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

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

1. 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

2. 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

3. Reeve JN, Bailey KA, Li WT, Marc F, Sandman K, and Soares DJ. Archaeal histones: structures, stability and DNA binding. Biochem Soc Trans. 2004 Apr;32(Pt 2):227-30. DOI:10.1042/bst0320227 |
4. Woese CR. Bacterial evolution. Microbiol Rev. 1987 Jun;51(2):221-71. DOI:10.1128/mr.51.2.221-271.1987 |
5. Forterre P. The great virus comeback-- from an evolutionary perspective. Res Microbiol. 2003 May;154(4):223-5. DOI:10.1016/s0923-2508(03)00111-6 |
6. Bamford DH. Do viruses form lineages across different domains of life?. Res Microbiol. 2003 May;154(4):231-6. DOI:10.1016/S0923-2508(03)00065-2 |
7. Daubin V and Ochman H. Start-up entities in the origin of new genes. Curr Opin Genet Dev. 2004 Dec;14(6):616-9. DOI:10.1016/j.gde.2004.09.004 |
8. Filée J and Forterre P. Viral proteins functioning in organelles: a cryptic origin?. Trends Microbiol. 2005 Nov;13(11):510-3. DOI:10.1016/j.tim.2005.08.012 |
9. ISBN:978-1555813093
10. Takemura M. Poxviruses and the origin of the eukaryotic nucleus. J Mol Evol. 2001 May;52(5):419-25. DOI:10.1007/s002390010171 |