Takeuchi N, Hogeweg P, Koonin EV. On the origin of DNA genomes: evolution of the division of labor between template and catalyst in model replicator systems.
PLoS Comput Biol 2011;
7:e1002024. [PMID:
21455287 PMCID:
PMC3063752 DOI:
10.1371/journal.pcbi.1002024]
[Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2010] [Accepted: 02/14/2011] [Indexed: 12/01/2022] Open
Abstract
The division of labor between template and catalyst is a fundamental property of
all living systems: DNA stores genetic information whereas proteins function as
catalysts. The RNA world hypothesis, however, posits that, at the earlier stages
of evolution, RNA acted as both template and catalyst. Why would such division
of labor evolve in the RNA world? We investigated the evolution of DNA-like
molecules, i.e. molecules that can function only as template, in minimal
computational models of RNA replicator systems. In the models, RNA can function
as both template-directed polymerase and template, whereas DNA can function only
as template. Two classes of models were explored. In the surface models,
replicators are attached to surfaces with finite diffusion. In the compartment
models, replicators are compartmentalized by vesicle-like boundaries. Both
models displayed the evolution of DNA and the ensuing division of labor between
templates and catalysts. In the surface model, DNA provides the advantage of
greater resistance against parasitic templates. However, this advantage is at
least partially offset by the disadvantage of slower multiplication due to the
increased complexity of the replication cycle. In the compartment model, DNA can
significantly delay the intra-compartment evolution of RNA towards catalytic
deterioration. These results are explained in terms of the trade-off between
template and catalyst that is inherent in RNA-only replication cycles: DNA
releases RNA from this trade-off by making it unnecessary for RNA to serve as
template and so rendering the system more resistant against evolving parasitism.
Our analysis of these simple models suggests that the lack of catalytic activity
in DNA by itself can generate a sufficient selective advantage for RNA
replicator systems to produce DNA. Given the widespread notion that DNA evolved
owing to its superior chemical properties as a template, this study offers a
novel insight into the evolutionary origin of DNA.
At the core of all biological systems lies the division of labor between the
storage of genetic information and its phenotypic implementation, in other
words, the functional differentiation between templates (DNA) and catalysts
(proteins). This fundamental property of life is believed to have been absent at
the earliest stages of evolution. The RNA world hypothesis, the most realistic
current scenario for the origin of life, posits that, in primordial replicating
systems, RNA functioned both as template and as catalyst. How would such
division of labor emerge through Darwinian evolution? We investigated the
evolution of DNA-like molecules in minimal computational models of RNA
replicator systems. Two models were considered: one where molecules are adsorbed
on surfaces and another one where molecules are compartmentalized by dividing
cellular boundaries. Both models exhibit the evolution of DNA and the ensuing
division of labor, revealing the simple governing principle of these processes:
DNA releases RNA from the trade-off between template and catalyst that is
inevitable in the RNA world and thereby enhances the system's resistance
against parasitic templates. Hence, this study offers a novel insight into the
evolutionary origin of the division of labor between templates and catalysts in
the RNA world.
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