Julius B. Lucks/Bibliography/Forterre-Biochimie-2005

Notes on [1]

• see also [2]
• NCBI virus invent DNA
• RNA genomes preceded DNA genomes
• 1st RNA world without proteins
• 2nd RNA world - ribozymes invented catalysing the peptide bond and had 1st draft of genetic code
• F2 - origin of RNA viruses from cell lines that could not compete with the line that evolved the ribosome precursor - these cells were predators with an extracellular part of the life cycle - then lost protein making machinery to become RNA viruses
• modern cells dNTPs made from rNTPs by ribonucleotide reductases (rNTP -> dNTP) and thymidylate synthases (dUMP -> dTMP)
  • reductase has 3 versions, I, II, III - all with complex cofactors with core region that is homologous - performs a complex radical-based reaction - could not have been done by RNA enzymes - so DNA appeared in 2nd stage of RNA world
• some bacterial viruses have U-DNA genomes (Bacillus subtilis phage)
• was a U-DNA world before T-DNA, and thymidylate synthases were evolved twice, independantly
• 2 reasons DNA preferred over RNA - 2'O of ribose in RNA is reactive and can attack phosphodiester bond; deamination of C -> U can be repaired in DNA, but not in RNA
  • DNA genomes can become larger and more complex, thus eventually outcompeting RNA genomes
• see (23) 'Modified bases in bacteriophoge genomes' - modern viruses alter their DNA to avoid host defenses - RNA viruses could have been the first to get DNA to avoid host RNAase's
  • many viruses encode ribonucleotide reductases and thymidylate synthases that are only distantly related to their hosts versions (21)
• Viruses could have transferred the complete complex DNA world to RNA cells (Fig 4)
  • 'It is clear now that the majority of DNA viruses are not lytic or lysogenic, but live most of the time in a carrier state in their cellular hosts.'
  • IDEA: if Fig 4 were correct, wouldn't we see more modern DNA cells with capsid protein homologs that were not due to prophages?
• likely that plasmids evolved from viruses because easier to lose capsid genes than to acquire them
• the tempo of evolution was higher at time of Last Universal Comman Ancestor (LUCA) then now (37,38)
• Archea and Eukarya share homol informational proteins (ribosomes), but Bacteria and Eukarya share homol membrane structure and composition
• F7 - phylogeny for RNA polymerase including large dsDNA viruses
• 3 viruses, 3 domains of life hypothesis

References

1. Forterre P. The two ages of the RNA world, and the transition to the DNA world: a story of viruses and cells. Biochimie. 2005 Sep-Oct;87(9-10):793-803. DOI:10.1016/j.biochi.2005.03.015 |

   Notes

2. Forterre P. Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: a hypothesis for the origin of cellular domain. Proc Natl Acad Sci U S A. 2006 Mar 7;103(10):3669-74. DOI:10.1073/pnas.0510333103 |

   Notes