Plasmids, viruses and virus-like membrane vesicles from Thermococcales

Biochemical Society Transactions

Volumn 39, Issue 1, 2011, Pages 36-44

  Soler, Nicolas ^a,c   Gaudin, Marie ^a   Marguet, Evelyne ^a   Forterre, Patrick ^a,b  

^a UNIVERSITÉ PARIS SACLAY   (France)

^b INSTITUT PASTEUR   (France)

^c INSTITUT COCHIN   (France)

Author keywords

Archaea; Membrane vesicle; Plasmid; Thermococcales; Virus

Indexed keywords

CONFERENCE PAPER; DNA REPLICATION; EUKARYOTE; GENE POOL; HYPERTHERMOPHILIC ARCHAEON; MEMBRANE VESICLE; NONHUMAN; PLASMID; PRIORITY JOURNAL; PROTEIN FAMILY; PYROCOCCUS FURIOSUS; PYROCOCCUS HORIKOSHII; SULFOLOBUS ACIDOCALDARIUS; THERMOCOCCALES; THERMOCOCCUS GAMMATOLERANS; THERMOCOCCUS KODAKARENSIS; THERMOCOCCUS NAUTILUS; THERMOCOCCUS ONNURINEUS; VIRUS ENVELOPE;

ARCHAEAL VIRUSES; BIOLOGICAL EVOLUTION; CELL MEMBRANE; DNA REPLICATION; DNA, ARCHAEAL; HUMANS; NUCLEIC ACID CONFORMATION; PLASMIDS; THERMOCOCCALES; TRANSPORT VESICLES; VIRAL PROTEINS;

ARCHAEA; EUKARYOTA; NAUTILUS; THERMOCOCCALES; THERMOCOCCUS;

EID: 79551496302     PISSN: 03005127     EISSN: 14708752     Source Type: Journal    
DOI: 10.1042/BST0390036     Document Type: Conference Paper

References (57)

1. Harrison, P.W., Lower, R.P., Kim, N.K. and Young, J.P. (2010) Introducing the bacterial 'chromid': not a chromosome, not a plasmid. Trends Microbiol. 18, 141-148
2. Cohen, S., Agmon, N., Sobol, O. and Segal, D. (2010) Extrachromosomal circles of satellite repeats and 5S ribosomal DNA in human cells. Mob. DNA 1, 11
3. Lipps, G. (2008) Archaeal plasmids. In Plasmids: Current Research and Future Trends (Lipps, G., ed), pp. 25-50, Caister Academic Press, Caister
4. Arnold, H.P., She, Q., Phan, H., Stedman, K., Prangishvili, D., Holz, I., Kristjansson, J.K., Garrett, R. and Zillig, W. (1999) The genetic element pSSVx of the extremely thermophilic crenarchaeon Sulfolobus is a hybrid between a plasmid and a virus. Mol. Microbiol. 34, 217-226
5. Wang, Y., Duan, Z., Zhu, H., Guo, X., Wang, Z., Zhou, J., She, Q. and Huang, L. (2007) A novel Sulfolobus non-conjugative extrachromosomal genetic element capable of integration into the host genome and spreading in the presence of a fusellovirus. Virology 363, 124-133
6. Roine, E., Kukkaro, P., Paulin, L., Laurinavicius, S., Domanska, A., Somerharju, P. and Bamford, D.H. (2010) New, closely related haloarchaeal viral elements with different nucleic acid types. J. Virol. 84, 3682-3689
7. Cortez, D., Forterre, P. and Gribaldo, S. (2009) A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes. Genome Biol. 10, R65
8. Koonin, E.V., Senkevich, T.G. and Dolja, V.V. (2006) The ancient virus world and evolution of cells. Biol. Direct 1, 29
9. Forterre, P. and Prangishvili, D. (2009) The origin of viruses. Res. Microbiol. 160, 466-472
10. Moreira, D. and Lopez-Garcia, P. (2009) Ten reasons to exclude viruses from the tree of life. Nat. Rev. Microbiol. 7, 306-311
11. Brochier, C., Forterre, P. and Gribaldo, S. (2005) An emerging phylogenetic core of Archaea: phylogenies of transcription and translation machineries converge following addition of new genome sequences. BMC Evol. Biol. 5, 36
12. Prieur, D., Erauso, G., Geslin, C., Lucas, S., Gaillard, M., Bidault, A., Mattenet, A.C., Rouault, K., Flament, D., Forterre, P. and Le Romancer, M. (2004) Genetic elements of Thermococcales. Biochem. Soc. Trans. 32, 184-187
13. Lepage, E., Marguet, E., Geslin, C., Matte-Tailliez, O., Zillig, W., Forterre, P. and Tailliez, P. (2004) Molecular diversity of new Thermococcales isolates from a single area of hydrothermal deep-sea vents as revealed by randomly amplified polymorphic DNA fingerprinting and 16S rRNA gene sequence analysis. Appl. Environ. Microbiol. 70, 1277-1286
14. Geslin, C., Le Romancer, M., Gaillard, M., Erauso, G. and Prieur, D. (2003) Observation of virus-like particles in high temperature enrichment cultures from deep-sea hydrothermal vents. Res. Microbiol. 154, 303-307
15. Soler, N., Marguet, E., Cortez, D., Desnoues, N., Keller, J., van Tilbeurgh, H., Sezonov, G. and Forterre, P. (2010) Two novel families of plasmids from hyperthermophilic archaea encoding new families of replication proteins. Nucleic Acids Res. 38, 5088-5104
16. Charbonnier, F., Erauso, G., Barbeyron, T., Prieur, D. and Forterre, P. (1992) Evidence that a plasmid from a hyperthermophilic archaebacterium is relaxed at physiological temperatures. J. Bacteriol. 174, 6103-6108
17. Lucas, S., Toffin, L., Zivanovic, Y., Charlier, D., Moussard, H., Forterre, P., Prieur, D. and Erauso, G. (2002) Construction of a shuttle vector for, and spheroplast transformation of, the hyperthermophilic archaeon Pyrococcus abyssi. Appl. Environ. Microbiol 68, 5528-5536
18. Santangelo, T.J., Cubonova, L. and Reeve, J.N. (2008) Shuttle vector expression in Thermococcus kodakaraensis: contributions of cis elements to protein synthesis in a hyperthermophilic archaeon. Appl. Environ. Microbiol. 74, 3099-3104
19. Waege, I., Schmid, G., Thumann, S., Thomm, M. and Hausner, W. (2010) Shuttle vector-based transformation system for Pyrococcus furiosus. Appl. Environ. Microbiol. 76, 3308-3313
20. Soler, N., Marguet, E., Verbavatz, J.M. and Forterre, P. (2008) Virus-like vesicles and extracellular DNA produced by hyperthermophilic archaea of the order Thermococcales. Res. Microbiol. 159, 390-399
21. Erauso, G., Charbonnier, F., Barbeyron, T., Forterre, P. and Prieur, D. (1992) Preliminary characterization of an ultrathermophilic archaebacterium with a plasmid isolated from North Fiji basinhydrothermal vent. C.R. Acad. Sci. 314, 387-393
22. Kikuchi, A. and Asai, K. (1984) Reverse gyrase: a topoisomerase which introduces positive superhelical turns into DNA. Nature 309, 677-681
23. Forterre, P., Mirambeau, G., Jaxel, C., Nadal, M. and Duguet, M. (1985) High positive supercoiling in vitro catalyzed by an ATP and polyethylene glycol-stimulated topoisomerase from Sulfolobus acidocaldarius. EMBO J. 4, 2123-2128
24. Nadal, M., Mirambeau, G., Forterre, P., Reiter, W.D. and Duguet, M. (1986) Positively supercoiled DNA in a virus-like particle of an archaebacterium. Nature 321, 256-258
25. Marguet, E., Zivanovic, Y. and Forterre, P. (1996) DNA topological change in the hyperthermophilic archaeon Pyrococcus abyssi exposed to low temperature. FEMS Microbiol. Lett. 142, 31-36
26. Lopez-Garcia, P. and Forterre, P. (1997) DNA topology in hyperthermophilic archaea: reference states and their variation with growth phase, growth temperature, and temperature stresses. Mol. Microbiol. 23, 1267-1279
27. Lopez-Garcia, P. and Forterre, P. (2000) DNA topology and the thermal stress response, a tale from mesophiles and hyperthermophiles. BioEssays 22, 738-746
28. Marguet, E. and Forterre, P. (1994) DNA stability at temperatures typical for hyperthermophiles. Nucleic Acids Res. 22, 1681-1686
29. D'Amaro, A., Rossi, M. and Ciaramella, M. (2007) Reverse gyrase: an unusual DNA manipulator of hyperthermophilic organisms. Ital. J. Biochem. 56, 103-109
30. Nadal, M. (2007) Reverse gyrase: an insight into the role of DNA-topoisomerases. Biochimie 89, 447-455
31. Forterre, P. (2002) The origin of DNA genomes and DNA replication proteins. Curr. Opin. Microbiol. 5, 525-532
32. Atomi, H., Matsumi, R. and Imanaka, T. (2004) Reverse gyrase is not a prerequisite for hyperthermophilic life. J. Bacteriol. 186, 4829-4833
33. Erauso, G., Marsin, S., Benbouzid-Rollet, N., Baucher, M.F., Barbeyron, T., Zivanovic, Y., Prieur, D. and Forterre, P. (1996) Sequence of plasmid pGT5 from the archaeon Pyrococcus abyssi: evidence for rolling-circle replication in a hyperthermophile. J. Bacteriol. 178, 3232-3237
34. Ilyina, T.V. and Koonin, E.V. (1992) Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria. Nucleic Acids Res. 20, 3279-3285
35. Marsin, S. and Forterre, P. (1998) A rolling circle replication initiator protein with a nucleotidyl-transferase activity encoded by the plasmid pGT5 from the hyperthermophilic archaeon Pyrococcus abyssi. Mol. Microbiol. 27, 1183-1192
36. Marsin, S. and Forterre, P. (1999) The active site of the rolling circle replication protein Rep75 is involved in site-specific nuclease, ligase and nucleotidyl transferase activities. Mol. Microbiol. 33, 537-545
37. Marsin, S., Marguet, E. and Forterre, P. (2000) Topoisomerase activity of the hyperthermophilic replication initiator protein Rep75. Nucleic Acids Res. 28, 2251-2255
38. Soler, N., Justome, A., Quevillon-Cheruel, S., Lorieux, F., Le Cam, E., Marguet, E. and Forterre, P. (2007) The rolling-circle plasmid pTN1 from the hyperthermophilic archaeon Thermococcus nautilus. Mol. Microbiol. 66, 357-370
39. Santangelo, T.J. and Reeve, J.N. (2010) Deletion of switch 3 results in an archaeal RNA polymerase that is defective in transcript elongation. J. Biol. Chem. 285, 23908-23915
40. Ward, D.E., Revet, I.M., Nandakumar, R., Tuttle, J.H., de Vos, W.M., Van Der Oost, J. and DiRuggiero, J. (2002) Characterization of plasmid pRT1 from Pyrococcus sp. strain JT1. J. Bacteriol. 184, 2561-2566
41. Gonnet, M., Erauso, G., Prieur, D. and Le Romancer, M. (2010) pAMT11, a novel plasmid isolated from a Thermococcus sp. strain closely related to the virus-like integrated element TKV1 of the Thermococcus kodakaraensis genome. Res. Microbiol., doi:10.1016/j.resmic.2010.11.003
42. Geslin, C., Le Romancer, M., Erauso, G., Gaillard, M., Perrot, G. and Prieur, D. (2003) PAV1, the first virus-like particle isolated from a hyperthermophilic euryarchaeote, "Pyrococcus abyssi". J. Bacteriol. 185, 3888-3894
43. Geslin, C., Gaillard, M., Flament, D., Rouault, K., Le Romancer, M., Prieur, D. and Erauso, G. (2007) Analysis of the first genome of a hyperthermophilic marine virus-like particle, PAV1, isolated from Pyrococcus abyssi. J. Bacteriol. 189, 4510-4519
44. Grigoriev, A. (1999) Strand-specific compositional asymmetries in double-stranded DNA viruses. Virus Res. 60, 1-19
45. Chattoraj, D.K. (2000) Control of plasmid DNA replication by iterons: no longer paradoxical. Mol. Microbiol. 37, 467-476
46. Prangishvili, D., Forterre, P. and Garrett, R.A. (2006) Viruses of the Archaea: a unifying view. Nat. Rev. Microbiol. 4, 837-848
47. Krupovic, M. and Bamford, D.H. (2008) Archaeal proviruses TKV4 and MVV extend the PRD1-adenovirus lineage to the phylum Euryarchaeota. Virology 375, 292-300
48. Iyer, L.M., Koonin, E.V., Leipe, D.D. and Aravind, L. (2005) Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members. Nucleic Acids Res. 33, 3875-3896
49. Fukui, T., Atomi, H., Kanai, T., Matsumi, R., Fujiwara, S. and Imanaka, T. (2005) Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes. Genome Res. 15, 352-363 (Pubitemid 40467776)
50. Zivanovic, Y., Armengaud, J., Lagorce, A., Leplat, C., Guerin, P., Dutertre, M., Anthouard, V., Forterre, P., Wincker, P. and Confalonieri, F. (2009) Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea. Genome Biol. 10, R70
51. She, Q., Peng, X., Zillig, W. and Garrett, R.A. (2001) Gene capture in archaeal chromosomes. Nature 409, 478
52. Keller, J., Leulliot, N., Soler, N., Collinet, B., Vincentelli, R., Forterre, P. and van Tilbeurgh, H. (2009) A protein encoded by a new family of mobile elements from Euryarchaea exhibits three domains with novel folds. Protein Sci. 18, 850-855
53. Krupovic, M., Gribaldo, S., Bamford, D.H. and Forterre, P. (2010) The evolutionary history of archaeal MCM helicases: a case study of vertical evolution combined with hitch-hiking of mobile genetic elements. Mol. Biol. Evol. 27, 2716-2732
54. Krupovic, M. and Bamford, D.H. (2008) Virus evolution: how far does the double β-barrel viral lineage extend? Nat. Rev. Microbiol. 6, 941-948
55. Renelli, M., Matias, V., Lo, R.Y. and Beveridge, T.J. (2004) DNA-containing membrane vesicles of Pseudomonas aeruginosa PAO1 and their genetic transformation potential. Microbiology 150, 2161-2169
56. Forterre, P. (2010) Manipulation of cellular syntheses and the nature of viruses: the virocell concept. C.R. Chim., doi:10.1016/j.crci.2010.06.007
57. Brochier-Armanet, C., Boussau, B., Gribaldo, S. and Forterre, P. (2008) Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nat. Rev. Microbiol. 6, 245-252