Kinetic Selection of Template Polymer with Complex Sequences

Matsubara, Yoshiya J.; Kaneko, Kunihiko

doi:10.1103/physrevlett.121.118101

Cited by 14 publications

(6 citation statements)

References 40 publications

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“…Recall that the information encoded in the composition is different from that encoded in RNA as the combinatorial diversity of sequences. Still, it is interesting to note that, under a limited flow of monomer resources, the sequence of catalytic polymers increases their complexity as has been shown recently [23].…”

Section: Discussionmentioning

confidence: 93%

Molecular Diversity and Network Complexity in Growing Protocells

Kamimura

Kaneko

2019

Preprint

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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.

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Section: Discussionmentioning

confidence: 93%

Molecular Diversity and Network Complexity in Growing Protocells

Kamimura

Kaneko

2019

Preprint

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“…Recall that the information encoded in the composition is different from that encoded in RNA as the combinatorial diversity of sequences. Still, it is interesting to note that under a limited flow of monomer resources, the sequence of catalytic polymers increases their complexity as has been shown recently [21].…”

Section: Discussionmentioning

confidence: 99%

Molecular Diversity and Network Complexity in Growing Protocells

Kamimura

Kaneko

2019

Life

Self Cite

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

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“…Previous theoretical studies considering growth via templated ligation generally explored effective models that reduce the state space to (sub-)sequences without considering complex formation explicitly [33,77,[84][85][86][87][88][89][90][91][92]. Such approaches do not treat (de-)hybridization and ligation as elementary steps.…”

Section: Prior Work Our Model and Future Extensionsmentioning

confidence: 99%

Thermodynamic and Kinetic Sequence Selection in Enzyme-Free Polymer Self-Assembly inside a Non-equilibrium RNA Reactor

Göppel

Rosenberger

Altaner

et al. 2022

Life

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The RNA world is one of the principal hypotheses to explain the emergence of living systems on the prebiotic Earth. It posits that RNA oligonucleotides acted as both carriers of information as well as catalytic molecules, promoting their own replication. However, it does not explain the origin of the catalytic RNA molecules. How could the transition from a pre-RNA to an RNA world occur? A starting point to answer this question is to analyze the dynamics in sequence space on the lowest level, where mononucleotide and short oligonucleotides come together and collectively evolve into larger molecules. To this end, we study the sequence-dependent self-assembly of polymers from a random initial pool of short building blocks via templated ligation. Templated ligation requires two strands that are hybridized adjacently on a third strand. The thermodynamic stability of such a configuration crucially depends on the sequence context and, therefore, significantly influences the ligation probability. However, the sequence context also has a kinetic effect, since non-complementary nucleotide pairs in the vicinity of the ligation site stall the ligation reaction. These sequence-dependent thermodynamic and kinetic effects are explicitly included in our stochastic model. Using this model, we investigate the system-level dynamics inside a non-equilibrium `RNA reactor’ enabling a fast chemical activation of the termini of interacting oligomers. Moreover, the RNA reactor subjects the oligomer pool to periodic temperature changes inducing the reshuffling of the system. The binding stability of strands typically grows with the number of complementary nucleotides forming the hybridization site. While shorter strands unbind spontaneously during the cold phase, larger complexes only disassemble during the temperature peaks. Inside the RNA reactor, strand growth is balanced by cleavage via hydrolysis, such that the oligomer pool eventually reaches a non-equilibrium stationary state characterized by its length and sequence distribution. How do motif-dependent energy and stalling parameters affect the sequence composition of the pool of long strands? As a critical factor for self-enhancing sequence selection, we identify kinetic stalling due to non-complementary base pairs at the ligation site. Kinetic stalling enables cascades of self-amplification that result in a strong reduction of occupied states in sequence space. Moreover, we discuss the significance of the symmetry breaking for the transition from a pre-RNA to an RNA world.

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Kinetic Selection of Template Polymer with Complex Sequences

Cited by 14 publications

References 40 publications

Molecular Diversity and Network Complexity in Growing Protocells

Molecular Diversity and Network Complexity in Growing Protocells

Molecular Diversity and Network Complexity in Growing Protocells

Thermodynamic and Kinetic Sequence Selection in Enzyme-Free Polymer Self-Assembly inside a Non-equilibrium RNA Reactor

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