Oscillations in rat liver cytosolic enzyme activities of the urea cycle

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.

Ammonia-lowering activities and carbamoyl phosphate synthetase 1 (Cps1) induction mechanism of a natural flavonoid

OBJECTIVE

Ammonia detoxification is essential for physiological well-being, and the urea cycle in liver plays a predominant role in ammonia disposal. Nobiletin (NOB), a natural dietary flavonoid, is known to exhibit various physiological efficacies. In the current study, we investigated a potential role of NOB in ammonia control and the underlying cellular mechanism.

MATERIALS/METHODS

C57BL/6 mice were fed with regular chow (RC), high-fat (HFD) or high-protein diet (HPD) and treated with either vehicle or NOB. Serum and/or urine levels of ammonia and urea were measured. Liver expression of genes encoding urea cycle enzymes and C/EBP transcription factors was determined over the circadian cycle. Luciferase reporter assays were carried out to investigate function of CCAAT consensus elements on the carbamoyl phosphate synthetase (Cps1) gene promoter. A circadian clock-deficient mouse mutant, Clock (Δ19/Δ19) , was utilized to examine a requisite role of the circadian clock in mediating NOB induction of Cps1.

RESULTS

NOB was able to lower serum ammonia levels in mice fed with RC, HFD or HPD. Compared with RC, HFD repressed the mRNA and protein expression of Cps1, encoding the rate-limiting enzyme of the urea cycle. Interestingly, NOB rescued CPS1 protein levels under the HFD condition via induction of the transcription factors C/EBPα and C/EBPβ. Expression of other urea cycle genes was also decreased by HFD relative to RC and again restored by NOB to varying degrees, which, in conjunction with Cps1 promoter reporter analysis, suggested a C/EBP-dependent mechanism for the co-induction of urea cycle genes by NOB. In comparison, HPD markedly increased CPS1 levels relative to RC, yet NOB did not further enrich CPS1 to a significant extent. Using the circadian mouse mutant Clock (Δ19/Δ19) , we also showed that a functional circadian clock, known to modulate C/EBP and CPS1 expression, was required for NOB induction of CPS1 under the HFD condition.

CONCLUSION

NOB, a dietary flavonoid, exhibits a broad activity in ammonia control across varying diets, and regulates urea cycle function via C/EBP-and clock-dependent regulatory mechanisms.

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.

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.

The metabolic core and catalytic switches are fundamental elements in the self-regulation of the systemic metabolic structure of cells

BACKGROUND

Experimental observations and numerical studies with dissipative metabolic networks have shown that cellular enzymatic activity self-organizes spontaneously leading to the emergence of a metabolic core formed by a set of enzymatic reactions which are always active under all environmental conditions, while the rest of catalytic processes are only intermittently active. The reactions of the metabolic core are essential for biomass formation and to assure optimal metabolic performance. The on-off catalytic reactions and the metabolic core are essential elements of a Systemic Metabolic Structure which seems to be a key feature common to all cellular organisms.

METHODOLOGY/PRINCIPAL FINDINGS

In order to investigate the functional importance of the metabolic core we have studied different catalytic patterns of a dissipative metabolic network under different external conditions. The emerging biochemical data have been analysed using information-based dynamic tools, such as Pearson's correlation and Transfer Entropy (which measures effective functionality). Our results show that a functional structure of effective connectivity emerges which is dynamical and characterized by significant variations of bio-molecular information flows.

CONCLUSIONS/SIGNIFICANCE

We have quantified essential aspects of the metabolic core functionality. The always active enzymatic reactions form a hub--with a high degree of effective connectivity--exhibiting a wide range of functional information values being able to act either as a source or as a sink of bio-molecular causal interactions. Likewise, we have found that the metabolic core is an essential part of an emergent functional structure characterized by catalytic modules and metabolic switches which allow critical transitions in enzymatic activity. Both, the metabolic core and the catalytic switches in which also intermittently-active enzymes are involved seem to be fundamental elements in the self-regulation of the Systemic Metabolic Structure.

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.

Global self-regulation of the cellular metabolic structure

BACKGROUND

Different studies have shown that cellular enzymatic activities are able to self-organize spontaneously, forming a metabolic core of reactive processes that remain active under different growth conditions while the rest of the molecular catalytic reactions exhibit structural plasticity. This global cellular metabolic structure appears to be an intrinsic characteristic common to all cellular organisms. Recent work performed with dissipative metabolic networks has shown that the fundamental element for the spontaneous emergence of this global self-organized enzymatic structure could be the number of catalytic elements in the metabolic networks.

METHODOLOGY/PRINCIPAL FINDINGS

In order to investigate the factors that may affect the catalytic dynamics under a global metabolic structure characterized by the presence of metabolic cores we have studied different transitions in catalytic patterns belonging to a dissipative metabolic network. The data were analyzed using non-linear dynamics tools: power spectra, reconstructed attractors, long-term correlations, maximum Lyapunov exponent and Approximate Entropy; and we have found the emergence of self-regulation phenomena during the transitions in the metabolic activities.

CONCLUSIONS/SIGNIFICANCE

The analysis has also shown that the chaotic numerical series analyzed correspond to the fractional Brownian motion and they exhibit long-term correlations and low Approximate Entropy indicating a high level of predictability and information during the self-regulation of the metabolic transitions. The results illustrate some aspects of the mechanisms behind the emergence of the metabolic self-regulation processes, which may constitute an important property of the global structure of the cellular metabolism.

The number of catalytic elements is crucial for the emergence of metabolic cores

Background

Different studies show evidence that several unicellular organisms display a cellular metabolic structure characterized by a set of enzymes which are always in an active state (metabolic core), while the rest of the molecular catalytic reactions exhibit on-off changing states. This self-organized enzymatic configuration seems to be an intrinsic characteristic of metabolism, common to all living cellular organisms. In a recent analysis performed with dissipative metabolic networks (DMNs) we have shown that this global functional structure emerges in metabolic networks with a relatively high number of catalytic elements, under particular conditions of enzymatic covalent regulatory activity.

Methodology/Principal Findings

Here, to investigate the mechanism behind the emergence of this supramolecular organization of enzymes, we have performed extensive DMNs simulations (around 15,210,000 networks) taking into account the proportion of the allosterically regulated enzymes and covalent enzymes present in the networks, the variation in the number of substrate fluxes and regulatory signals per catalytic element, as well as the random selection of the catalytic elements that receive substrate fluxes from the exterior. The numerical approximations obtained show that the percentages of DMNs with metabolic cores grow with the number of catalytic elements, converging to 100% for all cases.

Conclusions/Significance

The results show evidence that the fundamental factor for the spontaneous emergence of this global self-organized enzymatic structure is the number of catalytic elements in the metabolic networks. Our analysis corroborates and expands on our previous studies illustrating a crucial property of the global structure of the cellular metabolism. These results also offer important insights into the mechanisms which ensure the robustness and stability of living cells.

Daily oscillations in liver function: diurnal vs circadian rhythmicity

The rodent suprachiasmatic nucleus (SCN), a site in the brain that contains a light-entrained biological (circadian) clock, has been thought of as the master oscillator, regulating processes as diverse as cell division, reproductive cycles, sleep, and feeding. However, a second circadian system exists that can be entrained by meal feeding and has an influence over metabolism and behavior. Recent advances in the molecular genetics of circadian clocks are revealing clock characteristics such as rhythmic clock gene expression in a variety of non-neural tissues such as liver. Although little is known regarding the function of these clock genes in the liver, there is a large literature that addresses the capabilities of this organ to keep time. This time-keeping capability may be an adaptive function allowing for the prediction of mealtime and therefore improved digestion and energy usage. Consequently, an understanding of these rhythms is of great importance. This review summarizes the results of studies on diurnal and circadian rhythmicity in the rodent liver. We hope to lend support to the hypothesis that there are functionally important circadian clocks outside of the brain that are not light- or SCN-dependent. Rather, these clocks are largely responsive to stimuli involved in nutrient intake. The interaction between these two systems may be very important for the ability of organisms to synchronize their internal physiology.