title: Circularity and self-cleavage as a strategy for the emergence of a chromosome in the RNA-based protocell.
abstract: BACKGROUND
  It is now popularly accepted that an "RNA world" existed in early evolution. During division of RNA-based protocells, random distribution of individual genes (simultaneously as ribozymes) between offspring might have resulted in gene loss, especially when the number of gene types increased. Therefore, the emergence of a chromosome carrying linked genes was critical for the prosperity of the RNA world. However, there were quite a few immediate difficulties for this event to occur. For example, a chromosome would be much longer than individual genes, and thus more likely to degrade and less likely to replicate completely; the copying of the chromosome might start at middle sites and be only partial; and, without a complex transcription mechanism, the synthesis of distinct ribozymes would become problematic.
  
  
  RESULTS
  Inspired by features of viroids, which have been suggested as "living fossils" of the RNA world, we supposed that these difficulties could have been overcome if the chromosome adopted a circular form and small, self-cleaving ribozymes (e.g. the hammer head ribozymes) resided at the sites between genes. Computer simulation using a Monte-Carlo method was conducted to investigate this hypothesis. The simulation shows that an RNA chromosome can spread (increase in quantity and be sustained) in the system if it is a circular one and its linear "transcripts" are readily broken at the sites between genes; the chromosome works as genetic material and ribozymes "coded" by it serve as functional molecules; and both circularity and self-cleavage are important for the spread of the chromosome.
  
  
  CONCLUSIONS
  In the RNA world, circularity and self-cleavage may have been adopted as a strategy to overcome the immediate difficulties for the emergence of a chromosome (with linked genes). The strategy suggested here is very simple and likely to have been used in this early stage of evolution. By demonstrating the possibility of the emergence of an RNA chromosome, this study opens on the prospect of a prosperous RNA world, populated by RNA-based protocells with a number of genes, showing complicated functions.
authors: College of Life Sciences, Wuhan University, Wuhan 430072, P,R, China. mwt@whu.edu.cn
authors: Wentao
authors: W
authors: Ma
authors: Chunwu
authors: C
authors: Yu
authors: Wentao
authors: W
authors: Zhang
mesh_terms: D058045:Artificial Cells / Q000166:cytology / Q000378:metabolism*; D002875:Chromosomes / Q000737:chemistry / Q000502:physiology*; D019143:Evolution, Molecular; D008040:Genetic Linkage; D009010:Monte Carlo Method; D012313:RNA / Q000737:chemistry*; D016337:RNA, Catalytic / Q000737:chemistry / Q000235:genetics; D012324:RNA-Dependent RNA Polymerase / Q000737:chemistry / Q000235:genetics
chemical_list: D016337:RNA, Catalytic; D012313:RNA; D012324:RNA-Dependent RNA Polymerase
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