Julius B. Lucks/Bibliography/Forterre-PNAS-2006

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Notes on [1]

  • see also [2]
  • transition from RNA to DNA genomes could have been carried out by viruses (to protect from host RNA defenses)
    • cellular DNA and replication machineries originated by transfers from DNA viruses to RNA cells
      • 3 seperate such transfers could be at origin of Archea, Bacteria, and Eukarya - could explain why each domain has a specific DNA replication apparatus
    • plasmids transitional forms between DNA viruses and cellular chromosomes
  • unification of cellular life - all cells share a common mechanism for protein synthesis with same genetic code and thus originated from common ancestor: Last Universal Cellular Ancestor (LUCA)
    • each domain characterized by a different type of ribosome
  • introduction reviews pre-genomic theories to explain how these domains originated and what evolutionary relationships among them
  • archea have histones [3]
  • thought that archea evolved from bacteria by adaptation to hyperthermophily, but are cases of regular hyperthermophilic bacteria that use bacterial versions of their proteins
  • Woese [4]: suggestion that the rate of protein evolution higher in time frame between LUCA and last common ancestor of each domain today
  • all this analysis based on translation and transcription apparatus
  • major proteins in bacterial DNA replication (DNA polymerase, primase, helicase) not homologous to archael/eukaryotic homologs - one version of DnaG primase (bacterial), and 2 in other branches
    • cellular DNA informational proteins found in only 1 or 2, not 3 versions
    • can explain violation of 'one family, three versions' rule by considering multi-cellularity and viruses
  • see also [5, 6]
    • structural similarities between capsid proteins and replicating enzymes of viruses infecting different domains - viruses older than thought [6]
  • viruses can be sources of new proteins for cells [7]
    • evolution of mitochondria from alpha-proteobacteria - original bacteria RNA polymerase, DNA polymerase and helicase replaced by T3/T7-related viral proteins [8]
  • viruses could have invented DNA to counteract host RNA defenses - many modern viruses encode viral-specific versions of ribonucleotide reductases and thymidylate synthases (needed to make DNA precursors)
    • see also [9]
  • host RNA could have been transformed to DNA by a persistent viral infection (via a plasmid), with gradual accumulation of host genome as more stable DNA
  • propose here that this happened three, independent times giving rise to 2 DNA replication machineries (Bacteria and Archea/Eukarya) and three ribosomal machineries
    • ancestral RNA cells out-competed by DNA cells which could have larger and more stable genomes - also once these DNA cells took over, would have 'fixed' the three domains
  • encoding by DNA would have caused drastic drop in mutation rate, thus rate of evolution
  • archael lipids have opposite chirality than bacterial and eukaryotic lipids
  • plasmids originated from viruses (not vice versa because then a plasmid would have to 'invent' a capsid protein)
    • archea and bacteria have plasmids, eukarya do not
  • postulate that the virus that gave rise the eukarya had a linear DNA genome (possible multiple chromosomes)
    • several Eukaryotic RNA and DNA polymerases could suggest eukarya was caused by integration of several viruses
  • nucleocytoplasmic large DNA viruses, ex: poxviruses - replicate in cytoplasm, form small nuclei, produce envelope by recruiting membrane from ER
    • such a system could have evolved into the eukaryotic nucleus
    • mimivirus NCLDV with 1.2 Mb genome
      • capsid proteins homol to Adenoviruses and several bacterial and archael viruses suggesting existed before formation of eukaryotes [10]
  • can test experimentally by designing RNA plasmids with reverse transcriptase and see how much gets transferred to DNA genome
  • can test informatically by looking at all viral DNA informational proteins - should be viruses still around that closely resemble the founding viruses
    • recent discovery bacterial prophage homolog of archaeal replicative helicase minichromosome maintenance protein (MCM)


References

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  1. Error fetching PMID 16505372: [Forterre-PNAS-2006]
    Notes

  2. Error fetching PMID 16164990: [Forterre-Biochimie-2005]
    Notes

  3. Error fetching PMID 15046577: [Reeve-BiochemSocTrans-2004]
  4. Error fetching PMID 2439888: [Woese-MicrobiolRev-1987]
  5. Error fetching PMID 12901366: [Forterre-ResMicrobiol-2003]
  6. Error fetching PMID 12798226: [Bamford-ResMirobiol-2003]
  7. Error fetching PMID 15531155: [Daubin-CurrOpinGenetDev-2004]
  8. Error fetching PMID 16157484: [Filee-TrendsMicrobiol-2005]
  9. isbn:978-1555813093. [Villarreal-VirusesAndTheEvolutionOfLife-2005]
  10. Error fetching PMID 11443345: [Takemura-JMolEvol-2001]
All Medline abstracts: PubMed HubMed
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