Molecular Diversity and Network Complexity in Growing Protocells

Abstract

A great variety of molecular components is encapsulated in cells. Each of these components is replicated for cell reproduction. To address an essential role of the huge diversity of cellular components, we study a model of protocells that convert resources into catalysts with the aid of a catalytic reaction network. As the resources are limited, it is shown that diversity in intracellular components is increased to allow the use of diverse resources for cellular growth. Scaling relation is demonstrated between resource abundances and molecular diversity. We then study how the molecule species diversify and complex catalytic reaction networks develop through the evolutionary course. It is shown that molecule species first appear, at some generations, as parasitic ones that do not contribute to replication of other molecules. Later, the species turn to be host species that support the replication of other species. With this successive increase of host species, a complex joint network evolves. The present study sheds new light on the origin of molecular diversity and complex reaction network at the primitive stage of a cell.

Protobiotic network reproducers are compositional attractors: enhanced probability for life’s origin

“…The distillation is shown in Figure 6B,C, depicting an enrichment of high catalytic values in the attractor as compared to the original distribution. The concept of repertoire diminution en route to more effective catalytic network is also inferred in a different network model (11), showing that a minimum network with essential components would achieve a higher reproduction rate. The emerging diminution is reminiscent of the transition from prebiotic messy chemistry (1) to life, as exemplified by the fact that living cells utilize a small subset of the possible assortment within compound classes such as amino acids, sugars and lipids (15).…”

“…Computer program and basal data used in the computer simulations are deposited in public databases, with accession numbers and brief description of the relevant datasets provided in the Methods. (11), shown here in simplified form, the catalytic power varies in a limited interval and the momentary molecular concentrations within a cell are all equal. The top row provides information on the model's mode of containment: being within a lipid phase such as a micelle or a bilayer, hence defined as an integral part of the catalytic network (A); Enclosed in an implicit container without molecular identity or transport properties (B); Enclosed by a molecularly undefined cellular entity with specified molecular transport.…”

“…Its supporters posit that life began with spatially demarcated assemblages of small organic molecules, not necessarily resembling those of present life organic repertoire. At the heart of this scenario is the assumption that the assemblies would build up mutually catalytic networks, whose function rests on simple organocatalysts (10)(11)(12). Under certain quantitatively defined kinetic constraints, similar to those that govern present-day metabolism, such multimolecular networks would reproduce and evolve (12)(13)(14)(15).…”

The Universal Evolution and the Origin of Life

“…67 Atsushi Kamimura and her colleague Kunihiko Kaneko, both from the University of Tokyo, have proposed what they call the cluster model. 68 They argue that in the case of the origin of cells, the evolution acted on clusters of interacting organic molecules that gradually increased their complexity and improved copy fidelity. In other words, prokaryotes and all their important features emerged as a product of clusters of interacting organic molecules.…”

“…The verdict is still out as to whether the emergence of prokaryotic cells was a result of assembly of individual components or, as Kamimura and Kaneko theorize, it was a product of interactions among molecules in clusters that gradually increased their complexity and improved copy fidelity. 109 The scenario proposed by Kamimura and Kaneko appears to be more promising as it solves several problems at the same time: the origin of heredity, metabolism, and compartmentalization. 110 However, no matter what the final verdict is going to be, both paths point to the importance of conservation, as well as adaptation and assimilation as two vital aspects of combining and equilibrating required for creating prokaryotes.…”