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

Notes on Forterre-PNAS-2006

 * see also Forterre-Biochimie-2005
 * 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 Reeve-BiochemSocTrans-2004
 * 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 Woese-MicrobiolRev-1987 : 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 Forterre-ResMicrobiol-2003 Bamford-ResMirobiol-2003
 * structural similarities between capsid proteins and replicating enzymes of viruses infecting different domains - viruses older than thought Bamford-ResMirobiol-2003
 * viruses can be sources of new proteins for cells Daubin-CurrOpinGenetDev-2004
 * evolution of mitochondria from alpha-proteobacteria - original bacteria RNA polymerase, DNA polymerase and helicase replaced by T3/T7-related viral proteins Filee-TrendsMicrobiol-2005
 * 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 Villarreal-VirusesAndTheEvolutionOfLife-2005
 * 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 Takemura-JMolEvol-2001
 * 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)