Thermodynamic basis for the emergence of genomes during prebiotic evolution

• Published in: PLoS computational biology Vol. 8; no. 5; p. e1002534
• Main Authors: Woo, Hyung-June, Vijaya Satya, Ravi, Reifman, Jaques
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.05.2012; Public Library of Science (PLoS)
• Subjects: Armed forces; Behavior; Biology; Chemical evolution (Origin of life); Chemistry; Crystallization; DNA-Directed DNA Polymerase - metabolism; Evolution, Molecular; Genome; Genomes; Hypotheses; Kinetics; Models, Genetic; Mutation; Natural history; Origin of Life; Physics; Population; Ribonucleic acid; RNA; RNA - metabolism; RNA, Catalytic - metabolism; Stochastic Processes; Theory; Thermodynamics; United States; RNA, Catalytic; Thermodynamics; RNA; Stochastic Processes; Models, Genetic; Biogenesis; Genome; DNA-Directed DNA Polymerase; Evolution, Molecular
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.1002534

The RNA world hypothesis views modern organisms as descendants of RNA molecules. The earliest RNA molecules must have been random sequences, from which the first genomes that coded for polymerase ribozymes emerged. The quasispecies theory by Eigen predicts the existence of an error threshold limiting genomic stability during such transitions, but does not address the spontaneity of changes. Following a recent theoretical approach, we applied the quasispecies theory combined with kinetic/thermodynamic descriptions of RNA replication to analyze the collective behavior of RNA replicators based on known experimental kinetics data. We find that, with increasing fidelity (relative rate of base-extension for Watson-Crick versus mismatched base pairs), replications without enzymes, with ribozymes, and with protein-based polymerases are above, near, and below a critical point, respectively. The prebiotic evolution therefore must have crossed this critical region. Over large regions of the phase diagram, fitness increases with increasing fidelity, biasing random drifts in sequence space toward 'crystallization.' This region encloses the experimental nonenzymatic fidelity value, favoring evolutions toward polymerase sequences with ever higher fidelity, despite error rates above the error catastrophe threshold. Our work shows that experimentally characterized kinetics and thermodynamics of RNA replication allow us to determine the physicochemical conditions required for the spontaneous crystallization of biological information. Our findings also suggest that among many potential oligomers capable of templated replication, RNAs may have evolved to form prebiotic genomes due to the value of their nonenzymatic fidelity.