Temporal order of evolution of DNA replication systems inferred by comparison of cellular and viral DNA polymerases

Biology Direct

Volumn 1, Issue , 2006, Pages

  Koonin, Eugene V ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA;

EID: 34248220998     PISSN: None     EISSN: 17456150     Source Type: Journal    
DOI: 10.1186/1745-6150-1-39     Document Type: Article

References (59)

1. Kornberg A Baker TS DNA Replication San Francisco, Freeman 2nd 1992
2. Forterre P Bergera A Gadelle D Elie C Lottspeich F Confalonieri F Duguet M Holmes M Dyall-Smith M Evolution of DNA topoisomerases and DNA-polymerases - a persepctive from Archaea. Syst Appl Microbiol 1994 16 746-758
3. Mushegian AR Koonin EV A minimal gene set for cellular life derived by comparison of complete bacterial genomes Proc Natl Acad Sci U S A 1996 93 19 10268-10273 38373 8816789 10.1073/pnas.93.19.10268
4. Edgell DR Doolittle WF Archaea and the origin(s) of DNA replication proteins Cell 1997 89 7 995-998 10.1016/S0092-8674(00)80285-8 9215620
5. Leipe DD Aravind L Koonin EV Did DNA replication evolve twice independently? Nucleic Acids Res 1999 27 17 3389-3401 148579 10446225 10.1093/nar/27.17.3389
6. Koonin EV Comparative genomics, minimal gene-sets and the last universal common ancestor Nat Rev Microbiol 2003 1 2 127-136 10.1038/nrmicro751 15035042
7. Harris JK Kelley ST Spiegelman GB Pace NR The genetic core of the universal ancestor Genome Res 2003 13 3 407-412 430263 12618371 10.1101/ gr.652803
8. Woese CR Fox GE The concept of cellular evolution J Mol Evol 1977 10 1 1-6 10.1007/BF01796132 903983
9. Kelman Z White MF Archaeal DNA replication and repair Curr Opin Microbiol 2005 8 6 669-676 16242991
10. Keck JL Roche DD Lynch AS Berger JM Structure of the RNA polymerase domain of E. coli primase Science 2000 287 5462 2482-2486 10.1126/ science.287.5462.2482 10741967
11. Podobnik M McInerney P O'Donnell M Kuriyan J A TOPRIM domain in the crystal structure of the catalytic core of Escherichia coli primase confirms a structural link to DNA topoisomerases J Mol Biol 2000 300 2 353-362 10.1006/jmbi.2000.3844 10873470
12. Augustin MA Huber R Kaiser JT Crystal structure of a DNA-dependent RNA polymerase (DNA primase) Nat Struct Biol 2001 8 1 57-61 10.1038/83060 11135672
13. Lipps G Weinzierl AO von Scheven G Buchen C Cramer P Structure of a bifunctional DNA primase-polymerase Nat Struct Mol Biol 2004 11 2 157-162 10.1038/nsmb723 14730355
14. Wang J Sattar AK Wang CC Karam JD Konigsberg WH Steitz TA Crystal structure of a pol alpha family replication DNA polymerase from bacteriophage RB69 Cell 1997 89 7 1087-1099 10.1016/ S0092-8674(00)80296-2 9215631
15. Hopfner KP Eichinger A Engh RA Laue F Ankenbauer W Huber R Angerer B Crystal structure of a thermostable type B DNA polymerase from Thermococcus gorgonarius Proc Natl Acad Sci U S A 1999 96 7 3600-3605 22340 10097083 10.1073/pnas.96.7.3600
16. Bailey S Wing RA Steitz TA The Structure of T. aquaticus DNA Polymerase III Is Distinct from Eukaryotic Replicative DNA Polymerases Cell 2006 126 5 893-904 10.1016/j.cell.2006.07.027 16959569
17. Lamers MH Georgescu RE Lee SG O'Donnell M Kuriyan J Crystal Structure of the Catalytic alpha Subunit of E. coli Replicative DNA Polymerase III Cell 2006 126 5 881-892 10.1016/j.cell.2006.07.028 16959568
18. Cann IK Komori K Toh H Kanai S Ishino Y A heterodimeric DNA polymerase: evidence that members of Euryarchaeota possess a distinct DNA polymerase Proc Natl Acad Sci U S A 1998 95 24 14250-14255 24359 9826686 10.1073/ pnas.95.24.14250
19. Ishino Y Komori K Cann IK Koga Y A novel DNA polymerase family found in Archaea J Bacteriol 1998 180 8 2232-2236 107154 9555910
20. Forterre P Gribaldo S Brochier C [Luca: The last universal common ancestor] Med Sci (Paris) 2005 21 10 860-865 16197904
21. 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 3 457-465 10.1046/ j.1365-2958.1999.01497.x 10417637
22. Forterre P The origin of DNA genomes and DNA replication proteins Curr Opin Microbiol 2002 5 5 525-532 10.1016/S1369-5274(02)00360-0 12354562
23. Forterre P The two ages of the RNA world, and the transition to the DNA world: A story of viruses and cells Biochimie 2005 87 9-10 793-803 10.1016/j.biochi.2005.03.015 16164990
24. Forterre P The origin of viruses and their possible roles in major evolutionary transitions Virus Res 2006 117 1 5-16 10.1016/ j.virusres.2006.01.010 16476498
25. 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 103 10 3669-3674 1450140 16505372 10.1073/pnas.0510333103
26. Koonin EV Senkevich TG Dolja VV The ancient virus world and evolution of cells Biol Direct 2006 1 1 29 1594570 16984643 10.1186/1745-6150-1-29
27. Baltimore D Viral genetic systems Trans N Y Acad Sci 1971 33 3 327-332 4327120
28. Agol VI Towards the system of viruses Biosystems 1974 6 2 113-132 10.1016/0303-2647(74)90003-3 4613396
29. Filee J Forterre P Laurent J The role played by viruses in the evolution of their hosts: A view based on informational protein phylogenies Res Microbiol 2003 154 4 237-243 10.1016/S0923-2508(03)00066-4 12798227
30. 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 6 763-773 10.1007/s00239-001-0078-x 12029358
31. Altschul SF Koonin EV PSI-BLAST - a tool for making discoveries in sequence databases Trends Biochem Sci 1998 23 444-447 10.1016/ S0968-0004(98)01298-5 9852764
32. Altschul SF Madden TL Schaffer AA Zhang J Zhang Z Miller W Lipman DJ Gapped BLAST and PSI-BLAST: A new generation of protein database search programs Nucleic Acids Res 1997 25 17 3389-3402 146917 9254694 10.1093/ nar/25.17.3389
33. Iyer LM Balaji S Koonin EV Aravind L Evolutionary genomics of nucleo-cytoplasmic large DNA viruses Virus Res 2006 117 1 156-184 10.1016/j.virusres.2006.01.009 16494962
34. Liu J Glazko G Mushegian A Protein repertoire of double-stranded DNA bacteriophages Virus Res 2006 117 1 68-80 10.1016/j.virusres.2006.01.015 16490276
35. Gefter ML Molineux IJ Kornberg T Khorana HG Deoxyribonucleic acid synthesis in cell-free extracts. 3. Catalytic properties of deoxyribonucleic acid polymerase II J Biol Chem 1972 247 10 3321-3326 4337512
36. Kornberg T Gefter ML Deoxyribonucleic acid synthesis in cell-free extracts. IV. Purification and catalytic properties of deoxyribonucleic acid polymerase III J Biol Chem 1972 247 17 5369-5375 4560196
37. Ito J Braithwaite DK Compilation and alignment of DNA polymerase sequences Nucleic Acids Res 1991 19 15 4045-4057 328540 1870963
38. Ilyina TV Koonin EV Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria Nucleic Acids Res 1992 20 13 3279-3285 312478 1630899
39. Angly FE Felts B Breitbart M Salamon P Edwards RA Carlson C Chan AM Haynes M Kelley S Liu H Mahaffy JM Mueller JE Nulton J Olson R Parsons R Rayhawk S Suttle CA Rohwer F The marine viromes of four oceanic regions PLoS Biol 2006 4 11 e368 1634881 17090214 10.1371/journal.pbio.0040368
40. Prangishvili D Garrett RA Koonin EV Evolutionary genomics of archaeal viruses: Unique viral genomes in the third domain of life Virus Res 2006 117 52-67 10.1016/j.virusres.2006.01.007 16503363
41. Prangishvili D Forterre P Garrett RA Viruses of the Archaea: A unifying view Nat Rev Microbiol 2006 4 11 837-848 10.1038/nrmicro1527 17041631
42. Embley TM Martin W Eukaryotic evolution, changes and challenges Nature 2006 440 7084 623-630 10.1038/nature04546 16572163
43. Martin W Koonin EV Introns and the origin of nucleus-cytosol compartmentation Nature 2006 440 41-45 10.1038/nature04531 16511485
44. Jablonski D Roy K Valentine JW Out of the tropics: Evolutionary dynamics of the latitudinal diversity gradient Science 2006 314 5796 102-106 10.1126/science.1130880 17023653
45. Rothwell PJ Waksman G Structure and mechanism of DNA polymerases Adv Protein Chem 2005 71 401-440 16230118
46. P atel PH Suzuki M Adman E Shinkai A Loeb LA Prokaryotic DNA polymerase I: Evolution, structure, and "base flipping" mechanism for nucleotide selection J Mol Biol 2001 308 5 823-837 10.1006/ jmbi.2001.4619 11352575
47. O'Reilly EK Kao CC Analysis of RNA-dependent RNA polymerase structure and function as guided by known polymerase structures and computer predictions of secondary structure Virology 1998 252 2 287-303 10.1006/ viro.1998.9463 9878607
48. Hickman AB Ronning DR Kotin RM Dyda F Structural unity among viral origin binding proteins: Crystal structure of the nuclease domain of adeno-associated virus Rep Mol Cell 2002 10 2 327-337 10.1016/ S1097-2765(02)00592-0 12191478
49. Aravind L Mazumder R Vasudevan S Koonin EV Trends in protein evolution inferred from sequence and structure analysis Curr Opin Struct Biol 2002 12 3 392-399 10.1016/S0959-440X(02)00334-2 12127460
50. Aravind L Koonin EV DNA polymerase beta-like nucleotidyltransferase superfamily: Identification of three new families, classification and evolutionary history Nucleic Acids Res 1999 27 7 1609-1618 148363 10075991 10.1093/nar/27.7.1609
51. Koonin EV Martin W On the origin of genomes and cells within inorganic compartments Trends Genet 2005 21 12 647-654 10.1016/j.tig.2005.09.006 16223546
52. Martin W Russell MJ On the origins of cells: A hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells Philos Trans R Soc Lond B Biol Sci 2003 358 1429 59-83; discussion 83-5 10.1098/ rstb.2002.1183 12594918
53. Pereto J Lopez-Garcia P Moreira D Ancestral lipid biosynthesis and early membrane evolution Trends Biochem Sci 2004 29 9 469-477 10.1016/ j.tibs.2004.07.002 15337120
54. Jekely G Did the last common ancestor have a biological membrane? Biol Direct 2006 1 35 1675992 17129384 10.1186/1745-6150-1-35
55. Koonin EV On the Origin of Cells and Viruses: A Comparative-Genomic Perspective Israel J Ecol Evol 2007 in press
56. Koonin EV Dolja VV Evolution of complexity in the viral world: The dawn of a new vision Virus Res 2006 117 1 1-4 10.1016/j.virusres.2006.01.018 16497406
57. Claverie JM Viruses take center stage in cellular evolution Genome Biol 2006 7 6 110 10.1186/gb-2006-7-6-110 16787527
58. NCBI Taxonomy 2006 http://www.ncbi.nlm.nih.gov/Taxonomy/ taxonomyhome.html/
59. Van Regenmortel MHV Fauquet CM Bishop DHL Carstens EB Estes MK Lemon SM Maniloff J Mayo MA McGeoch DJ Pringle CR Wickner RB 7th Report of the International Committee on Taxonomy of Viruses San Diego, Academic Press 2000