The origin of DNA genomes and DNA replication proteins

Current Opinion in Microbiology

Volumn 5, Issue 5, 2002, Pages 525-532

  Forterre, Patrick ^a  

^a UNIVERSITÉ PARIS SACLAY   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA DIRECTED RNA POLYMERASE; DNA POLYMERASE; DNA PRIMASE; DNA TOPOISOMERASE; DNA TOPOISOMERASE (ATP HYDROLYSING); DOUBLE STRANDED DNA; HELICASE; POLYDEOXYRIBONUCLEOTIDE SYNTHASE; REPLICATION PROTEIN A; RIBONUCLEOTIDE REDUCTASE; RNA; RNA DIRECTED DNA POLYMERASE; RNA DIRECTED RNA POLYMERASE; THYMIDINE PHOSPHATE; THYMIDYLATE SYNTHASE; THYMINE; URACIL;

DNA METABOLISM; DNA REPLICATION; GENOME; NONHUMAN; PHYLOGENY; PROGENOTE; REVIEW; TEMPERATURE;

DNA VIRUSES; EUKARYOTA; PROKARYOTA;

EID: 0036790008     PISSN: 13695274     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1369-5274(02)00360-0     Document Type: Review

References (51)

1. Yusupov MM, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, Cate JH, Noller HF: Crystal structure of the ribosome at 5.5 Ȧ resolution. Science 2001, 292:883-896.
2. Freeland SJ, Knight RD, Landweber LF: Do proteins predate DNA? Science 1999, 286:690-692.
3. Poole A, Penny D, Sjöberg B-M: Methyl-RNA: an evolutionary bridge between RNA and DNA? Chem Biol 2000, 7:R207-R216.
4. Forterre P: Genomic and early cellular evolution. The origin of the DNA world. CR Acad Sci Paris Life Sci 2001, 324:1067-1076.
5. Poole A, Penny D, Sjöberg B-M: Confounded cytosine! Tinkering and the evolution of DNA. Nat Rev Mol Cell Biol 2001, 2:147-151.
6. Lazcano A, Guerrero R, Margulis L, Oro J: The evolutionary transition from RNA to DNA in early cells. J Mol Evol 1988, 27:283-290.
7. Arezi B, Kuchta RD: Eukaryotic DNA primase. Trends Biochem Sci 2000, 25:572-576.
8. Balter M: Evolution on life's fringes. Science 2000, 289:1866-1867.
9. Filee J, Forterre P, Sen-Lin T, Laurent J: Evolution of DNA polymerase families: evidences for multiple gene exchange between cellular and viral proteins. J Mol Evol 2002, 54:763-773.
10. Forterre P: New hypotheses about the origins of viruses, prokaryotes and eukaryotes. In Frontiers of Life. Edited by Trân Thanh Vân JK, Mounolou JC, Shneider J, McKay C. Editions Frontières; Gif-sur-Yvette, France; 1992:221-234.
11. Forterre P: Displacement of cellular proteins by functional analogues from plasmids or viruses could explain puzzling phylogenies of many DNA informational proteins. Mol Microbiol 1999, 33:457-465.
12. Garcia AD, Aravind L, Koonin EV, Moss B: Bacterial-type DNA Holliday junction resolvases in eukaryotic viruses. Proc Natl Acad Sci USA 2000, 97:8926-8931.
13. Lakshminarayan MI, Aravind L, Koonin E: Common origin of four large families of large eukaryotic RNA viruses. J Virol 2001, 75:11720-11734.
14. Takemura M: Poxviruses and the origin of the eukaryotic nucleus. J Mol Evol 2001, 52:419-425.
15. Villarreal LP, DeFilippis A: Hypothesis for DNA viruses as the origin of eukaryotic replication proteins. J Virol 2000, 74:7079-7084.
16. Butcher SJ, Grimes JM, Makeyev EV, Bamford DH, Stuart DI: A mechanism for initiating RNA-dependent RNA polymerization. Nature 2001, 410:235-240.
17. Ng KK, Cherney MM, Vazquez AL, Machin A, Alonso JM, Parra F, James MN: Crystal structures of active and inactive conformations of a caliciviral RNA-dependent RNA polymerase. J Biol Chem 2002, 277:1381-1387.
18. Steitz TA: DNA polymerases: structural diversity and common mechanisms. J Biol Chem 1999, 74:17395-17398.
19. Hendrix RW, Lawrence JG, Hatfull GF, Casjens S: The origins and ongoing evolution of viruses. Trends Microbiol 2000, 8:504-508.
20. Myllykallio H, Lipowski G, Leduc D, Filee J, Forterre P, Liebl U: An alternative flavin-dependent mechanism for thymidylate synthesis. Science 2002, 297:105-107.
21. Stubbe JA: Ribonucleotide reductases: the link between an RNA and a DNA world? Curr Opin Struct Biol 2000, 10:731-736.
22. Buhler C, Lebbink JH, Bocs C, Ladenstein R, Forterre P: DNA topoisomerase VI generates ATP-dependent double-strand breaks with two-nucleotide overhangs. J Biol Chem 2001, 276:37215-37222.
23. Champoux JJ: DNA topoisomerases: structure, function and mechanism. Annu Rev Biochem 2001, 70:369-413.
24. Keck JL, Roche DD, Lynch AS, Berger JM: Structure of the RNA polymerase domain of E. coli primase. Science 2000, 287:2482-2486.
25. Martin IV, MacNeill SA: ATP-dependent DNA ligases. Genome Biol 2002, 3:REVIEWS3005.
26. Nichols MD, DeAngelis K, Keck JL, Berger JM: Structure and function of an archaeal topoisomerase VI subunit with homology to the meiotic recombination factor Spo 11. EMBO J 1999, 18:6177-6188.
27. Moreira D: Multiple independent horizontal transfers of informational genes from bacteria to plasmids and phages implications for the origin of bacterial replication machinery. Mol Microbiol 2000, 35:1-5.
28. Edgell DR, Doolittle WF: Archaea and the origin(s) of DNA replication proteins. Cell 1997, 89:995-998.
29. Leipe DD, Aravind L, Koonin EV: Did DNA replication evolve twice independently? Nucleic Acids Res 1999, 27:3389-3401.
30. Matsunaga F, Forterre P, Ishino Y, Myllykallio H: In vivo interactions of archaeal Cdc6/Orc1 and minichromosome maintenance proteins with the replication origin. Proc Natl Acad Sci USA 2001, 98:11152-11157.
31. Myllykallio H, Lopez P, Lopez-Garcia P, Heilig R, Saurin W, Zivanovic Y, Philippe H, Forterre P: Bacterial mode of replication with eukaryotic-like machinery in a hyperthermophilic archaeon. Science 2000, 288:2212-2215.
32. Bell PJL: Viral eukaryogenesis: was the ancestor of the nucleus a complex DNA virus? J Mol Evol 2001, 53:251-256.
33. MacNaughton TB, Shi ST, Modahl LE, Lai MM: Rolling circle replication of hepatitis delta virus RNA is carried out by two different cellular RNA Polymerases. J Virol 2002, 76:3920-3927.
34. Moraleda G, Taylor J: Host RNA polymerase requirements for transcription of the human hepatitis delta virus genome. J Virol 2001, 75:10161-10169.
35. Zivanovic Y, Lopez P, Philippe H, Forterre P: Pyrococcus genome comparison evidences chromosome shuffling-driven evolution. Nucleic Acids Res 2002, 30:1902-1910.
36. Woese CR: Interpreting the universal phylogenetic tree. Proc Natl Acad Sci USA 2000, 97:8392-8396.
37. Forterre P, Philippe H: Where is the root of the universal tree of life? Bioessays 1999, 21:871-879.
38. Penny D, Poole A: The nature of the last universal common ancestor. Curr Opin Genet Dev 1999, 9:672-677.
39. Glansdorff N: About the last common ancestor, the universal life-tree and lateral gene transfer: a reappraisal. Mol Microbiol 2000, 38:177-185.
40. Lopez-Garcia P, Moreira D: Metabolic symbiosis at the origin of eukaryotes. Trends Biochem Sci 1999, 24:88-93.
41. Caetano-Anollés G: Evolved RNA secondary structure and the rooting of the universal tree of life. J Mol Evol 2002, 54:333-345.
42. Gribaldo S, Philippe H: Ancient phylogenetic relationships. Theor Pop Biol 2002, in press.
43. MacNeill SA: DNA replication: partners in the Okazaki two-step. Curr Biol 2001, 11:R842-R844.
44. Moulton V, Gardner PP, Pointon RF, Creamer LK, Jameson GB, Penny D: RNA folding argues against a hot-start origin of life. J Mol Evol 2000, 51:416-421.
45. Marguet E, Forterre P: DNA stability at temperatures typical for hyperthermophiles. Nucleic Acids Res 1994, 22:1681-1686.
46. Forterre P: A hot story from comparative genomics: reverse gyrase is the only hyperthermophile-specific protein. Trends Genet 2002, 18:236-237.
47. Forterre P, Bouthier De La Tour C, Philippe H, Duguet M: Reverse gyrase from hyperthermophiles: probable transfer of a thermoadaptation trait from archaea to bacteria. Trends Genet 2000, 16:152-154.
48. Galtier N, Tourasse N, Gouy M: A non hyperthermophilic common ancestor to extant life forms. Science 1999, 283:220-221.
49. Matte-Taillez O, Brochier C, Forterre P, Philippe H: Archaeal phylogeny based on ribosomal proteins. Mol Biol Evol 2002, 19:631-639.
50. Brochier C, Philippe H: A non-hyperthermophilic ancestor for bacteria. Nature 2002, 417:244.
51. Daubin V, Gouy M, Perriére G: Bacterial phylogeny using supertree approach. Genome Informatics 2001, 155-164.