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

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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 | PubMed ID:16164990 | HubMed [Forterre-Biochimie-2005]
    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 | PubMed ID:16505372 | HubMed [Forterre-PNAS-2006]
    Notes
All Medline abstracts: PubMed | HubMed