A DNA topoisomerase IB in Thaumarchaeota testifies for the presence of this enzyme in the last common ancestor of Archaea and Eucarya

Biology Direct

Volumn 3, Issue , 2008, Pages

  Brochier Armanet, Céline ^a   Gribaldo, Simonetta ^b   Forterre, Patrick ^b,c  

^a AIX MARSEILLE UNIVERSITÉ   (France)

^b INSTITUT PASTEUR   (France)

^c UNIVERSITÉ PARIS SACLAY   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA;

DNA TOPOISOMERASE;

ARCHAEBACTERIUM; ARTICLE; BACTERIUM; CHEMISTRY; ENZYMOLOGY; EUKARYOTIC CELL; GENETICS; PHYLOGENY; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT; STATISTICAL MODEL; VIRUS;

ARCHAEA; BACTERIA; DNA TOPOISOMERASES, TYPE I, EUKARYOTIC; EUKARYOTIC CELLS; LIKELIHOOD FUNCTIONS; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; VIRUSES;

EID: 58249106878     PISSN: None     EISSN: 17456150     Source Type: Journal    
DOI: 10.1186/1745-6150-3-54     Document Type: Review

References (30)

1. Champoux JJ DNA topoisomerases: Structure, function, and mechanism Annu Rev Biochem 2001, 70:369-413 10.1146/annurev.biochem.70.1.369 11395412
2. Corbett KD Berger JM Structure, molecular mechanisms, and evolutionary relationships in DNA topoisomerases Annu Rev Biophys Biomol Struct 2004, 33:95-118 10.1146/annurev.biophys.33.110502.140357 15139806
3. Wang JC Cellular roles of DNA topoisomerases: A molecular perspective Nat Rev Mol Cell Biol 2002, 3:430-440 10.1038/nrm831 12042765
4. Schoeffler AJ Berger JM DNA topoisomerases: Harnessing and constraining energy to govern chromosome topology Q Rev Biophys 2008, 41:41-101 18755053
5. Forterre P DNA topoisomerase V: A new fold of mysterious origin Trends Biotechnol 2006, 24:245-247 10.1016/j.tibtech.2006.04.006 16650908
6. Forterre P Gribaldo S Gadelle D Serre MC Origin and evolution of DNA topoisomerases Biochimie 2007, 89:427-446 10.1016/j.biochi.2006.12.009 17293019
7. Gadelle D Filee J Buhler C Forterre P Phylogenomics of type II DNA topoisomerases Bioessays 2003, 25:232-242 10.1002/bies.10245 12596227
8. Aravind L Leipe DD Koonin EV Toprim - a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins Nucleic Acids Res 1998, 26:4205-4213 147817 9722641 10.1093/nar/26.18.4205
9. Cheng C Kussie P Pavletich N Shuman S Conservation of structure and mechanism between eukaryotic topoisomerase I and site-specific recombinases Cell 1998, 92:841-850 10.1016/S0092-8674(00)81411-7 9529259
10. Taneja B Patel A Slesarev A Mondragon A Structure of the N-terminal fragment of topoisomerase V reveals a new family of topoisomerases Embo J 2006, 25:398-408 1383508 16395333 10.1038/sj.emboj.7600922
11. Benarroch D Claverie JM Raoult D Shuman S Characterization of mimivirus DNA topoisomerase IB suggests horizontal gene transfer between eukaryal viruses and bacteria J Virol 2006, 80:314-321 1317558 16352556 10.1128/ JVI.80.1.314-321.2006
12. Champoux JJ Dulbecco R An activity from mammalian cells that untwists superhelical DNA - a possible swivel for DNA replication (polyoma-ethidium bromide-mouse-embryo cells-dye binding assay) Proc Natl Acad Sci USA 1972, 69:143-146 427563 4333036 10.1073/pnas.69.1.143
13. Garinther WI Schultz MC Topoisomerase function during replication-independent chromatin assembly in yeast Mol Cell Biol 1997, 17:352-3526 232205 9199287
14. Kim RA Wang JC Function of DNA topoisomerases as replication swivels in Saccharomyces cerevisiae J Mol Biol 1989, 208:257-267 10.1016/ 0022-2836(89)90387-2 2549254
15. Brill SJ DiNardo S Voelkel-Meiman K Sternglanz R Need for DNA topoisomerase activity as a swivel for DNA replication for transcription of ribosomal RNA Nature 1987, 326:414-416 10.1038/326414a0 2436053
16. Liu LF Desai SD Li TK Mao Y Sun M Sim SP Mechanism of action of camptothecin Ann N Y Acad Sci 2000, 922:1-10 11193884
17. Bauer WR Ressner EC Kates J Patzke JV A DNA nicking-closing enzyme encapsidated in vaccinia virus: Partial purification and properties Proc Natl Acad Sci USA 1977, 74:1841-1845 431023 17115 10.1073/pnas.74.5.1841
18. Shuman S Vaccinia virus DNA topoisomerase: A model eukaryotic type IB enzyme Biochim Biophys Acta 1998, 1400:321-337 9748643
19. Krogh BO Shuman S Catalytic mechanism of DNA topoisomerase IB Mol Cell 2000, 5:1035-1041 10.1016/S1097-2765(00)80268-3 10911997
20. Tian L Shuman S Vaccinia topoisomerase mutants illuminate roles for Phe59, Gly73, Gln69 and Phe215 Virology 2007, 359:466-476 10.1016/ j.virol.2006.08.056 17059840
21. Osheroff N Unraveling the structure of the variola topoisomerase IB-DNA complex: A possible new twist on smallpox therapy Mol Interv 2006, 6:245-248 10.1124/mi.6.5.4 17035663
22. Krogh BO Shuman S A poxvirus-like type IB topoisomerase family in bacteria Proc Natl Acad Sci USA 2002, 99:1853-1858 122283 11830640 10.1073/pnas.032613199
23. Hallam SJ Konstantinidis KT Putnam N Schleper C Watanabe Y Sugahara J Preston C de la Torre J Richardson PM DeLong EF Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum Proc Natl Acad Sci USA 2006, 103:18296-18301 1643844 17114289 10.1073/pnas.0608549103
24. Brochier-Armanet C Boussau B Gribaldo S Forterre P Mesophilic Crenarchaeota: Proposal for a third archaeal phylum, the Thaumarchaeota Nat Rev Microbiol 2008, 6:245-252 10.1038/nrmicro1852 18274537
25. Konneke M Bernhard AE de la Torre JR Walker CB Waterbury JB Stahl DA Isolation of an autotrophic ammonia-oxidizing marine archaeon Nature 2005, 437:543-546 10.1038/nature03911 16177789
26. Venter JC Remington K Heidelberg JF Halpern AL Rusch D Eisen JA Wu D Paulsen I Nelson KE Nelson W et al Environmental genome shotgun sequencing of the Sargasso Sea Science 2004, 304:66-74 10.1126/ science.1093857 15001713
27. Makarova KS Sorokin AV Novichkov PS Wolf YI Koonin EV Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea Biol Direct 2007, 2:33 2222616 18042280 10.1186/1745-6150-2-33
28. Kwapisz M Beckouet F Thuriaux P Early evolution of eukaryotic DNA-dependent RNA polymerases Trends Genet 2008, 24:211-215 10.1016/ j.tig.2008.02.002 18384908
29. Lecompte O Ripp R Thierry JC Moras D Poch O Comparative analysis of ribosomal proteins in complete genomes: An example of reductive evolution at the domain scale Nucleic Acids Res 2002, 30:5382-5390 140077 12490706 10.1093/nar/gkf693
30. 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 USA 2006, 103:3669-3674 1450140 16505372 10.1073/pnas.0510333103