Evolution of Eukaryotic DNA Polymerases via Interaction Between Cells and Large DNA Viruses

Journal of Molecular Evolution

Volumn 81, Issue 1-2, 2015, Pages 24-33

  Takemura, Masaharu ^a   Yokobori, Shin Ichi ^b   Ogata, Hiroyuki ^c  

^a TOKYO UNIVERSITY OF SCIENCE   (Japan)

^b TOKYO UNIVERSITY OF PHARMACY AND LIFE SCIENCES   (Japan)

^c KYOTO UNIVERSITY   (Japan)

Author keywords

DNA polymerase; Eukaryogenesis; Mimivirus; NCLDV; Pandoravirus; Poxvirus

Indexed keywords

DNA VIRUSES; EUKARYOTA; MIMIVIRUS; POXVIRIDAE;

DNA DIRECTED DNA POLYMERASE; DNA VIRUS;

CELL NUCLEUS; COMPARATIVE STUDY; ENZYMOLOGY; EUKARYOTE; EUKARYOTIC CELL; GENETICS; HORIZONTAL GENE TRANSFER; METABOLISM; MOLECULAR EVOLUTION; PHYLOGENY; SEQUENCE ALIGNMENT;

CELL NUCLEUS; DNA VIRUSES; DNA-DIRECTED DNA POLYMERASE; EUKARYOTA; EUKARYOTIC CELLS; EVOLUTION, MOLECULAR; GENE TRANSFER, HORIZONTAL; PHYLOGENY; SEQUENCE ALIGNMENT;

EID: 84939473142     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-015-9690-z     Document Type: Article

References (38)

1. Bell PJL (2001) Viral eukaryogenesis: was the ancestor of the nucleus a complex DNA virus? J Mol Evol 53:251–256
2. Bell PJL (2009) The viral eukaryogenesis hypothesis. Annu N Y Acad Sci 1178:91–105
3. Burgers PMJ (2009) Polymerase dynamics at the eukaryotic DNA replication fork. J Biol Chem 284:4041–4045
4. Cavalier-Smith T (2010) Origin of the cell nucleus, mitosis and sex: roles of intracellular coevolution. Biol Direct 5:7
5. Claverie JM (2006) Viruses take center stage in cellular evolution. Genome Biol 7:110
6. Claverie JM, Abergel C (2013) Open questions about giant viruses. Adv Virus Res 85:25–56
7. Darriba D, Taboada GL, Doallo R, Posada D (2011) ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 27:1164–1165
8. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797
9. Edgell DR, Malik S-B, Doolittle WF (1998) Evidence of independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases. Mol Biol Evol 15:1207–1217
10. Filée J, Forterre P, Sen-Lin T, Laurent J (2002) Evolution of DNA polymerase families: evidence for multiple gene exchange between cellular and viral proteins. J Mol Evol 54:763–773
11. Fuerst JA, Sagulenko E (2012) Keys to eukaryality: planctomycetes and ancestral evolution of cellular complexity. Front Microbiol 3:167
12. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59:307–321
13. Hübscher U, Maga G, Spadari S (2002) Eukaryotic DNA polymerases. Annu Rev Biochem 71:133–163
14. Iyer LM, Aravind L, Koonin EV (2001) Common origin of four diverse families of large eukaryotic DNA viruses. J Virol 75:11720–11734
15. Iyer LM, Balaji S, Koonin EV, Aravind L (2006) Evolutionary genomics of nucleo-cytoplasmic large DNA viruses. Virus Res 117:156–184
16. Kuznetsov YG, Klose T, Rossmann M, McPherson A (2013) Morphogenesis of mimivirus and its viral factories: an atomic force microscopy study of infected cells. J Virol 87:11200–11213
17. Lartillot N, Philippe H (2004) A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol Biol Evol 21:1095–1109
18. Lundin D, Poole AM, Sjöberg BM, Högbom M (2012) Use of structural phylogenetic networks for classification of the ferritin-like super family. J Biol Chem 287:20565–20575
19. Martin W (2005) Archaebacteria (Archaea) and the origin of the eukaryotic nucleus. Curr Opin Microbiol 8:630–637
20. Monier A, Claverie JM, Ogata H (2008) Taxonomic distribution of large DNA viruses in the sea. Genome Biol 9:R106
21. Ogata H, Claverie JM (2007) Unique genes in giant viruses: regular substitution pattern and anomalously short size. Genome Res 17:1353–1361
22. Ogata H, Raoult D, Claverie JM (2005) A new example of viral intein in Mimivirus. Virol J 2:8
23. Philippe N et al (2013) Pandoraviruses: amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic eukaryotes. Science 341:281–286
24. Raoult D et al (2004) The 1.2-megabase genome sequence of mimivirus. Science 306:1344–1350
25. Ronquist F et al (2012) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61:539–542
26. Schramm B, Locker JK (2005) Cytoplasmic organization of POXvirus DNA replication. Traffic 6:839–846
27. Tahirov TH, Makarova KS, Rogozin IB, Pavlov YI, Koonin EV (2009) Evolution of DNA polymerases: an inactivated polymerase-exonuclease module in Pol ε and a chimeric origin of eukaryotic polymerases from two classes of archaeal ancestors. Biol Direct 4:11
28. Takemura M (2001) Poxviruses and the origin of the eukaryotic nucleus. J Mol Evol 52:419–425
29. Takemura M (2002) Evolution and degeneration of eukaryotic DNA replication system. BioSystems 65:139–145
30. Takemura M (2005) Evolutionary history of the retinoblastoma gene from archaea to eukarya. BioSystems 82:266–272
31. Takemura M (2011) Function of DNA polymerase α in a replication fork and its putative roles in genomic stability and eukaryotic evolution. In: Kušić-Tišma (ed) Fundamental aspects of DNA replication, InTech-Open Access Publisher, p 187–204
32. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729
33. Tolonen N et al (2001) Vaccinia virus DNA replication occurs in endoplasmic reticulum-enclosed cytoplasmic mini-nuclei. Mol Biol Cell 12:2031–2046
34. Villarreal LP, DeFilippis VR (2000) A hypothesis for DNA viruses as the origin of eukaryotic replication proteins. J Virol 74:7079–7084
35. Wang TSF (1991) Eukaryotic DNA polymerases. Annu Rev Biochem 60:513–552
36. Wilkinson M, McInerney JO, Hirt RP, Foster PG, Embley TM (2007) Of clades and clans: terms for phylogenetic relationships in unrooted trees. Trends Eco Evol 22:114–115
37. Williams TA, Foster PG, Cox CJ, Embley TM (2013) An archaeal origin of eukaryotes supports only two primary domains of life. Nature 504:231–236
38. Yamada T (2011) Giant viruses in the environment: their origins and evolution. Curr Opin Virol 1:58–62