Coevolution of compositional protocells and their environment

Abstract

The coevolution of environment and living organisms is well known in nature. Here, it is suggested that similar processes can take place before the onset of life, where protocellular entities, rather than full-fledged living systems, coevolve along with their surroundings. Specifically, it is suggested that the chemical composition of the environment may have governed the chemical repertoire generated within molecular assemblies, compositional protocells, while compounds generated within these protocells altered the chemical composition of the environment. We present an extension of the graded autocatalysis replication domain (GARD) model--the environment exchange polymer GARD (EE-GARD) model. In the new model, molecules, which are formed in a protocellular assembly, may be exported to the environment that surrounds the protocell. Computer simulations of the model using an infinite-sized environment showed that EE-GARD assemblies may assume several distinct quasi-stationary compositions (composomes), similar to the observations in previous variants of the GARD model. A statistical analysis suggested that the repertoire of composomes manifested by the assemblies is independent of time. In simulations with a finite environment, this was not the case. Composomes, which were frequent in the early stages of the simulation disappeared, while others emerged. The change in the frequencies of composomes was found to be correlated with changes induced on the environment by the assembly. The EE-GARD model is the first GARD model to portray a possible time evolution of the composomes repertoire.

Lack of evolvability in self-sustaining autocatalytic networks constraints metabolism-first scenarios for the origin of life

“…Template-free systems like composomes could only have had the limited role of accumulating prebiotic material and increasing environmental patchiness. One can enlarge by various means the chemical generativity of GARD-like systems (40) without cracking the problem of the origin of unlimited heredity. It should also be said that, although in the ordinary differential equations, infinite-size populations, both in the GARD as well as the sequential quasispecies models, naturally settle down to a unique equilibrium, in realistic scenarios the evolution of sequences is open-ended as a result of finite population size, the practically infinite size of sequence space, and the structure of the fitness landscape (see, e.g., ref.…”

Compositional Inheritance: Comparison of Self-assembly and Catalysis

“…Dimerization reactions were in fact included in the original GARD model (Segré et al 1998), but were later removed. Dimers and trimers have been re-added in the latest version (Shenhav et al 2007). Chemical reactions create a much higher degree of diversity than would be present in the environment, and they lead to the possibility of forming an autocatalytic set of reactions that remains in a non-equilibrium state, like the metabolism of a cell.…”

Emergence of Life from Multicomponent Mixtures of Chemicals: The Case for Experiments with Cycling Physicochemical Gradients

“…The transition from crowded lifeless prebiotic soups to living systems thus involves the coevolution of three complex (crowded, multicomponent, and multiphase) chemistries: (i) that of permeable walls-leading to extant membrane vectorial chemistry (oriented water-insoluble proteins within lipid bilayers); (ii) that of crowded prebiotic soups within the permeable walls-leading to extant crowded cytoplasm (nucleic acids, proteins, and their multicomplexes, particularly ribosomes); and (iii) that of prebiotic soups outside the permeable walls-leading to nutrients, which early cells utilized to grow and evolve (Shenhav et al, 2007;England et al, 2010). Regarding the first two coevolution requirements for life's emergence, there is phylogenetic evidence for the coevolution of protomembranes and proto-bio-macromolecules within, as ATPases and protein folds that interact with ATP appear to be very ancient, both from genetic and metabolic standpoints (Caetano-Anollés et al, 2009;Koonin, 2009).…”