Abstract
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.
Highlights
Reviewed by: Miyako Kusano, University of Tsukuba/RIKEN Center for Sustainable Resource Science, Japan Thomas Nägele, University of Vienna, Austria
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
Transfer entropy analysis of the dissipative metabolic networks (DMNs) showed that in addition to the network’s topological structure, characterized by the specific location of enzymatic subsystems, molecular substrate fluxes and regulatory signals, there is another functional structure of biomolecular information flow which is modular, dynamic and able to modify the catalytic activities of all the enzymatic sets (De la Fuente et al, 2011)
Summary
Reviewed by: Miyako Kusano, University of Tsukuba/RIKEN Center for Sustainable Resource Science, Japan Thomas Nägele, University of Vienna, Austria. 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. Analyses of the proteome of Saccharomyces cerevisiae have shown that at least 83% of proteins form complexes comprised of 2–83 proteins (Gavin et al, 2002) This kind of associative organization occurs in all sorts of cells, both eukaryotes and prokaryotes (Uetz et al, 2000; Ito et al, 2001; Ho et al, 2002; Bobik, 2006; Sutter et al, 2008; Yeates et al, 2008). Analysis of conserved sequences in biochemical reactions has shown that cellular metabolism contains basic functional units which tend to correspond to traditional metabolic pathways These functional multi-enzymatic units seem to be the catalytic building blocks of cellular metabolism (Kanehisa, 2013; Muto et al, 2013). Another kind of functional catalytic association is the interactome which
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