The temporal architecture of eukaryotic growth

The main sources of molecular organization in the cell. Atlas of self-organized and self-regulated dynamic biostructures

One of the most important goals of contemporary biology is to understand the principles of the molecular order underlying the complex dynamic architecture of cells. Here, we present an overview of the main driving forces involved in the cellular molecular complexity and in the emergent functional dynamic structures, spanning from the most basic molecular organization levels to the complex emergent integrative systemic behaviors. First, we address the molecular information processing which is essential in many complex fundamental mechanisms such as the epigenetic memory, alternative splicing, regulation of transcriptional system, and the adequate self-regulatory adaptation to the extracellular environment. Next, we approach the biochemical self-organization, which is central to understand the emergency of metabolic rhythms, circadian oscillations, and spatial traveling waves. Such a complex behavior is also fundamental to understand the temporal compartmentalization of the cellular metabolism and the dynamic regulation of many physiological activities. Numerous examples of biochemical self-organization are considered here, which show that practically all the main physiological processes in the cell exhibit this type of dynamic molecular organization. Finally, we focus on the biochemical self-assembly which, at a primary level of organization, is a basic but important mechanism for the order in the cell allowing biomolecules in a disorganized state to form complex aggregates necessary for a plethora of essential structures and physiological functions. In total, more than 500 references have been compiled in this review. Due to these main sources of order, systemic functional structures emerge in the cell, driving the metabolic functionality towards the biological complexity.

Disease Conditions

Since clock genes are involved in all physiological systems, their role in most disease conditions is not surprising. To complement the information reviewed in Part II for each physiological system considered separately, this chapter illustrates the interdigitating network of interactions taking place within multiple physiological systems in any given disease condition. Circadian disruption, a common factor in disease, is almost inseparable from disturbed sleep, which is present in conditions ranging from psychological to cardio-metabolic and neurodegenerative conditions. Sleep disruption also modifies the immune system. Herein, we highlight the pervasive role played by the circadian system in pathology based on a few examples of selected disease conditions, including some sleep disorders, mental disorders, neurodegenerative conditions, and cancer.

Studying the Human Microbiota: Advances in Understanding the Fundamentals, Origin, and Evolution of Biological Timekeeping

The recently observed circadian oscillations of the intestinal microbiota underscore the profound nature of the human-microbiome relationship and its importance for health. Together with the discovery of circadian clocks in non-photosynthetic gut bacteria and circadian rhythms in anucleated cells, these findings have indicated the possibility that virtually all microorganisms may possess functional biological clocks. However, they have also raised many essential questions concerning the fundamentals of biological timekeeping, its evolution, and its origin. This narrative review provides a comprehensive overview of the recent literature in molecular chronobiology, aiming to bring together the latest evidence on the structure and mechanisms driving microbial biological clocks while pointing to potential applications of this knowledge in medicine. Moreover, it discusses the latest hypotheses regarding the evolution of timing mechanisms and describes the functions of peroxiredoxins in cells and their contribution to the cellular clockwork. The diversity of biological clocks among various human-associated microorganisms and the role of transcriptional and post-translational timekeeping mechanisms are also addressed. Finally, recent evidence on metabolic oscillators and host-microbiome communication is presented.

Unconscious mind activates central cardiovascular network and promotes adaptation to microgravity possibly anti-aging during 1-year-long spaceflight

The intrinsic cardiovascular regulatory system (β, 0.00013–0.02 Hz) did not adapt to microgravity after a 6-month spaceflight. The infraslow oscillation (ISO, 0.01–0.10 Hz) coordinating brain dynamics via thalamic astrocytes plays a key role in the adaptation to novel environments. We investigate the adaptive process of a healthy astronaut during a 12-month-long spaceflight by analyzing heart rate variability (HRV) in the LF (0.01–0.05 Hz) and MF1 (0.05–0.10 Hz) bands for two consecutive days on four occasions: before launch, at 1-month (ISS01) and 11-month (ISS02) in space, and after return to Earth. Alteration of β during ISS01 improved during ISS02 (P = 0.0167). During ISS01, LF and MF1 bands, reflecting default mode network (DMN) activity, started to increase at night (by 43.1% and 32.0%, respectively), when suprachiasmatic astrocytes are most active, followed by a 25.9% increase in MF1-band throughout the entire day during ISS02, larger at night (47.4%) than during daytime. Magnetic declination correlated positively with β during ISS01 (r = 0.6706, P < 0.0001) and ISS02 (r = 0.3958, P = 0.0095). Magnetic fluctuations may affect suprachiasmatic astrocytes, and the DMN involving ISOs and thalamic astrocytes may then be activated, first at night, then during the entire day, a mechanism that could perhaps promote an anti-aging effect noted in other investigations.

Self-Organization and Information Processing: From Basic Enzymatic Activities to Complex Adaptive Cellular Behavior

One of the main aims of current biology is to understand the origin of the molecular organization that underlies the complex dynamic architecture of cellular life. Here, we present an overview of the main sources of biomolecular order and complexity spanning from the most elementary levels of molecular activity to the emergence of cellular systemic behaviors. First, we have addressed the dissipative self-organization, the principal source of molecular order in the cell. Intensive studies over the last four decades have demonstrated that self-organization is central to understand enzyme activity under cellular conditions, functional coordination between enzymatic reactions, the emergence of dissipative metabolic networks (DMN), and molecular rhythms. The second fundamental source of order is molecular information processing. Studies on effective connectivity based on transfer entropy (TE) have made possible the quantification in bits of biomolecular information flows in DMN. This information processing enables efficient self-regulatory control of metabolism. As a consequence of both main sources of order, systemic functional structures emerge in the cell; in fact, quantitative analyses with DMN have revealed that the basic units of life display a global enzymatic structure that seems to be an essential characteristic of the systemic functional metabolism. This global metabolic structure has been verified experimentally in both prokaryotic and eukaryotic cells. Here, we also discuss how the study of systemic DMN, using Artificial Intelligence and advanced tools of Statistic Mechanics, has shown the emergence of Hopfield-like dynamics characterized by exhibiting associative memory. We have recently confirmed this thesis by testing associative conditioning behavior in individual amoeba cells. In these Pavlovian-like experiments, several hundreds of cells could learn new systemic migratory behaviors and remember them over long periods relative to their cell cycle, forgetting them later. Such associative process seems to correspond to an epigenetic memory. The cellular capacity of learning new adaptive systemic behaviors represents a fundamental evolutionary mechanism for cell adaptation.

Resolution of Complex Issues in Genome Regulation and Cancer Requires Non-Linear and Network-Based Thermodynamics

The apparent lack of success in curing cancer that was evidenced in the last four decades of molecular medicine indicates the need for a global re-thinking both its nature and the biological approaches that we are taking in its solution. The reductionist, one gene/one protein method that has served us well until now, and that still dominates in biomedicine, requires complementation with a more systemic/holistic approach, to address the huge problem of cross-talk between more than 20,000 protein-coding genes, about 100,000 protein types, and the multiple layers of biological organization. In this perspective, the relationship between the chromatin network organization and gene expression regulation plays a fundamental role. The elucidation of such a relationship requires a non-linear thermodynamics approach to these biological systems. This change of perspective is a necessary step for developing successful 'tumour-reversion' therapeutic strategies.

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.

Recent Developments on the Origin and Nature of Reductive Sulfurous Off-Odours in Wine

Reductive sulfurous off-odors are still one of the main reasons for rejecting wines by consumers. In 2008 at the International Wine Challenge in London, approximately 6% of the more than 10,000 wines presented were described as faulty. Twenty-eight percent were described as faulty because they presented “reduced characters” similar to those presented by “cork taint” and in nearly the same portion. Reductive off-odors are caused by low volatile sulfurous compounds. Their origin may be traced back to the metabolism of the microorganisms (yeasts and lactic acid bacteria) involved in the fermentation steps during wine making, often followed by chemical conversions. The main source of volatile sulfur compounds (VSCs) are precursors from the sulfate assimilation pathway (SAP, sometimes named as the “sulfate reduction pathway” SRP), used by yeast to assimilate sulfur from the environment and incorporate it into the essential sulfur-containing amino acids methionine and cysteine. Reductive off-odors became of increasing interest within the last few years, and the method to remove them by treatment with copper (II) salts (sulfate or citrate) is more and more questioned: The effectiveness is doubted, and after prolonged bottle storage, they reappear quite often. Numerous reports within the last few years and an ongoing flood of publications dealing with this matter reflect the importance of this problem. In a recent detailed review, almost all relevant aspects were discussed on a scientific data basis, and a “decision tree” was formulated to support winemakers handling this problem. Since we are dealing with a very complicated matter with a multitude of black spots still remaining, these advices can only be realized using specific equipment and special chemicals, not necessarily found in small wineries. The main problem in dealing with sulfurous compounds arises from the high variability of their reactivities. Sulfur is a metalloid with a large valence span across eight electron transformations from S (−II) up to S (+VI). This allows it to participate in an array of oxidation, reduction and disproportionation reactions, both abiotic and linked to microbial metabolism. In addition, sulfur is the element with the most allotropes and a high tendency to form chains and rings, with different stabilities of defined species and a high interconvertibility among each other. We suppose, there is simply a lack of knowledge of what is transferred during filling into bottles after fermentation and fining procedures. The treatment with copper (II) salts to remove sulfurous off-odors before filling rather increases instead of solving the problem. This paper picks up the abundant knowledge from recent literature and tries to add some aspects and observations, based on the assumption that the formation of polythionates, hitherto not taken into consideration, may explain some of the mystery of the re-appearance of reductive off-odors.

Physiology, ecology and industrial applications of aroma formation in yeast

Yeast cells are often employed in industrial fermentation processes for their ability to efficiently convert relatively high concentrations of sugars into ethanol and carbon dioxide. Additionally, fermenting yeast cells produce a wide range of other compounds, including various higher alcohols, carbonyl compounds, phenolic compounds, fatty acid derivatives and sulfur compounds. Interestingly, many of these secondary metabolites are volatile and have pungent aromas that are often vital for product quality. In this review, we summarize the different biochemical pathways underlying aroma production in yeast as well as the relevance of these compounds for industrial applications and the factors that influence their production during fermentation. Additionally, we discuss the different physiological and ecological roles of aroma-active metabolites, including recent findings that point at their role as signaling molecules and attractants for insect vectors.

Biological Timekeeping: The Business of a Blind Watchmaker

Fundamental understanding of life depends on both structural and functional details at the molecular level. Continually improving means of measurement of spatial and dynamic properties of biochemical constituents and cellular components complement studies of whole organisms. Integration of the interaction of components to provide coherent behaviour depends on highly elaborate orchestration in space and time. Whereas spatial information on a nanometre resolution is available, and fast dynamic analyses provide biochemical reaction rates measured in nanoseconds, functional coordination of the system requires integrated time dependence. While we are well aware of the special complexity of living organisms, appreciation of temporal scales and their organisation in time is still fragmentary. This article summarises current developments in research on biological time on scales from nanoseconds to years, the networks that connect different time domains and the oscillations, rhythms and biological clocks that coordinate and synchronise the complexity of the living state.

“It is the pattern maintained by this homeostasis, which is the touchstone of our personal identity. Our tissues change as we live: the food we eat and the air we breathe become flesh of our flesh, and bone of our bone, and the momentary elements of our flesh and bone pass out of our body every day with our excreta. We are but whirlpools in a river of ever-flowing water. We are not the stuff that abides, but patterns that perpetuate themselves”60.

Wiener, 1954

“What are called structures are slow processes of long duration, functions are quick processes of short duration”61.

Von Bertalanffy, 1952

Elements of the cellular metabolic structure

A large number of studies have demonstrated the existence of metabolic covalent modifications in different molecular structures, which are able to store biochemical information that is not encoded by DNA. Some of these covalent mark patterns can be transmitted across generations (epigenetic changes). Recently, the emergence of Hopfield-like attractor dynamics has been observed in self-organized enzymatic networks, which have the capacity to store functional catalytic patterns that can be correctly recovered by specific input stimuli. Hopfield-like metabolic dynamics are stable and can be maintained as a long-term biochemical memory. In addition, specific molecular information can be transferred from the functional dynamics of the metabolic networks to the enzymatic activity involved in covalent post-translational modulation, so that determined functional memory can be embedded in multiple stable molecular marks. The metabolic dynamics governed by Hopfield-type attractors (functional processes), as well as the enzymatic covalent modifications of specific molecules (structural dynamic processes) seem to represent the two stages of the dynamical memory of cellular metabolism (metabolic memory). Epigenetic processes appear to be the structural manifestation of this cellular metabolic memory. Here, a new framework for molecular information storage in the cell is presented, which is characterized by two functionally and molecularly interrelated systems: a dynamic, flexible and adaptive system (metabolic memory) and an essentially conservative system (genetic memory). The molecular information of both systems seems to coordinate the physiological development of the whole cell.

Function of metabolic and organelle networks in crowded and organized media

(Macro)molecular crowding and the ability of the ubiquitous cytoskeleton to dynamically polymerize–depolymerize are prevalent cytoplasmic conditions in prokaryotic and eukaryotic cells. Protein interactions, enzymatic or signaling reactions - single, sequential or in complexes - whole metabolic pathways and organelles can be affected by crowding, the type and polymeric status of cytoskeletal proteins (e.g., tubulin, actin), and their imparted organization. The self-organizing capability of the cytoskeleton can orchestrate metabolic fluxes through entire pathways while its fractal organization can frame the scaling of activities in several levels of organization. The intracellular environment dynamics (e.g., biochemical reactions) is dominated by the orderly cytoskeleton and the intrinsic randomness of molecular crowding. Existing evidence underscores the inherent capacity of intracellular organization to generate emergent global behavior. Yet unknown is the relative impact on cell function provided by organelle or functional compartmentation based on transient proteins association driven by weak interactions (quinary structures) under specific environmental challenges or functional conditions (e.g., hypoxia, division, differentiation). We propose a qualitative, integrated structural–functional model of cytoplasmic organization based on a modified version of the Sierspinsky–Menger–Mandelbrot sponge, a 3D representation of a percolation cluster, and examine its capacity to accommodate established experimental facts.

On the dynamics of the adenylate energy system: homeorhesis vs homeostasis

Biochemical energy is the fundamental element that maintains both the adequate turnover of the biomolecular structures and the functional metabolic viability of unicellular organisms. The levels of ATP, ADP and AMP reflect roughly the energetic status of the cell, and a precise ratio relating them was proposed by Atkinson as the adenylate energy charge (AEC). Under growth-phase conditions, cells maintain the AEC within narrow physiological values, despite extremely large fluctuations in the adenine nucleotides concentration. Intensive experimental studies have shown that these AEC values are preserved in a wide variety of organisms, both eukaryotes and prokaryotes. Here, to understand some of the functional elements involved in the cellular energy status, we present a computational model conformed by some key essential parts of the adenylate energy system. Specifically, we have considered (I) the main synthesis process of ATP from ADP, (II) the main catalyzed phosphotransfer reaction for interconversion of ATP, ADP and AMP, (III) the enzymatic hydrolysis of ATP yielding ADP, and (IV) the enzymatic hydrolysis of ATP providing AMP. This leads to a dynamic metabolic model (with the form of a delayed differential system) in which the enzymatic rate equations and all the physiological kinetic parameters have been explicitly considered and experimentally tested in vitro. Our central hypothesis is that cells are characterized by changing energy dynamics (homeorhesis). The results show that the AEC presents stable transitions between steady states and periodic oscillations and, in agreement with experimental data these oscillations range within the narrow AEC window. Furthermore, the model shows sustained oscillations in the Gibbs free energy and in the total nucleotide pool. The present study provides a step forward towards the understanding of the fundamental principles and quantitative laws governing the adenylate energy system, which is a fundamental element for unveiling the dynamics of cellular life.

Time resolved DNA occupancy dynamics during the respiratory oscillation uncover a global reset point in the yeast growth program

The structural dynamics of chromatin have been implicated in the regulation of fundamental eukaryotic processes, such as DNA transcription, replication and repair. Although previous studies have revealed that the chromatin landscape, nucleosome remodeling and histone modification events are intimately tied into cellular energetics and redox state, few studies undertake defined time-resolved measurements of these state variables. Here, we use metabolically synchronous, continuously-grown yeast cultures to measure DNA occupancy and track global patterns with respect to the metabolic state of the culture. Combined with transcriptome analyses and ChIP-qPCR experiments, these paint an intriguing picture where genome-wide nucleosome focusing occurs during the recovery of energy charge, followed by clearance of the promoter regions and global transcriptional slow-down, thus indicating a nucleosome-mediated “reset point” for the cycle. The reset begins at the end of the catabolic and stress-response transcriptional programs and ends prior to the start of the anabolic and cell-growth transcriptional program, and the histones on genes from both the catabolic and anabolic superclusters are deacetylated.

Quantifying periodicity in omics data

Oscillations play a significant role in biological systems, with many examples in the fast, ultradian, circadian, circalunar, and yearly time domains. However, determining periodicity in such data can be problematic. There are a number of computational methods to identify the periodic components in large datasets, such as signal-to-noise based Fourier decomposition, Fisher's g-test and autocorrelation. However, the available methods assume a sinusoidal model and do not attempt to quantify the waveform shape and the presence of multiple periodicities, which provide vital clues in determining the underlying dynamics. Here, we developed a Fourier based measure that generates a de-noised waveform from multiple significant frequencies. This waveform is then correlated with the raw data from the respiratory oscillation found in yeast, to provide oscillation statistics including waveform metrics and multi-periods. The method is compared and contrasted to commonly used statistics. Moreover, we show the utility of the program in the analysis of noisy datasets and other high-throughput analyses, such as metabolomics and flow cytometry, respectively.

Encystment in Acanthamoeba castellanii: a review

Differentiation of Acanthamoeba castellanii trophozoites involves massive turnover of cellular components and remodelling of organelle structure and function so as to produce a cryptobiotic cell, resistant to desiccation, heat, freezing, and chemical treatments. This review presents a summary of a decade of research on the most studied aspects of the biochemistry of this process, with emphasis on problems of biocide and drug resistances, putative new targets, molecular and cell biology of the process of encystment, and the characteristics of the encysted state. As well as the intrinsic pathogenicity of the organism towards the cornea, and the ability of related species to invade the human brain, its propensity for harbouring and transmitting pathogenic bacteria and viruses is considerable and leads to increasing concerns. The long-term survival and resistance of cysts to drugs and biocides adds another layer of complexity to the problem of their elimination.

Elucidating the adaptation and temporal coordination of metabolic pathways using in-silico evolution

Cellular metabolism, the interconversion of small molecules by chemical reactions, is a tightly coordinated process that requires integration of diverse environmental and intracellular cues. While for many organisms the topology of the network of metabolic reactions is increasingly known, the regulatory principles that shape the network's adaptation to diverse and changing environments remain largely elusive. To investigate the principles of metabolic adaptation and regulation in metabolic pathways, we propose a computational approach based on in-silico evolution. Rather than analyzing existing regulatory schemes, we let a population of minimal, prototypical metabolic cells evolve rate constants and appropriate regulatory schemes that allow for optimal growth in static and fluctuating environments. Applying our approach to a small, but already sufficiently complex, minimal system reveals intricate transitions between metabolic modes. These results have implications for trade-offs in resource allocation. Going from static to varying environments, we show that for fluctuating nutrient availability, active metabolic regulation results in a significantly increased overall rate of metabolism.

Nature of Pre-Earthquake Phenomena and their Effects on Living Organisms

Earthquakes occur when tectonic stresses build up deep in the Earth before catastrophic rupture. During the build-up of stress, processes that occur in the crustal rocks lead to the activation of highly mobile electronic charge carriers. These charge carriers are able to flow out of the stressed rock volume into surrounding rocks. Such outflow constitutes an electric current, which generates electromagnetic (EM) signals. If the outflow occurs in bursts, it will lead to short EM pulses. If the outflow is continuous, the currents may fluctuate, generating EM emissions over a wide frequency range. Only ultralow and extremely low frequency (ULF/ELF) waves travel through rock and can reach the Earth surface. The outflowing charge carriers are (i) positively charged and (ii) highly oxidizing. When they arrive at the Earth surface from below, they build up microscopic electric fields, strong enough to field-ionize air molecules. As a result, the air above the epicentral region of an impending major earthquake often becomes laden with positive airborne ions. Medical research has long shown that positive airborne ions cause changes in stress hormone levels in animals and humans. In addition to the ULF/ELF emissions, positive airborne ions can cause unusual reactions among animals. When the charge carriers flow into water, they oxidize water to hydrogen peroxide. This, plus oxidation of organic compounds, can cause behavioral changes among aquatic animals.

Oscillation of oxygenation in skeletal muscle at rest and in light exercise

The aim of the present study was to compare the frequency of oxygenation determined in the vastus lateralis by near-infrared spectroscopy (NIRS) in light exercise with that at rest. A subject rested in a recumbent position for 5 min and changed body position to a sitting position on a cycle ergometer for 9 min. Then exercise with low intensity (work rate of 60% of maximal oxygen uptake) was carried out for 30 min. Total hemoglobin and myoglobin (THb/Mb) suddenly decreased after the start of exercise and gradually increased for 6 min. Oxygenated hemoglobin and myoglobin (Hb/MbO2) suddenly decreased and returned to a steady-state after the start of exercise. The difference between Hb/MbO2 and THb/Mb showed a sudden decrease and then a steady-state. This difference was analyzed by fast Fourier transform. The peak frequencies of the power spectrum density (PSD) were 0.0169 ± 0.0076 Hz at rest and 0.0117 ± 0.0042 Hz in exercise. The peak frequency of PSD was significantly decreased in exercise. In exercise, the range of frequencies was expanded. It is concluded that there are oscillations at rest as well as in exercise and that the frequency of peak PSD becomes lower in exercise than at rest.

Increased growth and germination success in plants following hydrogen sulfide administration

This study presents a novel way of enhancing plant growth through the use of a non-petroleum based product. We report here that exposing either roots or seeds of multicellular plants to extremely low concentrations of dissolved hydrogen sulfide at any stage of life causes statistically significant increases in biomass including higher fruit yield. Individual cells in treated plants were smaller (~13%) than those of controls. Germination success and seedling size increased in, bean, corn, wheat, and pea seeds while time to germination decreases. These findings indicated an important role of H2S as a signaling molecule that can increase the growth rate of all species yet tested. The increased crop yields reported here has the potential to effect the world's agricultural output.

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.

Adaptation of organisms by resonance of RNA transcription with the cellular redox cycle

Sequence variation in organisms differs across the genome and the majority of mutations are caused by oxidation, yet its origin is not fully understood. It has also been shown that the reduction-oxidation reaction cycle is the fundamental biochemical cycle that coordinates the timing of all biochemical processes in the cell, including energy production, DNA replication, and RNA transcription. We show that the temporal resonance of transcriptome biosynthesis with the oscillating binary state of the reduction-oxidation reaction cycle serves as a basis for non-random sequence variation at specific genome-wide coordinates that change faster than by accumulation of chance mutations. This work demonstrates evidence for a universal, persistent and iterative feedback mechanism between the environment and heredity, whereby acquired variation between cell divisions can outweigh inherited variation.

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.

PSK2 coordinates glucose metabolism and utilization to maintain ultradian clock-coupled respiratory oscillation in Saccharomyces cerevisiae yeast

Ultradian clock-coupled respiratory oscillation (UCRO) in an aerobic continuous culture of Saccharomyces cerevisiae S288C is principally regulated by control of certain redox reactions of energy metabolism. It is also modulated by the metabolism of storage carbohydrates during adaptation to environmental change. However, the mechanism of cell sensing and response to environmental nutrients in UCRO is unknown. The purpose of the present study was to determine the role of PSK2 kinase in UCRO in yeast. S. cerevisiae in culture showed oscillation in PSK2 mRNA levels with a definite phase relationship to the respiratory oscillation. Furthermore, inactivation of Psk2 by gene disruption severely affected UCRO and its decline to undetectable levels within 2days. In addition, the extracellular and intracellular glucose concentrations of PSK2 deletion mutants in culture were higher and lower, respectively, than those of the wild type. PSK2 mutant cells showed no alteration in redox state. Furthermore, the levels of storage carbohydrates such as glycogen and trehalose fluctuated in PSK2 mutants with attenuated amplitudes comparable to those in the wild type. The results indicated that PSK2 kinase is important for the uptake of glucose and regulation of storage-carbohydrate synthesis and hence the maintenance of an unperturbed continuously oscillating state.

Quantitative analysis of cellular metabolic dissipative, self-organized structures

One of the most important goals of the postgenomic era is understanding the metabolic dynamic processes and the functional structures generated by them. Extensive studies during the last three decades have shown that the dissipative self-organization of the functional enzymatic associations, the catalytic reactions produced during the metabolite channeling, the microcompartmentalization of these metabolic processes and the emergence of dissipative networks are the fundamental elements of the dynamical organization of cell metabolism. Here we present an overview of how mathematical models can be used to address the properties of dissipative metabolic structures at different organizational levels, both for individual enzymatic associations and for enzymatic networks. Recent analyses performed with dissipative metabolic networks have shown that unicellular organisms display a singular global enzymatic structure common to all living cellular organisms, which seems to be an intrinsic property of the functional metabolism as a whole. Mathematical models firmly based on experiments and their corresponding computational approaches are needed to fully grasp the molecular mechanisms of metabolic dynamical processes. They are necessary to enable the quantitative and qualitative analysis of the cellular catalytic reactions and also to help comprehend the conditions under which the structural dynamical phenomena and biological rhythms arise. Understanding the molecular mechanisms responsible for the metabolic dissipative structures is crucial for unraveling the dynamics of cellular life.

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.

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.

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.

Interaction of iron ions with oxygen or nitrogen monoxide in chromosomes triggers synchronous expression/suppression oscillations of compact gene groups ("genomewide oscillation"): hypothesis

It has been proposed that the "oxygen-endogenous reductants" system responsible for oscillatory changes in the redox potential of the cell fulfills the function of a "central oscillator" by inducing synchronous oscillations of an immense array of genes in the cell genome (so-called "genomewide oscillation"). The effect of the redox potential on the genome can be mediated by copper or iron ions. Copper ions can induce oscillating change of the DNA double helix stability through the change of guanine-cytosine pair stability depending from valence state of copper ions. Iron ions can have a redox potential effect on the genome mediated by iron+thiol groups localized in chromosomes. Cyclic changes in the thiol content concomitant with oxidation of thiols to disulfides trigger oscillatory changes in the activity of multiple redox-sensitive transcription factors eventually resulting in genomewide oscillation. In the presence of nitric oxide, oscillatory changes in thiol levels in chromosomes can be induced by S-nitrosylation of thiols. The latter is catalyzed by iron ions and results in incorporation of nitric oxide into dinitrosyl complexes with thiol-containing ligands. It is not excluded that by virtue of their ability to react with S-nitrosothiols, thiols and nitric oxide, these complexes contribute to the formation of a steady-state self-regulating oscillating chemical system and thus fulfill the function of "central regulators" of genomewide oscillation.

Reactive biomolecular divergence in genetically altered yeast cells and isolated mitochondria as measured by biocavity laser spectroscopy: rapid diagnostic method for studying cellular responses to stress and disease

We report an analysis of four strains of baker's yeast (Saccharomyces cerevisiae) using biocavity laser spectroscopy. The four strains are grouped in two pairs (wild type and altered), in which one strain differs genetically at a single locus, affecting mitochondrial function. In one pair, the wild-type rho+ and a rho0 strain differ by complete removal of mitochondrial DNA (mtDNA). In the second pair, the wild-type rho+ and a rho- strain differ by knock-out of the nuclear gene encoding Cox4, an essential subunit of cytochrome c oxidase. The biocavity laser is used to measure the biophysical optic parameter Deltalambda, a laser wavelength shift relating to the optical density of cell or mitochondria that uniquely reflects its size and biomolecular composition. As such, Deltalambda is a powerful parameter that rapidly interrogates the biomolecular state of single cells and mitochondria. Wild-type cells and mitochondria produce Gaussian-like distributions with a single peak. In contrast, mutant cells and mitochondria produce leptokurtotic distributions that are asymmetric and highly skewed to the right. These distribution changes could be self-consistently modeled with a single, log-normal distribution undergoing a thousand-fold increase in variance of biomolecular composition. These features reflect a new state of stressed or diseased cells that we call a reactive biomolecular divergence (RBD) that reflects the vital interdependence of mitochondria and the nucleus.

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.

Gene expression waves. Cell cycle independent collective dynamics in cultured cells

The ergodic hypothesis, which assumes the independence of each cell of the ensemble from all the others, is a necessary prerequisite to attach single cell based explanations to the grand averages taken from population data. This was the prevailing view about the interpretation of cellular biology experiments that typically are performed on colonies of billions of cells. By analysing gene expression data of different cells going from yeast to mammalian cell cultures, we demonstrate that cell cultures display a sort of "ecology-in-a-plate" giving rise to a rich dynamics of gene expression that are independent from reproductive cycles, hence contradicting simple ergodic assumptions The aspecific character of the observed coordinated gene expression activity inhibits any simple mechanistic hypothesis and highlights the need to consider population effects in the interpretation of data coming from cell cultures.

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.

Single and cell population respiratory oscillations in yeast: a 2-photon scanning laser microscopy study

Two-photon scanning laser and confocal microscopies were used to image metabolic dynamics of single or cell populations of Saccharomyces cerevisiae strain 28033. Autofluorescence of reduced nicotinamide nucleotides, and mitochondrial membrane potential (DeltaPsim), were simultaneously monitored. Spontaneous, large-scale synchronized oscillations of NAD(P)H and DeltaPsim throughout the entire population of yeasts occurred under perfusion with aerated buffer in a continuous single-layered film of organisms. These oscillations stopped in the absence of perfusion and the intracellular NAD(P)H pool became reduced. Individual mitochondria within a single yeast also showed in-phase synchronous responses with the cell population, in both tetramethylrhodamine ethyl ester (or tetramethylrhodamine methyl ester) and autofluorescence. A single, localized, laser flash also triggered mitochondrial oscillations in single cells suggesting that the mitochondrion may behave as an autonomous oscillator. We conclude that spontaneous oscillations of S. cerevisiae mitochondrial redox states and DeltaPsim occur within individual yeasts, and synchrony of populations of organisms indicates the operation of an efficient system of cell-cell interaction to produce concerted metabolic multicellular behaviour on the minute time scale in both cases.

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.

Hydrogen sulfide: clandestine microbial messenger?

Although the toxicity of hydrogen sulfide (H(2)S) has been substantiated for almost 230 years, its pivotal roles in both aerobic and anaerobic organisms have only recently become evident. In low oxygen environments with millimolar concentrations of H(2)S, it functions as an electron donor and as an energy source in some systems. At micromolar levels, intracellular H(2)S in aerobic organisms has a vital role in redox balancing. At even lower concentrations, H(2)S provides essential signals in yeast, in the brain and in smooth and cardiac muscles. Here, other possible coordinating roles within and between microorganisms are suggested, including the possibility that H(2)S functions as a signalling mediator in prokaryotes. It is expected that future research will uncover a host of novel functions, not only in eukaryotes but also in prokaryotic species.