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DNA replication has three main steps: initiation, elongation, and termination. Replication in prokaryotes begins when initiator proteins bind to the single origin of replication (ori) on the cell's circular chromosome. Replication then proceeds around the entire circle of the chromosome in each direction from the two replication forks, resulting in two DNA molecules.
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DNA replication is initiated at sites containing predefined DNA sequences known as origins of replication. DNA is unwound at these sites by the minichromosome maintenance (MCM) helicase and other factors such as Cdc45 and the associated GINS complex.The unwound single strands are protected by replication protein A (RPA) until DNA polymerase starts synthesizing DNA at the 5’ end of the strand in the same direction as the replication fork. To prevent the replication fork from falling apart,...
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DNA replication is carried out by a large complex of proteins that act in a coordinated matter to achieve high-fidelity DNA replication. Together this complex is known as the DNA replication machinery or the replisome.
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Direct Restart of a Replication Fork Stalled by a Head-On RNA Polymerase
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Host-parasite oscillation dynamics and evolution in a compartmentalized RNA replication system.

Yohsuke Bansho1, Taro Furubayashi2, Norikazu Ichihashi3

  • 1Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan; Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo 102-0083, Japan;

Proceedings of the National Academy of Sciences of the United States of America
|April 2, 2016
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Summary

Compartmentalization enables self-replicating RNA systems to exhibit complex ecological behaviors like population oscillations, unlike bulk conditions where parasites dominate. This suggests early life

Keywords:
RNA replicationcompartmentevolutionoscillationparasite

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Area of Science:

  • Origin of life studies
  • Systems chemistry
  • Theoretical biology

Background:

  • Cellular functions, including self-replication, have been reconstituted in vitro using DNA, RNA, and proteins.
  • A key challenge is reconstituting interactive networks of self-replicating species to understand emergent ecological behaviors.

Purpose of the Study:

  • To synthesize and study a simple, two-species RNA replication system composed of host and parasitic RNA.
  • To investigate the impact of compartmentalization on the population dynamics and coevolution of these self-replicating RNAs.

Main Methods:

  • Synthesis of a minimal replication system with two self-replicating RNA species: a host and a parasite.
  • Experimental observation of RNA population dynamics under both bulk and compartmentalized conditions.
  • Analysis of population oscillations and host RNA evolution within the compartmentalized system.

Main Results:

  • In bulk conditions, the parasitic RNA eradicated the host RNA.
  • In compartmentalized conditions, a continuous oscillation pattern in the population dynamics of the two RNAs emerged.
  • The oscillation patterns evolved over time, primarily due to changes in the host RNA.

Conclusions:

  • Cell-like compartments are crucial for generating complex host-parasite ecological dynamics in self-replicating systems.
  • The findings suggest that host-parasite coevolution may have originated in the early stages of life's evolution within compartmentalized environments.