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
- cellular DNA and replication machineries originated by transfers from DNA viruses to RNA cells
- 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
- 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 pmid:16505372.
Notes - 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 pmid:16164990.
- 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/ pmid:15046577.
- Woese CR. Bacterial evolution. Microbiol Rev 1987 Jun; 51(2) 221-71. pmid:2439888.
- Forterre P. The great virus comeback-- from an evolutionary perspective. Res Microbiol 2003 May; 154(4) 223-5. pmid:12901366.
- 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 pmid:12798226.
- 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 pmid:15531155.
- 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 pmid:16157484.
- Luis P. Villarreal. Viruses And The Evolution Of Life. ASM Press. isbn:978-1555813093.
- Takemura M. Poxviruses and the origin of the eukaryotic nucleus. J Mol Evol 2001 May; 52(5) 419-25. doi:10.1007/s002390010171 pmid:11443345.
