, Volume 23, Issue 1, pp 141–149 | Cite as

Increase of positive supercoiling in a hyperthermophilic archaeon after UV irradiation

  • A. GorlasEmail author
  • R. Catchpole
  • E. Marguet
  • P. Forterre
Original Paper


Diverse DNA repair mechanisms are essential to all living organisms. Some of the most widespread repair systems allow recovery of genome integrity in the face of UV radiation. Here, we show that the hyperthermophilic archaeon Thermococcus nautili possesses a remarkable ability to recovery from extreme chromosomal damage. Immediately following UV irradiation, chromosomal DNA of T. nautili is fragmented beyond recognition. However, the extensive UV-induced double-stranded breaks (DSB) are repaired over the course of several hours, allowing restoration of growth. DSBs also disrupted plasmid DNA in this species. Similar to the chromosome, plasmid integrity was restored during an outgrowth period. Intriguingly, the topology of recovered pTN1 plasmids differed from control strain by being more positively supercoiled. As reverse gyrase (RG) is the only enzyme capable of inducing positive supercoiling, our results suggest the activation of RG activity by UV-induced stress. We suggest simple UV stress could be used to study archaeal DNA repair and responses to DSB.


UV irradiation Double-strand breaks Plasmid Topology 



A.G and P.F were funded by the Agence Nationale de la Recherche, project Thermovésicules (ANR 12-BSV3-003-01). P.F and R.C were supported by the European Research council, project EVOMOBIL (FP/2007-2013)—ERC Grant agreement no. 340440 to PF.


  1. Ajon M, Fröls S, van Wolferen M, Stoecker K, Teichmann D, Driessen AJ, Grogan DW, Albers SV, Schleper C (2011) UV-inducible DNA exchange in hyperthermophilic archaea mediated by type IV pili. Mol Microbiol 82:807–817CrossRefGoogle Scholar
  2. Atomi H, Matsumi R, Imanaka T (2004) Reverse gyrase is not a prerequisite for hyperthermophilic life. J Bacteriol 186:4829–4833CrossRefGoogle Scholar
  3. Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J (2004) Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1. Genome Res 14:1025–1035CrossRefGoogle Scholar
  4. Britt AB (2004) Repair of DNA damage induced by solar UV. Photosynth Res 81:105–112CrossRefGoogle Scholar
  5. Brochier-Armanet C, Forterre P (2007) Widespread distribution of archaeal reverse gyrase in thermophilic bacteria suggests a complex history of vertical inheritance and lateral gene transfers. Archaea 2:83–93CrossRefGoogle Scholar
  6. Charbonnier F, Forterre P (1994) Comparison of plasmid DNA topology among mesophilic and thermophilic eubacteria and archaebacteria. J Bacteriol 176:1251–1259CrossRefGoogle Scholar
  7. Charbonnier F, Erauso G, Barbeyron T, Prieur D, Forterre P (1992) Evidence that a plasmid from a hyperthermophilic archaebacterium is relaxed at physiological temperatures. J Bacteriol 174:6103–6108CrossRefGoogle Scholar
  8. D’Ari R (1985) The SOS system. Biochimie 67:343–347CrossRefGoogle Scholar
  9. DiRuggiero J, Santangelo N, Nackerdien Z, Ravel J, Robb FT (1997) Repair of extensive ionizing-radiation DNA damage at 95 degrees C in the hyperthermophilic archaeon Pyrococcus furiosus. J Bacteriol 179:4643–4645CrossRefGoogle Scholar
  10. Drlica K (1992) Control of bacterial DNA supercoiling. Mol Microbiol 6:425–433CrossRefGoogle Scholar
  11. Duguet M (1993) The helical repeat of DNA at high temperature. Nucleic Acids Res 21:463–468CrossRefGoogle Scholar
  12. Forterre P (2002) A hot story from comparative genomics: reverse gyrase is the only hyperthermophile-specific protein. Trends Genet 18:236–237CrossRefGoogle Scholar
  13. Forterre P, Mirambeau G, Jaxel C, Nadal M, Duguet M (1985) High positive supercoiling in vitro catalyzed by an ATP and polyethylene glycol-stimulated topoisomerase from Sulfolobus acidocaldarius. EMBO J 4:2123–2128CrossRefGoogle Scholar
  14. Forterre P, Confalonieri F, Charbonnier F, Duguet M (1995) Speculations on the origin of life and thermophily: review of available information on reverse gyrase suggests that hyperthermophilic procaryotes are not so primitive. Orig Life Evol Biosph 25:235–249CrossRefGoogle Scholar
  15. Friedberg EC, Aguilera A, Gellert M, Hanawalt PC, Hays JB, Lehmann AR, Lindahl T, Lowndes N, Sarasin A, Wood RD (2006) DNA repair: from molecular mechanism to human disease. DNA Repair 5:986–996CrossRefGoogle Scholar
  16. Fröls S, Gordon PM, Panlilio MA, Duggin IG, Bell SD, Sensen CW, Schleper C (2007) Response of the hyperthermophilic archaeon Sulfolobus solfataricus to UV damage. J Bacteriol 189:8708–8718CrossRefGoogle Scholar
  17. Fröls S, Ajon M, Wagner M, Teichmann D, Zolghadr B, Folea M, Boekema EJ, Driessen AJ, Schleper C, Albers SV (2008) UV-inducible cellular aggregation of the hyperthermophilic archaeon Sulfolobus solfataricus is mediated by pili formation. Mol Microbiol 70:938–952CrossRefGoogle Scholar
  18. Fröls S, White MF, Schleper C (2009) Reactions to UV damage in the model archaeon Sulfolobus solfataricus. Biochem Soc Trans 37:36–41CrossRefGoogle Scholar
  19. Gaudin M, Krupovic M, Marguet E, Gauliard E, Cvirkaite-Krupovic V, Le Cam E, Oberto J, Forterre P (2014) Extracellular membrane vesicles harbouring viral genomes. Environ Microbiol 16:1167–1175CrossRefGoogle Scholar
  20. Gérard E, Jolivet E, Prieur D, Forterre P (2001) DNA protection mechanisms are not involved in the radioresistance of the hyperthermophilic archaea Pyrococcus abyssi and P. furiosus. Mol Genet Genom 266:72–78CrossRefGoogle Scholar
  21. Gorlas A, Koonin EV, Bienvenu N, Prieur D, Geslin C (2012) TPV1, the first virus isolated from the hyperthermophilic genus Thermococcus. Environ Microbiol 14:503–516CrossRefGoogle Scholar
  22. Gorlas A, Alain K, Bienvenu N, Geslin C (2013) Thermococcus prieurii sp. nov., a hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 63:2920–2926CrossRefGoogle Scholar
  23. Gorlas A, Croce O, Oberto J, Gauliard E, Forterre P, Marguet E (2014) Thermococcus nautili sp. nov., a hyperthermophilic archaeon isolated from a hydrothermal deep-sea vent. Int J Syst Evol Microbiol 64:1802–1810CrossRefGoogle Scholar
  24. Götz D, Paytubi S, Munro S, Lundgren M, Bernander R, White MF (2007) Responses of hyperthermophilic crenarchaea to UV irradiation. Genome Biol 8:R220CrossRefGoogle Scholar
  25. Higgins NP, Vologodskii AV (2015) Topological behavior of plasmid DNA. Microbiol Spectr. Google Scholar
  26. Kampmann M, Stock D (2004) Reverse gyrase has heat-protective DNA chaperone activity independent of supercoiling. Nucleic Acids Res 32:3537–3545CrossRefGoogle Scholar
  27. Kikuchi A, Asai K (1984) Reverse gyrase—a topoisomerase which introduces positive superhelical turns into DNA. Nature 309:677–681CrossRefGoogle Scholar
  28. Krupovic M, Quemin ER, Bamford DH, Forterre P, Prangishvili D (2014) Unification of the globally distributed spindle-shaped viruses of the Archaea. J Virol 88:2354–2358CrossRefGoogle Scholar
  29. Lankinen MH, Vilpo LM, Vilpo JA (1996) UV- and gamma-irradiation-induced DNA single-strand breaks and their repair in human blood granulocytes and lymphocytes. Mutat Res 352:31–38CrossRefGoogle Scholar
  30. Lepage E, Marguet E, Geslin C, Matte-Tailliez O, Zillig W, Forterre P, 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 70:1277–1286CrossRefGoogle Scholar
  31. Lipscomb GL, Hahn EM, Crowley AT, Adams MWW (2017) Reverse gyrase is essential for microbial growth at 95 C. Extremophiles 21:603–608CrossRefGoogle Scholar
  32. López-García P (1999) DNA supercoiling and temperature adaptation: a clue to early diversification of life? J Mol Evol 49:439–452CrossRefGoogle Scholar
  33. López-García P, Forterre P (1997) DNA topology in hyperthermophilic archaea: reference states and their variation with growth phase, growth temperature, and temperature stresses. Mol Microbiol 23:1267–1279CrossRefGoogle Scholar
  34. López-García P, Forterre P (1999) Control of DNA topology during thermal stress in hyperthermophilic archaea: DNA topoisomerase levels, activities and induced thermotolerance during heat and cold shock in Sulfolobus. Mol Microbiol 33:766–777CrossRefGoogle Scholar
  35. López-García P, Forterre P (2000) DNA topology and the thermal stress response, a tale from mesophiles and hyperthermophiles. Bioessays 22:738–746CrossRefGoogle Scholar
  36. López-García P, Antón J, Abad JP, Amils R (1994) Halobacterial megaplasmids are negatively supercoiled. Mol Microbiol 11:421–427CrossRefGoogle Scholar
  37. López-García P, Forterre P, van der Oost J, Erauso G (2000) Plasmid pGS5 from the hyperthermophilic archaeon Archaeoglobus profundus is negatively supercoiled. J Bacteriol 182:4998–5000CrossRefGoogle Scholar
  38. Lulchev P, Klostermeier D (2014) Reverse gyrase—recent advances and current mechanistic understanding of positive DNA supercoiling. Nucleic Acids Res 42:8200–8213CrossRefGoogle Scholar
  39. Ma J, Wang MD (2016) DNA supercoiling during transcription. Biophys Rev 8:S75–S87CrossRefGoogle Scholar
  40. Makarova KS, Aravind L, Grishin NV, Rogozin IB, Koonin EV (2002) A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. Nucleic Acids Res 30:482–496CrossRefGoogle Scholar
  41. Marguet E, Zivanovic Y, Forterre P (1996) DNA topological change in the hyperthermophilic archaeon Pyrococcus abyssi exposed to low temperature. FEMS Microbiol lett 142:31–36CrossRefGoogle Scholar
  42. Martin A, Yeats S, Janekovic D, Reiter WD, Aicher W, Zillig W (1984) SAV 1, a temperate uv-inducible DNA virus-like particle from the archaebacterium Sulfolobus acidocaldarius isolate B12. EMBO J 3:2165–2168CrossRefGoogle Scholar
  43. Matallana-Surget S, Wattiez R (2013) impact of solar radiation on gene expression in bacteria. Proteomes 1:70–86CrossRefGoogle Scholar
  44. McCready S, Müller JA, Boubriak I, Berquist BR, Ng WL, DasSarma S (2005) UV irradiation induces homologous recombination genes in the model archaeon, Halobacterium sp. NRC-1. Saline Syst 1:3CrossRefGoogle Scholar
  45. Mojica FJ, Charbonnier F, Juez G, Rodríguez-Valera F, Forterre P (1994) Effects of salt and temperature on plasmid topology in the halophilic archaeon Haloferax volcanii. J Bacteriol 176:4966–4973CrossRefGoogle Scholar
  46. Nadal M, Mirambeau G, Forterre P, Reiter WD, Duguet M (1986) Positively supercoiled DNA in a virus-like particle of an archaebacterium. Nature 321:256–258CrossRefGoogle Scholar
  47. Napoli A, Valenti A, Salerno V, Nadal M, Garnier F, Rossi M, Ciaramella M (2004) Reverse gyrase recruitment to DNA after UV light irradiation in Sulfolobus solfataricus. J Biol Chem 279:33192–33198CrossRefGoogle Scholar
  48. Oberto J, Gaudin M, Cossu M, Gorlas A, Slesarev A, Marguet E, Forterre P (2014) Genome sequence of a hyperthermophilic archaeon, Thermococcus nautili 30–1, that produces viral vesicles. Genome Announc. Google Scholar
  49. Perugino G, Valenti A, D’amaro A, Rossi M, Ciaramella M (2009) Reverse gyrase and genome stability in hyperthermophilic organisms. Biochem Soc Trans 37:69–73CrossRefGoogle Scholar
  50. Rastogi RP, Richa Kumar A, Tyagi MB, Sinha RP (2010) Molecular mechanisms of ultraviolet radiation-induced DNA damage and repair. J Nucleic Acids 2010:592980CrossRefGoogle Scholar
  51. Roca J (2009) Two-dimensional agarose gel electrophoresis of DNA topoisomers. Methods Mol Biol 582:27–37CrossRefGoogle Scholar
  52. Rolfsmeier ML, Laughery MF, Haseltine CA (2010) Repair of DNA double-strand breaks following UV damage in three Sulfolobus solfataricus strains. J Bacteriol 192:4954–4962CrossRefGoogle Scholar
  53. Salerno V, Napoli A, White MF, Rossi M, Ciaramella M (2003) Transcriptional response to DNA damage in the archaeon Sulfolobus solfataricus. Nucleic Acids Res 31:6127–6138CrossRefGoogle Scholar
  54. Schleper C, Kubo K, Zillig W (1992) The particle SSV1 from the extremely thermophilic archaeon Sulfolobus is a virus: demonstration of infectivity and of transfection with viral DNA. Proc Natl Acad Sci USA 89:7645–7649CrossRefGoogle Scholar
  55. Schmidt KJ, Beck KE, Grogan DW (1999) UV stimulation of chromosomal marker exchange in Sulfolobus acidocaldarius: implications for DNA repair, conjugation and homologous recombination at extremely high temperatures. Genetics 152:1407–1415Google Scholar
  56. Sinha RP, Häder DP (2002) UV-induced DNA damage and repair: a review. Photochem Photobiol Sci 1:225–236CrossRefGoogle Scholar
  57. Sinha RP, Dautz M, Häder DP (2001) A simple and efficient method for the quantitative analysis of thymine dimers in cyanobacteria, phytoplankton and macroalgae. Acta Protozool 40:187–195Google Scholar
  58. Soler N, Justome A, Quevillon-Cheruel S, Lorieux F, Le Cam E, Marguet E, Forterre P (2007) The rolling-circle plasmid pTN1 from the hyperthermophilic archaeon Thermococcus nautilus. Mol Microbiol 66:357–370CrossRefGoogle Scholar
  59. Soler N, Marguet E, Cortez D, Desnoues N, Keller J, van Tilbeurgh H, Sezonov G, Forterre P (2010) Two novel families of plasmids from hyperthermophilic archaea encoding new families of replication proteins. Nucleic Acids Res 38:5088–5104CrossRefGoogle Scholar
  60. Tapias A, Leplat C, Confalonieri F (2009) Recovery of ionizing-radiation damage after high doses of gamma ray in the hyperthermophilic archaeon Thermococcus gammatolerans. Extremophiles 13:333–343CrossRefGoogle Scholar
  61. Ward JF (1990) The yield of DNA double-strand breaks produced intracellularly by ionizing radiation: a review. Int J Radiat Biol 57:1141–1150CrossRefGoogle Scholar
  62. Williams E, Lowe TM, Savas J, DiRuggiero J (2007) Microarray analysis of the hyperthermophilic archaeon Pyrococcus furiosus exposed to gamma irradiation. Extremophiles 11:19–29CrossRefGoogle Scholar
  63. Wolferen M, Ajon M, Driessen AJ, Albers SV (2013) Molecular analysis of the UV-inducible pili operon from Sulfolobus acidocaldarius. Microbiologyopen 2:928–937CrossRefGoogle Scholar
  64. Wolferen M, Wagner A, van der Does C, Albers SV (2016) The archaeal ced system imports DNA. Proc Natl Acad Sci USA 113:2496–2501CrossRefGoogle Scholar
  65. Wood ER, Ghane F, Grogan DW (1997) Genetic responses of the hyperthermophilic archaeon Sulfolobus acidocaldarius to short-wavelength UV light. J Bacteriol 179:5693–5698CrossRefGoogle Scholar
  66. Zhang C, Tian B, Li S, Ao X, Dalgaard K, Gökce S, Liang Y, She Q (2013) Genetic manipulation in Sulfolobus islandicus and functional analysis of DNA repair genes. Biochem Soc Trans 41:405–410CrossRefGoogle Scholar
  67. Zillig W, Prangishvili D, Schleper C, Elferink M, Holz I, Albers S, Janekovic D, Götz D (1996) Viruses, plasmids and other genetic elements of thermophilic and hyperthermophilic Archaea. FEMS Microbiol Rev 18:225–236CrossRefGoogle Scholar

Copyright information

© Springer Japan KK, part of Springer Nature 2018

Authors and Affiliations

  • A. Gorlas
    • 1
    Email author
  • R. Catchpole
    • 1
    • 2
  • E. Marguet
    • 1
  • P. Forterre
    • 1
    • 2
  1. 1.Laboratoire de Biologie Cellulaire des ArchaeaInstitut de Biologie Intégrative de la Cellule, UMR8621/CNRSOrsay CedexFrance
  2. 2.Laboratoire de Biologie Moléculaire du Gène chez les ExtrémophilesInstitut PasteurParisFrance

Personalised recommendations