Clock control of ultradian respiratory oscillation found during yeast continuous culture

Temporal metabolic partitioning of the yeast and protist cellular networks: the cell is a global scale-invariant (fractal or self-similar) multioscillator

Britton Chance, electronics expert when a teenager, became an enthusiastic student of biological oscillations, passing on this enthusiasm to many students and colleagues, including one of us (DL). This historical essay traces BC's influence through the accumulated work of DL to DL's many collaborators. The overall temporal organization of mass-energy, information, and signaling networks in yeast in self-synchronized continuous cultures represents, until now, the most characterized example of in vivo elucidation of time structure. Continuous online monitoring of dissolved gases by direct measurement (membrane-inlet mass spectrometry, together with NAD(P)H and flavin fluorescence) gives strain-specific dynamic information from timescales of minutes to hours as does two-photon imaging. The predominantly oscillatory behavior of network components becomes evident, with spontaneously synchronized cellular respiration cycles between discrete periods of increased oxygen consumption (oxidative phase) and decreased oxygen consumption (reductive phase). This temperature-compensated ultradian clock provides coordination, linking temporally partitioned functions by direct feedback loops between the energetic and redox state of the cell and its growing ultrastructure. Multioscillatory outputs in dissolved gases with 13 h, 40 min, and 4 min periods gave statistical self-similarity in power spectral and relative dispersional analyses: i.e., complex nonlinear (chaotic) behavior and a functional scale-free (fractal) network operating simultaneously over several timescales.

The molecular basis of metabolic cycles and their relationship to circadian rhythms

Metabolic cycles result from the partitioning of oxidative and reductive metabolism into rhythmic phases of gene expression and oscillating post-translational protein modifications. Relatively little is known about how these switches in gene expression are controlled, although recent studies have suggested that transcription itself may play a central role. This review explores the molecular basis of the metabolic and gene-expression oscillations in the yeast Saccharomyces cerevisiae, as well as how they relate to other biological time-keeping mechanisms, such as circadian rhythms.

Autonomous Metabolic Oscillations Robustly Gate the Early and Late Cell Cycle

Eukaryotic cell division is known to be controlled by the cyclin/cyclin dependent kinase (CDK) machinery. However, eukaryotes have evolved prior to CDKs, and cells can divide in the absence of major cyclin/CDK components. We hypothesized that an autonomous metabolic oscillator provides dynamic triggers for cell-cycle initiation and progression. Using microfluidics, cell-cycle reporters, and single-cell metabolite measurements, we found that metabolism of budding yeast is a CDK-independent oscillator that oscillates across different growth conditions, both in synchrony with and also in the absence of the cell cycle. Using environmental perturbations and dynamic single-protein depletion experiments, we found that the metabolic oscillator and the cell cycle form a system of coupled oscillators, with the metabolic oscillator separately gating and maintaining synchrony with the early and late cell cycle. Establishing metabolism as a dynamic component within the cell-cycle network opens new avenues for cell-cycle research and therapeutic interventions for proliferative disorders.

The flavoproteome of the yeast Saccharomyces cerevisiae

Genome analysis of the yeast Saccharomyces cerevisiae identified 68 genes encoding flavin-dependent proteins (1.1% of protein encoding genes) to which 47 distinct biochemical functions were assigned. The majority of flavoproteins operate in mitochondria where they participate in redox processes revolving around the transfer of electrons to the electron transport chain. In addition, we found that flavoenzymes play a central role in various aspects of iron metabolism, such as iron uptake, the biogenesis of iron-sulfur clusters and insertion of the heme cofactor into apocytochromes. Another important group of flavoenzymes is directly (Dus1-4p and Mto1p) or indirectly (Tyw1p) involved in reactions leading to tRNA-modifications. Despite the wealth of genetic information available for S. cerevisiae, we were surprised that many flavoproteins are poorly characterized biochemically. For example, the role of the yeast flavodoxins Pst2p, Rfs1p and Ycp4p with regard to their electron donor and acceptor is presently unknown. Similarly, the function of the heterodimeric Aim45p/Cir1p, which is homologous to the electron-transferring flavoproteins of higher eukaryotes, in electron transfer processes occurring in the mitochondrial matrix remains to be elucidated. This lack of information extends to the five membrane proteins involved in riboflavin or FAD transport as well as FMN and FAD homeostasis within the yeast cell. Nevertheless, several yeast flavoproteins, were identified as convenient model systems both in terms of their mechanism of action as well as structurally to improve our understanding of diseases caused by dysfunctional human flavoprotein orthologs.

Visible light alters yeast metabolic rhythms by inhibiting respiration

Exposure of cells to visible light in nature or in fluorescence microscopy often is considered to be relatively innocuous. However, using the yeast respiratory oscillation (YRO) as a sensitive measurement of metabolism, we find that non-UV visible light has a significant impact on yeast metabolism. Blue/green wavelengths of visible light shorten the period and dampen the amplitude of the YRO, which is an ultradian rhythm of cell metabolism and transcription. The wavelengths of light that have the greatest effect coincide with the peak absorption regions of cytochromes. Moreover, treating yeast with the electron transport inhibitor sodium azide has similar effects on the YRO as visible light. Because impairment of respiration by light would change several state variables believed to play vital roles in the YRO (e.g., oxygen tension and ATP levels), we tested oxygen's role in YRO stability and found that externally induced oxygen depletion can reset the phase of the oscillation, demonstrating that respiratory capacity plays a role in the oscillation's period and phase. Light-induced damage to the cytochromes also produces reactive oxygen species that up-regulate the oxidative stress response gene TRX2 that is involved in pathways that enable sustained growth in bright visible light. Therefore, visible light can modulate cellular rhythmicity and metabolism through unexpectedly photosensitive pathways.

Dynamics of oscillatory phenotypes in Saccharomyces cerevisiae reveal a network of genome-wide transcriptional oscillators

Genetic and environmental factors are well-studied influences on phenotype; however, time is a variable that is rarely considered when studying changes in cellular phenotype. Time-resolved microarray data revealed genome-wide transcriptional oscillation in a yeast continuous culture system with ∼ 2 and ∼ 4 h periods. We mapped the global patterns of transcriptional oscillations into a 3D map to represent different cellular phenotypes of redox cycles. This map shows the dynamic nature of gene expression in that transcripts are ordered and coupled to each other through time and concentration space. Although cells differed in oscillation periods, transcripts involved in certain processes were conserved in a deterministic way. When oscillation period lengthened, the peak to trough ratio of transcripts increased and the fraction of cells in the unbudded (G0/G1) phase of the cell division cycle increased. Decreasing the glucose level in the culture medium was one way to increase the redox cycle, possibly from changes in metabolic flux. The period may be responding to lower glucose levels by increasing the fraction of cells in G1 and reducing S-phase gating so that cells can spend more time in catabolic processes. Our results support that gene transcripts are coordinated with metabolic functions and the cell division cycle.

Time-structure of the yeast metabolism in vivo

All previous studies on the yeast metabolome have yielded a plethora of information on the components, function and organisation of low molecular mass and macromolecular components involved in the cellular metabolic network. Here we emphasise that an understanding of the global dynamics of the metabolome in vivo requires elucidation of the temporal dynamics of metabolic processes on many time-scales. We illustrate this using the 40 min oscillation in respiratory activity displayed in auto-synchronous continuously grown cultures of Saccharomyces cerevisiae, where respiration cycles between a phase of increased respiration (oxidative phase) and decreased respiration (reductive phase). Thereby an ultradian clock, i.e. a timekeeping device that runs through many cycles during one day, is involved in the co-ordination of the vast majority of events and processes in yeast. Through continuous online measurements, we first show that mitochondrial and redox physiology are intertwined to produce the temporal landscape on which cellular events occur. Next we look at the higher order processes of DNA duplication and mitochondrial structure to reveal that both events are choreographed during the respiratory cycles. Furthermore, spectral analysis using the discrete Fourier transformation of high-resolution (10 Hz) time-series of NAD(P)H confirms the existence of higher frequency components of biological origin and that these follow a scale-free architecture even in stable oscillating modes. A different signal-processing approach using discrete wavelet transformations (DWT) indicates that there is a significant contribution to the overall signal from ` ~5, ~ 10 and ~ 20-minutes cycles and the amplitudes of these cycles are phase-dependent. Further investigation (derivative of Gaussian continuous wavelet transformation) reveals that the observed 20-minutes cycles are actually confined to the reductive phase and consist of two ~15-minutes cycles. Moreover, the 5 and 10-minutes cycles are restricted to the oxidative phase of the cycle. The mitochondrial origin of these signals was confirmed by pulse-injection of the cytochrome c oxidase inhibitor H(2)S. We next discuss how these multi-oscillatory states can impinge on the apparently complex reactome (represented as a phase diagram of 1,650 chemical species that show oscillatory behaviour). We conclude that biological processes can be considerably more comprehensible when dynamic in vivo time-structure is taken into account.

What yeast and cardiomyocytes share: ultradian oscillatory redox mechanisms of cellular coherence and survival

The coherent and robust, yet sensitively adaptable, nature of organisms is an astonishing phenomenon that involves massive parallel processing and concerted network performance at the molecular level. Unravelling the dynamic complexities of the living state underlines the essential operation of ultradian oscillations, rhythms and clocks for the establishment and maintenance of functional order simultaneously on fast and slower timescales. Non-invasive monitoring of respiration, mitochondrial inner membrane potentials, and redox states (especially those of NAD(P)H, flavin, and the monochlorobimane complex of glutathione), even after more than 50 years research, continue to provide both new insights and biomedical applications. Experiments with yeast and in cardiac cells reveal astonishing parallels and similarities in their dynamic biochemical organization.

Redox regulation in respiring Saccharomyces cerevisiae

BACKGROUND

In biological systems, redox reactions are central to most cellular processes and the redox potential of the intracellular compartment dictates whether a particular reaction can or cannot occur. Indeed the widespread use of redox reactions in biological systems makes their detailed description outside the scope of one review.

SCOPE OF THE REVIEW

Here we will focus on how system-wide redox changes can alter the reaction and transcriptional landscape of Saccharomyces cerevisiae. To understand this we explore the major determinants of cellular redox potential, how these are sensed by the cell and the dynamic responses elicited.

MAJOR CONCLUSIONS

Redox regulation is a large and complex system that has the potential to rapidly and globally alter both the reaction and transcription landscapes. Although we have a basic understanding of many of the sub-systems and a partial understanding of the transcriptional control, we are far from understanding how these systems integrate to produce coherent responses. We argue that this non-linear system self-organises, and that the output in many cases is temperature-compensated oscillations that may temporally partition incompatible reactions in vivo.

GENERAL SIGNIFICANCE

Redox biochemistry impinges on most of cellular processes and has been shown to underpin ageing and many human diseases. Integrating the complexity of redox signalling and regulation is perhaps one of the most challenging areas of biology. This article is part of a Special Issue entitled Systems Biology of Microorganisms.

The diversity and evolution of circadian clock proteins in fungi

Circadian rhythms are endogenous cellular patterns that associate multiple physiological and molecular functions with time. The Neurospora circadian system contains at least three oscillators: the FRQ/WC-dependent circadian oscillator (FWO), whose core components are the FRQ, WC-1, WC-2, FRH, and FWD-1 proteins; the WC-dependent circadian oscillator (WC-FLO); and one or more FRQ/ WC-independent oscillators (FLO). Little is known about the distribution of homologs of the Neurospora clock proteins or about the molecular foundations of circadian rhythms across fungi. Here, we examined 64 diverse fungal proteomes for homologs of all five Neurospora clock proteins and retraced their evolutionary history. The FRH and FWD-1 proteins were likely present in the fungal ancestor. WC-1 and WC-2 homologs are absent from the early diverging chytrids and Microsporidia but are present in all other major clades. In contrast to the deep origins of these four clock proteins FRQ homologs are taxonomically restricted within Sordariomycetes, Leotiomycetes and Dothideomycetes. The large number of FRH and FWD-1 homologs identified and their lack of concordance with the fungal species phylogeny indicate that they likely underwent multiple rounds of duplications and losses. In contrast, the FRQ, WC-1 and WC-2 proteins exhibit relatively few duplications and losses. A notable exception is the 10 FRQ-like proteins in Fusarium oxysporum, which resulted from nine duplication events. Our results suggest that the machinery required for FWO oscillator function is taxonomically restricted within Ascomycetes. Although the WC proteins are widely distributed, the functional diversity of the few non-Neurospora circadian oscillators suggests that a WC-FLO oscillator is unlikely to fully explain the observed rhythms. The contrast between the diversity of circadian oscillators and the conservation of most of their machinery is likely best explained by considering the centrality of noncircadian functions in which RNA helicase (FRH), F-box (FWD-1), WC-1 and WC-2 (light-sensing) proteins participate in fungi and eukaryotes.

Ultradian metabolic cycles in yeast

Budding yeast are capable of displaying various modes of oscillatory behavior. Such cycles can occur with a period ranging from 1 min up to many hours, depending on the growth and culturing conditions used to observe them. This chapter discusses the robust oscillations in oxygen consumption exhibited by high-density yeast cell populations during continuous, glucose-limited growth in a chemostat. These ultradian metabolic cycles offer a view of the life of yeast cells under a challenging, nutrient-poor growth environment and might represent useful systems to interrogate a variety of fundamental metabolic and regulatory processes.

Synchronous plasma membrane electrochemical potential oscillations during yeast colony development and aging

Microorganisms that survive in natural environments form organized multicellular communities, biofilms and colonies with specific properties. During stress and nutrient limitation, slow growing and senescent cells in such communities retain vital processes by maintaining plasma membrane integrity and retaining the ability to generate transmembrane electrochemical gradients. We report the use of a Saccharomyces cerevisiae colonial model to show that population growth in a multicellular community depends on nutrient diffusion and that resting cells start to accumulate from the beginning of the second acidic phase of colony development. Despite differentiation of colony members, synchronous transmembrane potential oscillation was detected in the organized colony. The electrochemical membrane potential periodically oscillated at frequencies between those for circadian to infradian rhythms during colony aging and transiently decreased at time points previously linked with rebuilding of yeast metabolism. Despite extensive decreases in the intracellular ATP concentration and in the amount and activity of the plasma membrane proton pump during nutrient limited growth and colony aging, the transmembrane electrochemical potential appeared to be maintained above a level critical for population survival.

Regulation of glycolytic oscillations by mitochondrial and plasma membrane H+-ATPases

We investigated the coupling between glycolytic and mitochondrial membrane potential oscillations in Saccharomyces cerevisiae under semianaerobic conditions. Glycolysis was measured as NADH autofluorescence, and mitochondrial membrane potential was measured using the fluorescent dye 3,3'-diethyloxacarbocyanine iodide. The responses of glycolytic and membrane potential oscillations to a number of inhibitors of glycolysis, mitochondrial electron flow, and mitochondrial and plasma membrane H(+)-ATPase were investigated. Furthermore, the glycolytic flux was determined as the rate of production of ethanol in a number of different situations (changing pH or the presence and absence of inhibitors). Finally, the intracellular pH was determined and shown to oscillate. The results support earlier work suggesting that the coupling between glycolysis and mitochondrial membrane potential is mediated by the ADP/ATP antiporter and the mitochondrial F(0)F(1)-ATPase. The results further suggest that ATP hydrolysis, through the action of the mitochondrial F(0)F(1)-ATPase and plasma membrane H(+)-ATPase, are important in regulating these oscillations. We conclude that it is glycolysis that drives the oscillations in mitochondrial membrane potential.

Spatio-temporal dynamics of yeast mitochondrial biogenesis: transcriptional and post-transcriptional mRNA oscillatory modules

Examples of metabolic rhythms have recently emerged from studies of budding yeast. High density microarray analyses have produced a remarkably detailed picture of cycling gene expression that could be clustered according to metabolic functions. We developed a model-based approach for the decomposition of expression to analyze these data and to identify functional modules which, expressed sequentially and periodically, contribute to the complex and intricate mitochondrial architecture. This approach revealed that mitochondrial spatio-temporal modules are expressed during periodic spikes and specific cellular localizations, which cover the entire oscillatory period. For instance, assembly factors (32 genes) and translation regulators (47 genes) are expressed earlier than the components of the amino-acid synthesis pathways (31 genes). In addition, we could correlate the expression modules identified with particular post-transcriptional properties. Thus, mRNAs of modules expressed “early” are mostly translated in the vicinity of mitochondria under the control of the Puf3p mRNA-binding protein. This last spatio-temporal module concerns mostly mRNAs coding for basic elements of mitochondrial construction: assembly and regulatory factors. Prediction that unknown genes from this module code for important elements of mitochondrial biogenesis is supported by experimental evidence. More generally, these observations underscore the importance of post-transcriptional processes in mitochondrial biogenesis, highlighting close connections between nuclear transcription and cytoplasmic site-specific translation.

In bacterial and eukaryotic cells, gene expression is regulated at both the transcriptional and translational levels. In eukaryotes these two processes cannot be directly coupled because the nuclear membrane separates the chromosomes from the ribosomes. Although the transcription levels in different cellular conditions have been widely examined, genome-wide post-transcriptional mechanisms are poorly documented and therefore, the connections between the two processes are difficult to explain. In this work, the time-regulated expression of the genes involved in the construction of the mitochondrion, an important organelle present in nearly all the eukaryotic cells, was scrutinized both at transcriptional and post-transcriptional levels. We observed that temporal transcriptional profiles coincide with groups of genes which are translated at specific cellular loci. The description of these relationships is functionally relevant since the genes which are transcribed early in mitochondria cycles are those which are translated to the vicinity of mitochondria. In addition, these early genes code for essential assembling factors or core elements of the protein complexes whereas the peripheral proteins are translated later in the cytoplasm. Also, these observations support the concerted action of important regulatory factors which control either the gene transcription level (transcription factors) or the mRNA localization (mRNA-binding proteins).

Invariant submanifold for series arrays of Josephson junctions

We study the nonlinear dynamics of series arrays of Josephson junctions in the large-N limit, where N is the number of junctions in the array. The junctions are assumed to be identical, overdamped, driven by a constant bias current, and globally coupled through a common load. Previous simulations of such arrays revealed that their dynamics are remarkably simple, hinting at the presence of some hidden symmetry or other structure. These observations were later explained by the discovery of N-3 constants of motion, the choice of which confines the resulting flow in phase space to a low-dimensional invariant manifold. Here we show that the dimensionality can be reduced further by restricting attention to a special family of states recently identified by Ott and Antonsen. In geometric terms, the Ott-Antonsen ansatz corresponds to an invariant submanifold of dimension one less than that found earlier. We derive and analyze the flow on this submanifold for two special cases: an array with purely resistive loading and another with resistive-inductive-capacitive loading. Our results recover (and in some instances improve) earlier findings based on linearization arguments.

Respiratory oscillations in yeasts

Respiratory oscillations in yeasts have been studied in three time domains with periods of (a) about a minute, (b) about 40 min, and (c) about a day. Reactive responses (damped oscillations), rhythms and temperature-compensated clocks have been described for (b) and (c), but a timekeeping clock has not yet been shown for (a). Synchronous populations reveal the time-structure that can only otherwise be studied in single organisms; this is because time-averaging through an asynchronous population conceals its fine structure. Early studies with synchronous cultures made by size selection methods indicated ultradian-clock driven oscillations in respiration, pools of adenylates, total protein, RNA synthesis and many enzyme activities (tau = 40 min in Schizosaccharomyces pombe, 30 min in Candida utilis), and more recently in self-synchronised continuous cultures of Saccharomyces cerevisiae (tau = 48 min). Most detailed understanding comes from the latter system, where continuous, noninvasive real-time monitoring (of 02 uptake, CO2 production, and NAD(P)H redox state) is combined with frequent discrete time samples (for other redox components, including H2S, GSH and cytochromes, metabolites, and mRNA levels). A redox switch lies at the heart of this ultradian clock and a plethora of outputs is optimized to a time-base that is genetically-determined and differs in different organisms. It is suggested that the entire temporal landscape of all eukaryotic organisms and the cells of higher plants and animals is constructed on this basis. A time frame for the coordination and coherence of all intracellular processes and the construction and assembly of cellular structures is provided by the ultradian clock The circadian clock matches these functions to the daily cycle of the external environment.

Real-time luminescence monitoring of cell-cycle and respiratory oscillations in yeast

The use of luciferase reporters has become a precise, noninvasive, high-throughput method for real-time monitoring of promoter activity in living cells, especially for rhythmic biological processes such as circadian rhythms. We developed a destabilized firefly luciferase as a reporter for rhythmic promoter activity in both the cell division and respiratory cycles of the budding yeast Saccharomyces cerevisiae in which real-time luminescence reporters have not been previously applied. The continuous output of light from luciferase reporters allowed us to explore the relationship between the cell division cycle and the yeast respiratory oscillation, including the observation of responses to chemicals that cause phase shifting of the respiratory oscillations. Destabilized firefly luciferase is a good reporter of cell cycle position in synchronized or partially synchronized yeast cultures, in both batch and continuous cultures. In addition, the oxygen dependence of luciferase can be used under certain conditions as a genetically encodable oxygen monitor. Finally, we use this reporter to show that there is a direct correlation between premature induction of cell division and phase resetting of the respiratory oscillation under the continuous culture conditions tested.

The scale-free dynamics of eukaryotic cells

Temporal organization of biological processes requires massively parallel processing on a synchronized time-base. We analyzed time-series data obtained from the bioenergetic oscillatory outputs of Saccharomyces cerevisiae and isolated cardiomyocytes utilizing Relative Dispersional (RDA) and Power Spectral (PSA) analyses. These analyses revealed broad frequency distributions and evidence for long-term memory in the observed dynamics. Moreover RDA and PSA showed that the bioenergetic dynamics in both systems show fractal scaling over at least 3 orders of magnitude, and that this scaling obeys an inverse power law. Therefore we conclude that in S. cerevisiae and cardiomyocytes the dynamics are scale-free in vivo. Applying RDA and PSA to data generated from an in silico model of mitochondrial function indicated that in yeast and cardiomyocytes the underlying mechanisms regulating the scale-free behavior are similar. We validated this finding in vivo using single cells, and attenuating the activity of the mitochondrial inner membrane anion channel with 4-chlorodiazepam to show that the oscillation of NAD(P)H and reactive oxygen species (ROS) can be abated in these two evolutionarily distant species. Taken together these data strongly support our hypothesis that the generation of ROS, coupled to redox cycling, driven by cytoplasmic and mitochondrial processes, are at the core of the observed rhythmicity and scale-free dynamics. We argue that the operation of scale-free bioenergetic dynamics plays a fundamental role to integrate cellular function, while providing a framework for robust, yet flexible, responses to the environment.

Redox rhythmicity: clocks at the core of temporal coherence

Ultradian rhythms are those that cycle many times in a day and are therefore measured in hours, minutes, seconds or even fractions of a second. In yeasts and protists, a temperature-compensated clock with a period of about an hour (30-90 minutes) provides the time base upon which all central processes are synchronized. A 40-minute clock in yeast times metabolic, respiratory and transcriptional processes, and controls cell division cycle progression. This system has at its core a redox cycle involving NAD(P)H and dithiol-disulfide interconversions. It provides an archetype for biological time keeping on longer time scales (e.g. the daily cycles driven by circadian clocks) and underpins these rhythms, which cannot be understood in isolation. Ultradian rhythms are the foundation upon which the coherent functioning of the organism depends.

Regulation of yeast oscillatory dynamics

When yeast cells are grown continuously at high cell density, a respiratory oscillation percolates throughout the population. Many essential cellular functions have been shown to be separated temporally during each cycle; however, the regulatory mechanisms involved in oscillatory dynamics remain to be elucidated. Through GC-MS analysis we found that the majority of metabolites show oscillatory dynamics, with 70% of the identified metabolite concentrations peaking in conjunction with NAD(P)H. Through statistical analyses of microarray data, we identified that biosynthetic events have a defined order, and this program is initiated when respiration rates are increasing. We then combined metabolic, transcriptional data and statistical analyses of transcription factor activity, identified the top oscillatory parameters, and filtered a large-scale yeast interaction network according to these parameters. The analyses and controlled experimental perturbation provided evidence that a transcriptional complex formed part of the timing circuit for biosynthetic, reductive, and cell cycle programs in the cell. This circuitry does not act in isolation because both have strong translational, proteomic, and metabolic regulatory mechanisms. Our data lead us to conclude that the regulation of the respiratory oscillation revolves around coupled subgraphs containing large numbers of proteins and metabolites, with a potential to oscillate, and no definable hierarchy, i.e., heterarchical control.

Observation of a chaotic multioscillatory metabolic attractor by real-time monitoring of a yeast continuous culture

We monitored a continuous culture of the yeast Saccharomyces cerevisiae by membrane-inlet mass spectrometry. This technique allows very rapid simultaneous measurements (one point every 12 s) of several dissolved gases. During our experiment, the culture exhibited a multioscillatory mode in which the dissolved oxygen and carbon dioxide records displayed periodicities of 13 h, 36 min and 4 min. The 36- and 4-min modes were not visible at all times, but returned at regular intervals during the 13-h cycle. The 4-min mode, which has not previously been described in continuous culture, can also be seen when the culture displays simpler oscillatory behavior. The data can be used to visualize a metabolic attractor of this system, i.e. the set of dissolved gas concentrations which are consistent with the multioscillatory state. Computation of the leading Lyapunov exponent reveals the dynamics on this attractor to be chaotic.

A tuneable attractor underlies yeast respiratory dynamics

Our understanding of the molecular structure and function in the budding yeast, Saccharomyces cerevisiae, surpasses that of all other eukaryotic cells. However, the fundamental properties of the complex processes and their control systems have been difficult to reconstruct from detailed dissection of their molecular components. Spontaneous oscillatory dynamics observed in self-synchronized continuous cultures is pervasive, involves much of the cellular network, and provides unique insights into integrative cell physiology. Here, in non-invasive experiments in vivo, we exploit these oscillatory dynamics to analyse the global timing of the cellular network to show the presence of a low-order chaotic component. Although robust to a wide range of environmental perturbations, the system responds and reacts to the imposition of harsh environmental conditions, in this case low pH, by dynamic re-organization of respiration, and this feeds upwards to affect cell division. These complex dynamics can be represented by a tuneable attractor that orchestrates cellular complexity and coherence to the environment.

Oscillatory reaction of catalase wrapped by liposome

To date we have been studying the enzymatic oscillatory reaction caused by gradual entry of substrate via semi-permeable membrane. It has been found that many enzymes cause oscillatory reaction. Here we present an oscillatory reaction of enzyme wrapped by liposome. We used catalase as an enzyme, since its oscillatory reaction has been already investigated in detail in the absence of liposome. Distinct oscillation with shorter period than without liposome was obtained. On the other hand, it was shown that the presence of liposome facilitated the permeation rate of hydrogen peroxide through semi-permeable membrane. This is thought to be factor of shortening the oscillation period compared with that in the absence of liposome. Oscillation was also temperature dependent. Our finding may provide an important insight into the study of enzyme reaction taking part in rhythms in living systems.

The temporal architecture of eukaryotic growth

Coherence of the time structure of growing organisms depends on a metronome-like orchestration. In a continuously perfused culture of Saccharomyces cerevisiae the redox state of the cell shows a temperature-compensated oscillation manifest in respiratory cycles, which are measured by continuous and non-invasive electrodes of probes such as dissolved oxygen and probes such as fluorometric NAD(P)H. Although the entire transcriptome exhibits low-amplitude oscillatory behaviour, transcripts involved in the vast majority of metabolism, stress response, cellular structure, protein turnover, mRNA turnover, and DNA synthesis are amongst the top oscillators and their orchestration occurs by an intricate network of transcriptional regulators. Therefore cellular auto-dynamism is a function of a large ensemble of excitable intracellular components of that self-organized temporally and spatially that encompasses mitochondrial, nuclear, transcriptional and metabolic dynamics, coupled by cellular redox state.

Genome-wide oscillation of transcription in yeast

Yeast cells growing under continuous conditions at high cellular density employ a robust metabolic cycle for energy generation in which a respiratory burst alternates with a non-respiratory, reductive phase. Two related studies have recently shown that global transcriptional co-regulation of genes defines the phases of this metabolic network in time and synchronizes cell division with metabolism. The finding that many fundamental and diverse cellular processes can be coordinated by global mRNA oscillations implies the existence of a more widespread metabolic clock that might also be present in higher eukaryotes.

Effects of uncoupling of mitochondrial energy conservation on the ultradian clock-driven oscillations in Saccharomyces cerevisiae continuous culture

Protonophores have several different perturbative effects on dissolved O2 concentrations in continuous cultures of Saccharomyces cerevisiae. As well as uncoupling energy conservation from mitochondrial electron transport in vivo, they reset ultradian clock-driven respiratory oscillations and produce cell cycle effects. Thus, additions at low concentration (1.25 microM) of either m-chlorocarbonyl-cyanide phenylhydrazone (CCCP) or 5-chloro-3-t-butyl-2-chloro-4(1)-nitrosalicylanilide (S13) led to phase resetting of the 48 min ultradian clock-driven respiratory oscillations. At 2.5 microM CCCP or 4 microM S13, transient inhibition of oscillatory respiration (for 5 h) preceded synchronisation of the cell division cycle seen as a slow (9 h period) wave that enveloped the 48 min oscillation. At still higher concentrations of CCCP (5 microM), the cell division cycle was prolonged by about 7 h, and during this phase, the respiratory oscillation became undetectable. The significance of these observations with respect to the time-keeping functions of the ultradian clock is discussed.

Ultradian metronome: timekeeper for orchestration of cellular coherence

Dynamic intracellular spatial and temporal organization emerges from spontaneous synchronization of a massive array of weakly coupled oscillators; the majority of subcellular processes are implicated in this integrated expression of cellular physiology. Evidence for this view comes mainly from studies of Saccharomyces cerevisiae growing in self-synchronized continuous cultures, in which a temperature-compensated ultradian clock (period of approximately 40 min) couples fermentation with redox state in addition to the transcriptome and cell-division-cycle progression. Functions for ultradian clocks have also been determined in other yeasts (e.g. Schizosaccharomyces pombe and Candida utilis), seven protists (e.g. Acanthamoeba castellanii and Paramecium tetraurelia), as well as cultured mammalian cells. We suggest that ultradian timekeeping is a basic universal necessity for coordinated intracellular coherence.

Autonomous oscillations in Saccharomyces cerevisiae during batch cultures on trehalose

We report that autonomous oscillations, which usually happen in aerobic glucose-limited continuous cultures of yeast at low dilution rate, were also observed in trehalose discontinuous cultures of Saccharomyces cerevisiae. This unexpected oscillatory behaviour was therefore examined using fast Fourier transformation of online gas measurements. This robust mathematical analysis underlined the existence of two types of oscillation. The first was found to be linked to the cell cycle because (a) the periodicity corresponded to a fraction of the generation time and (b) the oscillations were accompanied by a transient increase in the budding index, mobilization of storage carbohydrates, and fermentative activity. Moreover, these oscillations occurred in a range of specific growth rates between 0.04 and 0.15 h(-1). All these criteria were consistent with the cell-cycle-related metabolic oscillations observed in the same range of growth rates in glucose-limited continuous cultures. The second type were short-period respiratory oscillations, independent of the specific growth rate. Both types of oscillation were found to take place consecutively and/or simultaneously during batch culture on trehalose. In addition, mobilization of intracellular trehalose emerged as a key parameter for the sustainability of these autonomous oscillations as they were no longer observed in a mutant defective in neutral trehalase activity. We propose that batch culture on trehalose may be an excellent device for further investigation of the molecular mechanisms that underlie autonomous oscillations in yeast.

Cellular oscillators: rhythmic gene expression and metabolism

Many biological processes are driven by biological clocks that, depending on the frequency they generate, are classified into ultradian, circadian and infradian oscillators. In virtually all light-sensitive organisms from cyanobacteria to humans, a circadian timing system adapts cyclic physiology to geophysical time. Recent evidence suggests that even in mammals circadian oscillators function in a cell-autonomous manner. In yeast, an ultradian oscillator regulates cyclic respiratory activity and global gene expression. Circadian oscillators and the ultradian yeast respiratory clock share at least four properties: they follow limit-cycle kinetics, interweave with cellular metabolism, are temperature-compensated and influence the cell division clock.

Modeling the synchronization of yeast respiratory oscillations

The budding yeast Saccharomyces cerevisiae exhibits autonomous oscillations when grown aerobically in continuous culture with ethanol as the primary carbon source. A single cell model that includes the sulfate assimilation and ethanol degradation pathways recently has been developed to study these respiratory oscillations. We utilize an extended version of this single cell model to construct large cell ensembles for investigation of a proposed synchronization mechanism involving hydrogen sulfide. Ensembles with as many as 10,000 cells are used to simulate population synchronization and to compute transient number distributions from asynchronous initial cell states. Random perturbations in intracellular kinetic parameters are introduced to study the synchronization of single cells with small variations in their unsynchronized oscillation periods. The cell population model is shown to be consistent with available experimental data and to provide insights into the regulatory mechanisms responsible for the synchronization of yeast metabolic oscillations.

The mammalian circadian timing system: from gene expression to physiology

Many physiological processes in organisms from bacteria to man are rhythmic, and some of these are controlled by self-sustained oscillators that persist in the absence of external time cues. Circadian clocks are perhaps the best characterized biological oscillators and they exist in virtually all light-sensitive organisms. In mammals, they influence nearly all aspects of physiology and behavior, including sleep-wake cycles, cardiovascular activity, endocrinology, body temperature, renal activity, physiology of the gastro-intestinal tract, and hepatic metabolism. The master pacemaker is located in the suprachiasmatic nuclei, two small groups of neurons in the ventral part of the hypothalamus. However, most peripheral body cells contain self-sustained circadian oscillators with a molecular makeup similar to that of SCN (suprachiasmatic nucleus) neurons. This organization implies that the SCN must synchronize countless subsidiary oscillators in peripheral tissues, in order to coordinate cyclic physiology. In this review, we will discuss some recent studies on the structure and putative functions of the mammalian circadian timing system, but we will also point out some apparent inconsistencies in the currently publicized model for rhythm generation.

Circadian gene expression in mammalian fibroblasts revealed by real-time luminescence reporting: temperature compensation and damping

Mammalian cells such as rat-1 fibroblasts have been shown to exhibit daily oscillations in the expression of several gene transcripts in culture. After induction, these oscillations persist with a period of approximately 24 h for several days. This characteristic suggests that the oscillations are controlled by a circadian clock, but the crucial criterion of temperature compensation has not been demonstrated for rat-1 fibroblasts. We have developed an automated assay of circadian expression of the mPer1 promoter in rat-1 fibroblasts that have been stably transfected with a luciferase reporter. Using this cell culture-based in vitro luminescent reporter assay, we found that the daily oscillation of mPer1 promoter activity in rat-1 cells is temperature compensated over the range of 28.5-36.5 degrees C. This finding means that these oscillations are bona fide circadian rhythms. Moreover, the circadian clock of these homeothermic mammalian cells not only is temperature compensated but also is overcompensated such that it runs faster at cooler temperatures (Q10 of 0.85-0.88). The oscillations in rat-1 fibroblasts damp more rapidly at cooler temperatures, and damping is not due to cells becoming unhealthy because a second stimulus will reinitiate a robust rhythm. These data show that rat-1 cell cultures that are stably transfected with luminescence reporters are an excellent model system for studying circadian clocks at the cellular level in mammals.

Oscillatory metabolism of Saccharomyces cerevisiae: an overview of mechanisms and models

The budding yeast Saccharomyces cerevisiae displays steady oscillations in continuous cultures under certain conditions. Oscillatory responses are important both metabolically and in process applications. Although much information has become available, a definitive theory to explain and model these oscillations is yet to be formulated. Models of oscillatory cultivation have focussed primarily either on intracellular reactions or on transport processes coupled to substantially lumped intracellular kinetics. This review discusses the development of the models and the directions they provide for a comprehensive model of oscillatory metabolism.

The rhythm of yeast

Although yeast are unicellular and comparatively simple organisms, they have a sense of time which is not related to reproduction cycles. The glycolytic pathway exhibits oscillatory behaviour, i.e. the metabolite concentrations oscillate around phosphofructokinase. The frequency of these oscillations is about 1 min when using intact cells. Also a yeast cell extract can oscillate, though with a lower frequency. With intact cells the macroscopic oscillations can only be observed when most of the cells oscillate in concert. Transient oscillations can be observed upon simultaneous induction; sustained oscillations require an active synchronisation mechanism. Such an active synchronisation mechanism, which involves acetaldehyde as a signalling compound, operates under certain conditions. How common these oscillations are in the absence of a synchronisation mechanism is an open question. Under aerobic conditions an oscillatory metabolism can also be observed, but with a much lower frequency than the glycolytic oscillations. The frequency is between one and several hours. These oscillations are partly related to the reproductive cycle, i.e. the budding index also oscillates; however, under some conditions they are unrelated to the reproductive cycle, i.e. the budding index is constant. These oscillations also have an active synchronisation mechanism, which involves hydrogen sulfide as a synchronising agent. Oscillations with a frequency of days can be observed with yeast colonies on plates. Here the oscillations have a synchronisation mechanism which uses ammonia as a synchronising agent.

Generation and maintenance of synchrony in Saccharomyces cerevisiae continuous culture

Cultures of Saccharomyces cerevisiae grown continuously produce an autonomous oscillation in many metabolic outputs. The most conveniently measured variable, i.e., dissolved oxygen concentration, oscillates with a period of 40-55 min. Previously we have identified two compounds capable of resetting phase, acetaldehyde and hydrogen sulfide. The phase-response curves constructed for acetaldehyde show a strong (Type 0) response at 3.0 mM and a weak (Type 1) response at 1.0 mM. Ammonium sulfide phase-response curves (pulse injected at 1.0 microM and 3.0 microM) revealed that sulfide is only an effective perturbation agent when endogenous sulfide concentrations are at a maximum. Also only Type 1 phase responses were observed. When the phase-response curve for sulfite (at 3.0 M) was constructed, phase responses were at a maximum at 60 degrees, indicating the possible involvement of sulfite in cell synchronization. It is concluded that endogenously produced acetaldehyde and sulfite tune the oscillation of mitochondrial energization state whereas sulfide mediates population synchrony.

Respiratory oscillations in yeast: mitochondrial reactive oxygen species, apoptosis and time; a hypothesis

Oscillatory metabolic activities occur more widely than is generally realised; detectability requires observation over extended times of single yeast cells or synchrony of individuals to provide a coherent population. Where oscillations in intracellular metabolite concentrations are observed, the phenomenon has been ascribed to sloppy control, energetic optimisation, signalling, temporal compartmentation of incompatible reactions, or timekeeping functions. Here we emphasise the consequences of respiratory oscillations as a source of mitochondrially generated reactive O(2) metabolites. Temporal co-ordination of intracellular activities necessitates a time base. This is provided by an ultradian clock, and one result of its long-term operation is cyclic energisation of mitochondria, and thereby the generation of deleterious free radical species. Our hypothesis is that unrepaired cellular constituents and components (especially mitochondria) eventually lead to cellular senescence and apoptosis when a finite number of respiratory cycles has occurred.

The Gts1 protein stabilizes the autonomous oscillator in yeast

Continuous cultures of Saccharomyces cerevisiae show a robust autonomous temperature compensated oscillation in many metabolic functions. Respiratory activity, a convenient output to measure, oscillates with a period of 40 min. Deletion of GTS1, whose protein product has homology to the circadian per protein, has been implicated in temporal events within yeast, causes a reduction in periodicity to 18 min (wild-type period 40-60 min). The dilution rate was steadily increased from 0.04/h to 0.085/h and the oscillation stabilized after four to six dilutions. However, Gts1p's involvement in the maintenance and generation of metabolic synchrony, and in the central oscillating loop, appear to be minimal, as the mutant oscillation was robust and autonomous. Deletion of GTS1 did cause decreased temperature compensation of the period of the oscillation from Q(10) = 1.07 for the wild-type to Q(10) = 1.6 for the mutant. Also the degree of nutrient compensation observed for the wild-type was not observed in the GTS1-null mutant strain. It is postulated that Gts1p is involved in the mechanism that communicates external conditions, such as temperature, to the central oscillating loop.

Free intracellular amino acid pools during autonomous oscillations in Saccharomyces cerevisiae

In the present work dynamic changes of free intracellular amino acid pools during autonomous oscillations of Saccharomyces cerevisiae were quantified in glucose-limited continuous cultivations. At a dilution rate of D = 0.22 h(-1) cyclic changes with a period of 120 min were found for many variables such as carbon dioxide production rate, dissolved oxygen, pH, biomass content, and various metabolite concentrations. On the basis of the observed dynamic patterns, free intracellular amino acids were classified to show oscillatory, stationary, or chaotic behavior. Amino acid pools such as serine, alanine, valine, leucine, or lysine were subjected to clear oscillations with a frequency of 120 min, identical to that of other described cultivation variables, indicating that there is a direct correlation between the periodic changes of amino acid concentrations and the metabolic oscillations on the cellular level. The oscillations of these amino acids were unequally phase-delayed and had different amplitudes of oscillation. Accordingly, they exhibited different patterns in phase plane plots vs. intracellular trehalose. Despite the complex and marked metabolic changes during oscillation, selected intracellular amino acids such as histidine, threonine, isoleucine, or arginine remained about constant. Concentrations of glutamate and glutamine showed a chaotic behavior. However, the ratio of glutamate to glutamine concentration was found to be oscillatory, with a period of 60 min and a corresponding figure eight-shaped pattern in a plot vs. trehalose concentration. Considering the described diversity, it can be concluded that the observed periodic changes are neither just the consequence of low or high rates of protein biosynthesis/degradation nor correlated to changing cell volumes during oscillation. The ratio between doubling time (189 min) and period of oscillation of intracellular amino acids (120 min) was 1:6. The fact that there is a close relationship between doubling time and period of oscillation underlines that the described autonomous oscillations are cell-cycle-associated.

Cycles of mitochondrial energization driven by the ultradian clock in a continuous culture of Saccharomyces cerevisiae

A continuous culture of Saccharomyces cerevisiae IFO 0233, growing with glucose as the major carbon and energy source, shows oscillations of respiration with a period of 48 min. Samples taken at maxima and minima indicate that (i) periodic changes do not occur as a result of carbon depletion, (ii) intrinsic differences in respiratory activity occur in washed organisms and (iii) a respiratory inhibitor accumulates during respiratory oscillations. Plasma membrane and inner mitochondrial membranes generate transmembrane electrochemical potentials; changes in these can be respectively assessed using anionic or cationic fluorophores. Thus flow cytometric analyses indicated that an oxonol dye [DiBAC(4)(3); bis(1,3-dibutylbarbituric acid)trimethine oxonol] was excluded from yeasts to a similar extent (in >98% of the population) at all stages, showing that the plasma membrane potential was maintained at a steady value. However, uptake of Rhodamine 123 was greatest at that phase characterized by a low respiratory rate. Addition of uncouplers of energy conservation [CCCP (m-chlorocarbonylcyanide phenylhydrazone) or S-13(5-chloro-3-t-butyl-2-chloro-4(1)-nitrosalicylanilide)] to the continuous cultures increased the respiration, but had only a transient effect on the period of the oscillation. Electron microscopy showed changes in mitochondrial ultrastructure during the respiratory oscillation. At low respiration the cristae were more clearly defined due to swelling of the matrix; this corresponds to the 'orthodox' conformation. When respiration was high the mitochondrial configuration was 'condensed'. It has been shown previously that a temperature-compensated ultradian clock operates in S. cerevisiae. It is proposed that mitochondria undergo cycles of energization in response to energetic demands driven by this ultradian clock output.

Respiratory oscillations in yeast: clock-driven mitochondrial cycles of energization

Respiratory oscillations in continuous yeast cultures can be accounted for by cyclic energization of mitochondria, dictated by the demands of a temperature-compensated ultradian clock with a period of 50 min. Inner mitochondrial membranes show both ultrastructural modifications and electrochemical potential changes. Electron transport components (NADH and cytochromes c and c oxidase) show redox state changes as the organisms cycle between their energized and de-energized phases. These regular cycles are transiently perturbed by uncouplers of energy conservation, with amplitudes more affected than period; that the characteristic period is restored after only one prolonged cycle, indicates that mitochondrial energy generation is not part of the clock mechanism itself, but is responding to energetic requirement.