Tag mechanism as a strategy for the RNA replicase to resist parasites in the RNA world.

Sanmao Wu,Wentao Zhang,Yu Feng,Yong Chen,Shaolin Yin,Wentao Ma,Chunwu Yu,Lennart Randau

doi:10.1371/journal.pone.0172702

Abstract

The idea that life may have started with an “RNA world” is attractive. Wherein, a crucial event (perhaps at the very beginning of the scenario) should have been the emergence of a ribozyme that catalyzes its own replication, i.e., an RNA replicase. Although now there is experimental evidence supporting the chemical feasibility of such a ribozyme, the evolutionary dynamics of how the replicase could overcome the “parasite” problem (because other RNAs may also exploit this ribozyme) and thrive, as described in the scenario, remains unclear. It has been suggested that spatial limitation may have been important for the replicase to confront parasites. However, more studies showed that such a mechanism is not sufficient when this ribozyme’s altruistic trait is taken into full consideration. “Tag mechanism”, which means labeling the replicase with a short subsequence for recognition in replication, may be a further mechanism supporting the thriving of the replicase. However, because parasites may also “equip” themselves with the tag, it is far from clear whether the tag mechanism could take effect. Here, we conducted a computer simulation using a Monte-Carlo model to study the evolutionary dynamics surrounding the development of a tag-driven (polymerase-type) RNA replicase in the RNA world. We concluded that (1) with the tag mechanism the replicase could resist the parasites and become prosperous, (2) the main underlying reason should be that the parasitic molecules, especially those strong parasites, are more difficult to appear in the tag-driven system, and (3) the tag mechanism has a synergic effect with the spatial limitation mechanism–while the former provides “time” for the replicase to escape from parasites, the latter provides “space” for the replicase to escape. Notably, tags may readily serve as “control handles”, and once the tag mechanism was exploited, the evolution towards complex life may have been much easier.

Highlights

The idea that an RNA world [1] existed before the DNA and protein-based life has become a central hypothesis in regard of early evolution [2,3,4,5]
Darwinian evolution may have started at molecular level because molecules are natural, simple independent entities that may be subject to natural selection
The RNA replicase, which has been supposed to have initiated that hypothetic RNA world [5,6,7,8], is just such a candidate

Summary

Introduction

The idea that an RNA world [1] existed before the DNA and protein-based life has become a central hypothesis in regard of early evolution [2,3,4,5]. An interesting study demonstrated that such an RNA polymerase ribozyme may appear by assembling from simple RNA oligomers (e.g., about 30nt long, possibly arising from prebiotic chemistry) under certain conditions involving freeze-thaw cycles [17]. Even if such an RNA replicase is chemically feasible and may appear (as one or several molecules) in the early RNA world as well, how could the ribozyme be selfish enough to favor its own replication, while ignoring other RNA molecules under the same circumstances [6,7], and spread (thrive) in the system? This problem, which is referred to as the “parasite” problem, is not a chemical problem, but a problem of evolutionary dynamics [9]

Methods

Results

Conclusion