Origin of biochemical organization

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.

Global self-organization of the cellular metabolic structure

BACKGROUND

Over many years, it has been assumed that enzymes work either in an isolated way, or organized in small catalytic groups. Several studies performed using "metabolic networks models" are helping to understand the degree of functional complexity that characterizes enzymatic dynamic systems. In a previous work, we used "dissipative metabolic networks" (DMNs) to show that enzymes can present a self-organized global functional structure, in which several sets of enzymes are always in an active state, whereas the rest of molecular catalytic sets exhibit dynamics of on-off changing states. We suggested that this kind of global metabolic dynamics might be a genuine and universal functional configuration of the cellular metabolic structure, common to all living cells. Later, a different group has shown experimentally that this kind of functional structure does, indeed, exist in several microorganisms.

METHODOLOGY/PRINCIPAL FINDINGS

Here we have analyzed around 2.500.000 different DMNs in order to investigate the underlying mechanism of this dynamic global configuration. The numerical analyses that we have performed show that this global configuration is an emergent property inherent to the cellular metabolic dynamics. Concretely, we have found that the existence of a high number of enzymatic subsystems belonging to the DMNs is the fundamental element for the spontaneous emergence of a functional reactive structure characterized by a metabolic core formed by several sets of enzymes always in an active state.

CONCLUSIONS/SIGNIFICANCE

This self-organized dynamic structure seems to be an intrinsic characteristic of metabolism, common to all living cellular organisms. To better understand cellular functionality, it will be crucial to structurally characterize these enzymatic self-organized global structures.

Early assembly of cellular life

Popular hypotheses that attempt to explain the origin of prebiotic molecules and cellular life capable of growth and division are not always agreed upon. In this manuscript, information on early bacterial life on Earth is examined using information from several disciplines. For example, knowledge can be integrated from physics, thermodynamics, planetary sciences, geology, biogeochemistry, lipid chemistry, primordial cell structures, cell and molecular biology, microbiology, metabolism and genetics. The origin of life also required a combination of elements, compounds and environmental physical-chemical conditions that allowed cells to assemble in less than a billion years. This may have been widespread in the subsurface of the early Earth located at microscopic physical domains.