dramatically modified by the protein-based circadian oscillator.

Stability and lability of circadian period of gene expression in the cyanobacterium Synechococcus elongatus

Molecular aspects of the circadian clock in the cyanobacterium Synechococcus elongatus have been described in great detail. Three-dimensional structures have been determined for the three proteins, KaiA, KaiB and KaiC, that constitute a central oscillator of the clock. Moreover, a temperature-compensated circadian rhythm of KaiC phosphorylation can be reconstituted in vitro with the addition of KaiA, KaiB and ATP. These data suggest a relatively simple circadian system in which a single oscillator provides temporal information for all downstream processes. However, in vivo the situation is more complex, and additional components contribute to the maintenance of a normal period, the resetting of relative phases of circadian oscillations, and the control of rhythms of gene expression. We show here that two well-studied promoters in the S. elongatus genome report different circadian periods of expression under a given set of conditions in wild-type as well as mutant genetic backgrounds. Moreover, the period differs between these promoters with respect to modulation by light intensity, growth phase, and the presence or absence of a promoter-recognition subunit of RNA polymerase. These data contrast sharply with the current clock model in which a single Kai-based oscillator governs circadian period. Overall, these findings suggest that complex interactions among the circadian oscillator, perhaps other oscillators, and other cellular machinery result in a clock that is plastic and sensitive to the environment and to the physiological state of the cell.

Structural insights into a circadian oscillator

An endogenous circadian system in cyanobacteria exerts pervasive control over cellular processes, including global gene expression. Indeed, the entire chromosome undergoes daily cycles of topological changes and compaction. The biochemical machinery underlying a circadian oscillator can be reconstituted in vitro with just three cyanobacterial proteins, KaiA, KaiB, and KaiC. These proteins interact to promote conformational changes and phosphorylation events that determine the phase of the in vitro oscillation. The high-resolution structures of these proteins suggest a ratcheting mechanism by which the KaiABC oscillator ticks unidirectionally. This posttranslational oscillator may interact with transcriptional and translational feedback loops to generate the emergent circadian behavior in vivo. The conjunction of structural, biophysical, and biochemical approaches to this system reveals molecular mechanisms of biological timekeeping.

A cyanobacterial circadian clockwork

Cyanobacteria have become a major model system for analyzing circadian rhythms. The temporal program in this organism enhances fitness in rhythmic environments and is truly global--essentially all genes are regulated by the circadian system. The topology of the chromosome also oscillates and possibly regulates the rhythm of gene expression. The underlying circadian mechanism appears to consist of both a post-translational oscillator (PTO) and a transcriptional/translational feedback loop (TTFL). The PTO can be reconstituted in vitro with three purified proteins (KaiA, KaiB, and KaiC) and ATP. These three core oscillator proteins have been crystallized and structurally determined, the only full-length circadian proteins to be so characterized. The timing of cell division is gated by a circadian checkpoint, but the circadian pacemaker is not influenced by the status of the cell division cycle. This imperturbability may be due to the presence of the PTO that persists under conditions in which metabolism is repressed. Recent biochemical, biophysical, and structural discoveries have brought the cyanobacterial circadian system to the brink of explaining heretofore unexplainable biochemical characteristics of a circadian oscillator: the long time constant, precision, and temperature compensation.

Genome streamlining results in loss of robustness of the circadian clock in the marine cyanobacterium Prochlorococcus marinus PCC 9511

The core oscillator of the circadian clock in cyanobacteria consists of 3 proteins, KaiA, KaiB, and KaiC. All 3 have previously been shown to be essential for clock function. Accordingly, most cyanobacteria possess at least 1 copy of each kai gene. One exception is the marine genus Prochlorococcus, which we suggest here has suffered a stepwise deletion of the kaiA gene, together with significant genome streamlining. Nevertheless, natural Prochlorococcus populations and laboratory cultures are strongly synchronized by the alternation of day and night, displaying 24-h rhythms in DNA replication, with a temporal succession of G1, S, and G2-like cell cycle phases. Using quantitative real-time PCR, we show here that in Prochlorococcus marinus PCC 9511, the mRNA levels of the clock genes kaiB and kaiC, as well as a few other selected genes including psbA, also displayed marked diel variations when cultures were kept under a light-dark rhythm. However, both cell cycle and psbA gene expression rhythms damped very rapidly under continuous light. In the closely related Synechococcus sp. WH8102, which possesses all 3 kai genes, cell cycle rhythms persisted over several days, in agreement with established cyanobacterial models. These data indicate a correlation between the loss of kaiA and a loss of robustness in the endogenous oscillator of Prochlorococcus and raise questions about how a basic KaiBC system may function and through which mechanism the daily "lights-on" and "lights-off" signal could be mediated.

Biological Rhythms Workshop IA: molecular basis of rhythms generation

Current circadian models are based on genetic, biochemical, and structural data that, when combined, provide a comprehensive picture of the molecular basis for rhythms generation. These models describe three basic elements-input pathways, oscillator, and output pathways-to which each molecular component is assigned. The lines between these elements are often blurred because some proteins function in more than one element of the circadian system. The end result of these molecular oscillations is the same in each system (near 24-hour timing), yet the proteins involved, the interactions among those proteins, and the regulatory feedback loops differ. Here, the currentmodels for the molecular basis for rhythms generation are described for the prokaryotic cyanobacterium Synechococcus elongatus as well as the eukaryotic systems Neurospora crassa, Drosophila melanogaster, Arabidopsis thaliana, and mammals (particularly rodents).

Bacterial circadian programs

Twenty years ago, it was widely believed that prokaryotes were too "simple" to have evolved circadian programs. Since that time, however, the cyanobacterial circadian system has progressed from a curiosity to a major model system for analyzing clock phenomena. In addition to globally regulating gene expression, cyanobacteria are one of the only systems in which the adaptive fitness of a circadian system has been rigorously evaluated. Moreover, cyanobacteria are the only clock system in which all essential proteins of the core oscillator have been crystallized and structurally determined, namely, the KaiA, KaiB, and KaiC proteins. A biochemical oscillator can be reconstituted in vitro with these three purified Kai proteins and displays the key properties of temperature-compensated rhythmicity. This result spectacularly demonstrates that a strictly posttranslational clock is sufficient to elaborate circadian phenomena and that a transcription-translation feedback loop is not obligatory. The conjunction of structural information on essential clock proteins with a defined system that reconstitutes circadian oscillations in vitro leads to a turning point whereby biophysical and biochemical approaches bring analyses of circadian clock-work to an unprecedented level of molecular detail.

A cyanobacterial circadian clock based on the Kai oscillator

In the cyanobacterium Synechococcus elongatus PCC 7942, the products of three genes (kaiA, kaiB, and kaiC) have been identified as essential components of the circadian clock. Recently, we reconstituted the self-sustainable circadian oscillation of the KaiC phosphorylation state by incubating purified KaiC with KaiA, KaiB, and ATP. This in vitro oscillation persisted for at least three cycles and the period was compensated against temperature changes. Period lengths observed in vivo in various kaiC mutants were consistent with those measured using in vitro mixtures containing the respective mutant KaiC proteins. These results demonstrate that the oscillation of KaiC phosphorylation is the primary pacemaker of the cyanobacterial circadian clock and reveal a novel function of proteins as timing devices that govern cellular metabolism. We further analyzed four aspects of the KaiC phosphorylation cycle in vitro: the interactions among KaiA, KaiB, and KaiC; the functions of the two phosphorylation sites, the energetics that determine the circadian period, and the mechanisms that synchronize the components of the Kai oscillator. From these analyses, we have proposed a circadian program consisting of the three proteins that keeps biological time in a living cell.

Integrating the circadian oscillator into the life of the cyanobacterial cell

In two decades, the study of circadian rhythms in cyanobacteria has gone from observations of phenomena in intractable species to the development of a model organism for mechanistic study, atomic-resolution structures of components, and reconstitution of a circadian biochemical oscillation in vitro. With sophisticated biochemical, biophysical, genetic, and genomic tools in place, the circadian clock of the unicellular cyanobacterium Synechococcus elongatus is poised to be the first for which a systems-level understanding can be achieved.

Fluorescence staining of live cyanobacterial cells suggest non-stringent chromosome segregation and absence of a connection between cytoplasmic and thylakoid membranes

Background

In spite of their abundance and importance, little is known about cyanobacterial cell biology and their cell cycle. During each cell cycle, chromosomes must be separated into future daughter cells, i.e. into both cell halves, which in many bacteria is achieved by an active machinery that operates during DNA replication. Many cyanobacteria contain multiple identical copies of the chromosome, but it is unknown how chromosomes are segregated into future daughter cells, and if an active or passive mechanism is operative. In addition to an outer and an inner cell membrane, cyanobacteria contain internal thylakoid membranes that carry the active photosynthetic machinery. It is unclear whether thylakoid membranes are invaginations of the inner cell membrane, or an independent membrane system.

Results

We have used different fluorescent dyes to study the organization of chromosomes and of cell and thylakoid membranes in live cyanobacterial cells. FM1-43 stained the outer and inner cytoplasmic membranes but did not enter the interior of the cell. In contrast, thylakoid membranes in unicellular Synechocystis cells became visible through a membrane-permeable stain only. Furthermore, continuous supply of the fluorescent dye FM1-43 resulted in the formation of one to four intracellular fluorescent structures in Synechocystis cells, within occurred within 30 to 60 minutes, and may represent membrane vesicles. Using fluorescent DNA stains, we found that Synechocystis genomic DNA is compacted in the cell centre that is devoid of thylakoid membranes. Nucleoids segregated very late in the cell cycle, just before complete closing of the division septum. In striking contrast to Bacillus subtilis, which possesses an active chromosome segregation machinery, fluorescence intensity of stained nucleoids differed considerably between the two Synechocystis daughter cells soon after cell division.

Conclusion

Our experiments strongly support the idea that the cytoplasmic and thylakoid membranes are not directly connected, but separate entities, in unicellular cyanobacteria. Our findings suggest that a transport system may exist between the cytoplasmic membrane and thylakoids, which could mediate the extension of thylakoid membranes and possibly also protein transport from the cytoplasmic membrane to thylakoid membranes. The cell cycle studies in Synechocystis sp. PCC 6803 show that the multiple chromosome copies per cell segregate very late in the cell cycle and in a much less stringent manner than in B. subtilis cells, indicating that chromosomes may become segregated randomly and in a passive fashion, possibly through constriction of the division septum.