title: The evolution of strand preference in simulated RNA replicators with strand displacement: implications for the origin of transcription.
abstract: BACKGROUND
  The simplest conceivable example of evolving systems is RNA molecules that can replicate themselves. Since replication produces a new RNA strand complementary to a template, all templates would eventually become double-stranded and, hence, become unavailable for replication. Thus the problem of how to separate the two strands is considered a major issue for the early evolution of self-replicating RNA. One biologically plausible way to copy a double-stranded RNA is to displace a preexisting strand by a newly synthesized strand. Such copying can in principle be initiated from either the (+) or (-) strand of a double-stranded RNA. Assuming that only one of them, say (+), can act as replicase when single-stranded, strand displacement produces a new replicase if the (-) strand is the template. If, however, the (+) strand is the template, it produces a new template (but no replicase). Modern transcription exhibits extreme strand preference wherein anti-sense strands are always the template. Likewise, replication by strand displacement seems optimal if it also exhibits extreme strand preference wherein (-) strands are always the template, favoring replicase production. Here we investigate whether such strand preference can evolve in a simple RNA replicator system with strand displacement.
  
  
  RESULTS
  We first studied a simple mathematical model of the replicator dynamics. Our results indicated that if the system is well-mixed, there is no selective force acting upon strand preference per se. Next, we studied an individual-based simulation model to investigate the evolution of strand preference under finite diffusion. Interestingly, the results showed that selective forces "emerge" because of finite diffusion. Strikingly, the direction of the strand preference that evolves [i.e. (+) or (-) strand excess] is a complex non-monotonic function of the diffusion intensity. The mechanism underlying this behavior is elucidated. Furthermore, a speciation-like phenomenon is observed under certain conditions: two extreme replication strategies, namely replicase producers and template producers, emerge and coexist among competing replicators.
  
  
  CONCLUSIONS
  Finite diffusion enables the evolution of strand preference, the direction of which is a non-monotonic function of the diffusion intensity. By identifying the conditions under which strand preference evolves, this study provides an insight into how a rudimentary transcription-like pattern might have emerged in an RNA-based replicator system.
  
  
  METHODS
  This article was reviewed by Eugene V Koonin, Rob Kinght and István Scheuring (nominated by David H Ardell). For the full reviews, please go to the Reviewers' comments section.
authors.affiliation: Theoretical Biology and Bioinformatics Group, Utrecht University, Utrecht, The Netherlands. takeuchi.nobuto@gmail.com
authors.forename: Nobuto
authors.initials: N
authors.lastname: Takeuchi
authors.forename: Laura
authors.initials: L
authors.lastname: Salazar
authors.forename: Anthony M
authors.initials: AM
authors.lastname: Poole
authors.forename: Paulien
authors.initials: P
authors.lastname: Hogeweg
mesh_terms: D019143:Evolution, Molecular; D055641:Mathematical Concepts; D008957:Models, Genetic; D012330:RNA, Double-Stranded / Q000235:genetics* / Q000378:metabolism*; D013269:Stochastic Processes; D014158:Transcription, Genetic
chemical_list: D012330:RNA, Double-Stranded