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Global self-organization of the cellular metabolic structure.

De La Fuente IM, Martínez L, Pérez-Samartín AL, Ormaetxea L, Amezaga C, Vera-López A - PLoS ONE (2008)

Bottom Line: 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.Later, a different group has shown experimentally that this kind of functional structure does, indeed, exist in several microorganisms.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.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Matemáticas, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Vizcaya, Spain.

ABSTRACT

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.

Show MeSH
Dynamical patterns in the DMNs formed by two subsystems represented in the figure 1.(a) Periodic transitions in the mean amplitude A0 of the MSb1, and (b) their corresponding cycle of the different periodic behaviors belonging to the activity of the own metabolic subsystem; the δ threshold value is δ = 0.3, which represents the level of the covalent regulatory activity. (c) Complex periodic transitions in the mean amplitude A0 in the MSb2 for δ = 0.83 and (d) their corresponding patterns of its activity showing cycles of periodic oscillations with a steady state. The mean amplitude A0 is represented as a function of the number of transitions N. The activity C (sequences of periodic or stationary patterns) developed by each metabolic subsystem is represented as a function of the time t.
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pone-0003100-g002: Dynamical patterns in the DMNs formed by two subsystems represented in the figure 1.(a) Periodic transitions in the mean amplitude A0 of the MSb1, and (b) their corresponding cycle of the different periodic behaviors belonging to the activity of the own metabolic subsystem; the δ threshold value is δ = 0.3, which represents the level of the covalent regulatory activity. (c) Complex periodic transitions in the mean amplitude A0 in the MSb2 for δ = 0.83 and (d) their corresponding patterns of its activity showing cycles of periodic oscillations with a steady state. The mean amplitude A0 is represented as a function of the number of transitions N. The activity C (sequences of periodic or stationary patterns) developed by each metabolic subsystem is represented as a function of the time t.

Mentions: At small threshold values, for 0≤δ≤0.12 the MSb1 presents a single oscillatory behavior of one-period. In the interval 0.12<δ≤0.836 the first subsystem is always active and presents different cycles of transitions with 2, 3, 6, 12… and more of 100 periodic patterns. For instance, one can observe how for δ = 0.19 the MSb1, presents a cycle of period three, i.e. the output activity of the subsystem 1 makes uninterrupted transitions between three different kinds of periodic oscillations. In figure 2b, it can also be observed how, for δ = 0.3, a cycle of uninterrupted transitions between 8 different periodic oscillations emerges spontaneously in MSb1.


Global self-organization of the cellular metabolic structure.

De La Fuente IM, Martínez L, Pérez-Samartín AL, Ormaetxea L, Amezaga C, Vera-López A - PLoS ONE (2008)

Dynamical patterns in the DMNs formed by two subsystems represented in the figure 1.(a) Periodic transitions in the mean amplitude A0 of the MSb1, and (b) their corresponding cycle of the different periodic behaviors belonging to the activity of the own metabolic subsystem; the δ threshold value is δ = 0.3, which represents the level of the covalent regulatory activity. (c) Complex periodic transitions in the mean amplitude A0 in the MSb2 for δ = 0.83 and (d) their corresponding patterns of its activity showing cycles of periodic oscillations with a steady state. The mean amplitude A0 is represented as a function of the number of transitions N. The activity C (sequences of periodic or stationary patterns) developed by each metabolic subsystem is represented as a function of the time t.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2519785&req=5

pone-0003100-g002: Dynamical patterns in the DMNs formed by two subsystems represented in the figure 1.(a) Periodic transitions in the mean amplitude A0 of the MSb1, and (b) their corresponding cycle of the different periodic behaviors belonging to the activity of the own metabolic subsystem; the δ threshold value is δ = 0.3, which represents the level of the covalent regulatory activity. (c) Complex periodic transitions in the mean amplitude A0 in the MSb2 for δ = 0.83 and (d) their corresponding patterns of its activity showing cycles of periodic oscillations with a steady state. The mean amplitude A0 is represented as a function of the number of transitions N. The activity C (sequences of periodic or stationary patterns) developed by each metabolic subsystem is represented as a function of the time t.
Mentions: At small threshold values, for 0≤δ≤0.12 the MSb1 presents a single oscillatory behavior of one-period. In the interval 0.12<δ≤0.836 the first subsystem is always active and presents different cycles of transitions with 2, 3, 6, 12… and more of 100 periodic patterns. For instance, one can observe how for δ = 0.19 the MSb1, presents a cycle of period three, i.e. the output activity of the subsystem 1 makes uninterrupted transitions between three different kinds of periodic oscillations. In figure 2b, it can also be observed how, for δ = 0.3, a cycle of uninterrupted transitions between 8 different periodic oscillations emerges spontaneously in MSb1.

Bottom Line: 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.Later, a different group has shown experimentally that this kind of functional structure does, indeed, exist in several microorganisms.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.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Matemáticas, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Vizcaya, Spain.

ABSTRACT

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.

Show MeSH