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Extremophiles

, Volume 11, Issue 2, pp 315–327 | Cite as

Characterization of an ATP-dependent DNA ligase from the acidophilic archaeon “Ferroplasma acidarmanus” Fer1

  • Brian R. Jackson
  • Catherine Noble
  • Manuel Lavesa-Curto
  • Philip L. Bond
  • Richard P. Bowater
Original Paper

Abstract

Analysis of the genome of “Ferroplasma acidarmanus” Fer1, an archaeon that is an extreme acidophile, identified an open reading frame encoding a putative ATP-dependent DNA ligase, which we termed FaLig. The deduced amino acid sequence of FaLig contains 595 amino acids, with a predicted molecular mass of 67.8 kDa. “F. acidarmanus” Fer1 is classified as a Euryarchaeote, but phylogenetic analysis using amino acid sequences showed that FaLig is more similar to DNA ligases from Crenarchaeota, suggesting that lateral transfer of these genes has occurred among archaea. The gene sequence encoding FaLig was cloned into a bacterial expression vector harbouring an upstream His-tag to aid purification. Conditions for expression and purification from Escherichia coli were identified and recombinant FaLig was confirmed to be an ATP-dependent DNA ligase. Optimal conditions for nick-joining by the protein were pH 6–7, 0.5 mM ATP, in the presence of either Mg2+ or Mn2+. Using a range of nicked, double-stranded nucleic acids, ligation was detected with the same substrates as previously determined for other DNA ligases. Although FaLig is the DNA ligase from one of the most extreme acidophilic organism yet studied, this characterization suggests that its biochemical mechanism is analogous to that of enzymes from other cellular systems.

Keywords

DNA ligase Ferroplasma acidarmanus DNA nick-joining Acidophilic Archaea 

Abbreviations

DTT

Dithiothreitol

FaLig

Ferroplasma acidarmanus” Fer1 DNA ligase

IPTG

Isopropyl β-d-1-thiogalactopyranoside

LB

Luria-Bertani broth

T4Dnl

T4 DNA ligase

Notes

Acknowledgments

We thank Des Bullard and Heather Sayer for assistance with experiments and discussions about the project. This work was funded by the BBSRC and Society for General Microbiology.

References

  1. Bullard DR, Bowater RP (2006) Direct comparison of nick-joining activity of the nucleic acid ligases from bacteriophage T4. Biochem J 398:135–144PubMedCrossRefGoogle Scholar
  2. Castanie MP, Berges H, Oreglia J, Prere MF, Fayet O (1997) A set of pBR322-compatible plasmids allowing the testing of chaperone-assisted folding of proteins overexpressed in Escherichia coli. Anal Biochem 254:150–152PubMedCrossRefGoogle Scholar
  3. Chen Y, Song J, Sui SF, Wang DN (2003) DnaK and DnaJ facilitated the folding process and reduced inclusion body formation of magnesium transporter CorA overexpressed in Escherichia coli. Protein Expr Purif 32:221–231PubMedCrossRefGoogle Scholar
  4. Darland G, Brock TD, Samsonoff W, Conti SF (1970) A thermophilic, acidophilic mycoplasma isolated from a coal refuse pile. Science 170:1416–1418PubMedCrossRefGoogle Scholar
  5. Dermody JJ, Robinson GT, Sternglanz R (1979) Conditional-lethal deoxyribonucleic acid ligase mutant of Escherichia coli. J Bacteriol 139:701–704PubMedGoogle Scholar
  6. Doherty AJ, Suh SW (2000) Structural and mechanistic conservation in DNA ligases. Nucleic Acids Res 28:4051–4058PubMedCrossRefGoogle Scholar
  7. Dopson M, Baker-Austin C, Hind A, Bowman JP, Bond PL (2004) Characterization of Ferroplasma isolates and Ferroplasma acidarmanus sp. nov., extreme acidophiles from acid mine drainage and industrial bioleaching environments. Appl Environ Microbiol 70:2079–2088PubMedCrossRefGoogle Scholar
  8. Edwards KJ, Bond PL, Gihring TM, Banfield JF (2000) An archaeal iron-oxidizing extreme acidophile important in acid mine drainage. Science 287:1796–1799PubMedCrossRefGoogle Scholar
  9. Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer ELL, Bateman A (2006) Pfam: clans, web tools and services. Nucleic Acids Res 34:D247–D251PubMedCrossRefGoogle Scholar
  10. Futterer O, Angelov A, Liesegang H, Gottschalk G, Schepers B, Dock C, Antranikian G, Liebl W (2004) Genome sequence of Picrophilus torridus and its implications for life around pH 0. Proc Natl Acad Sci USA 101:9091–9096PubMedCrossRefGoogle Scholar
  11. Goenka S, Rao CM (2001) Expression of recombinant zeta-crystallin in Escherichia coli with the help of GroEL/ES and its purification. Protein Exp Purif 21:260–267CrossRefGoogle Scholar
  12. Golyshina OV, Golyshin PN, Timmis KN, Ferrer M (2006) The ‘pH optimum anomaly’ of intracellular enzymes of Ferroplasma acidiphilum. Environ Microbiol 8:416–425PubMedCrossRefGoogle Scholar
  13. Golyshina OV, Timmis KN (2005) Ferroplasma and relatives, recently discovered cell wall-lacking archaea making a living in extremely acid, heavy metal-rich environments. Environ Microbiol 7:1277–1288PubMedCrossRefGoogle Scholar
  14. Gunther S, Montes M, de DA, del VM, Atencia EA, Sillero A (2002) Thermostable Pyrococcus furiosus DNA ligase catalyzes the synthesis of (di)nucleoside polyphosphates. Extremophiles 6:45–50PubMedCrossRefGoogle Scholar
  15. Ho CK, Shuman S (2002) Bacteriophage T4 RNA ligase 2 (gp24.1) exemplifies a family of RNA ligases found in all phylogenetic domains. Proc Natl Acad Sci USA 99:12709–12714PubMedCrossRefGoogle Scholar
  16. Ho CK, Wang LK, Lima CD, Shuman S (2004) Structure and mechanism of RNA ligase. Struct (Camb) 12:327–339CrossRefGoogle Scholar
  17. Jeon SJ, Ishikawa K (2003) A novel ADP-dependent DNA ligase from Aeropyrum pernix K1. FEBS Lett 550:69–73PubMedCrossRefGoogle Scholar
  18. Kanugula S, Pauly GT, Moschel RC, Pegg AE (2005) A bifunctional DNA repair protein from Ferroplasma acidarmanus exhibits O6-alkylguanine-DNA alkyltransferase and endonuclease V activities. Proc Natl Acad Sci USA 102:3617–3622PubMedCrossRefGoogle Scholar
  19. Kelman Z, White MF (2005) Archaeal DNA replication and repair. Curr Opin Microbiol 8:669–676PubMedCrossRefGoogle Scholar
  20. Keppetipola N, Shuman S (2005) Characterization of a thermophilic ATP-dependent DNA ligase from the euryarchaeon Pyrococcus horikoshii. J Bacteriol 187:6902–6908PubMedCrossRefGoogle Scholar
  21. Kletzin A (1992) Molecular characterisation of a DNA ligase gene of the extremely thermophilic archaeon Desulfurolobus ambivalens shows close phylogenetic relationship to eukaryotic ligases. Nucleic Acids Res 20:5389–5396PubMedCrossRefGoogle Scholar
  22. Kodama KI, Barnes DE, Lindahl T (1991) In vitro mutagenesis and functional expression in Escherichia coli of a cDNA encoding the catalytic domain of human DNA ligase I. Nucleic Acids Res 19:6093–6099PubMedCrossRefGoogle Scholar
  23. Lai X, Shao H, Hao F, Huang L (2002) Biochemical characterization of an ATP-dependent DNA ligase from the hyperthermophilic crenarchaeon Sulfolobus shibatae. Extremophiles 6:469–477PubMedCrossRefGoogle Scholar
  24. Lavesa-Curto M, Sayer H, Bullard D, MacDonald A, Wilkinson A, Smith A, Bowater L, Hemmings A, Bowater R (2004) Characterisation of a temperature-sensitive DNA ligase from Escherichia coli. Microbiology 150:4171–4180PubMedCrossRefGoogle Scholar
  25. Lehman IR (1974) DNA ligase: structure, mechanism, and function. Science 186:790–797PubMedCrossRefGoogle Scholar
  26. Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar, Buchner A, Lai T, Steppi S, Jobb G, Forster W, Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, Konig A, Liss T, Lussmann R, May M, Nonhoff B, Reichel B, Strehlow R, Stamatakis A, Stuckmann N, Vilbig A, Lenke M, Ludwig T, Bode A, Schleifer KH (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32:1363–1371PubMedCrossRefGoogle Scholar
  27. Macalady JL, Vestling MM, Baumler D, Boekelheide N, Kaspar CW, Banfield JF (2004) Tetraether-linked membrane monolayers in Ferroplasma spp: a key to survival in acid. Extremophiles 8:411–419PubMedCrossRefGoogle Scholar
  28. Makarova KS, Koonin EV (2003) Comparative genomics of Archaea: how much have we learned in six years, and what’s next? Genome Biol 4:115PubMedCrossRefGoogle Scholar
  29. Makarova KS, Koonin EV (2005) Evolutionary and functional genomics of the Archaea. Curr Opin Microbiol 8:586–594PubMedCrossRefGoogle Scholar
  30. Marchler-Bauer A, Anderson JB, Cherukuri PF, DeWeese-Scott C, Geer LY, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Liebert CA, Liu C, Lu F, Marchler GH, Mullokandov M, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Yamashita RA, Yin JJ, Zhang D, Bryant SH (2005) CDD: a conserved domain database for protein classification. Nucleic Acids Res 33:D192–D196PubMedCrossRefGoogle Scholar
  31. Martins A, Shuman S (2004) An RNA Ligase from Deinococcus radiodurans. J Biol Chem 279:50654–50661PubMedCrossRefGoogle Scholar
  32. Nakatani M, Ezaki S, Atomi H, Imanaka T (2000) A DNA ligase from a hyperthermophilic archaeon with unique cofactor specificity. J Bacteriol 182:6424–6433PubMedCrossRefGoogle Scholar
  33. Nandakumar J, Ho CK, Lima CD, Shuman S (2004) RNA substrate specificity and structure-guided mutational analysis of bacteriophage T4 RNA ligase 2. J Biol Chem 279:31337–31347PubMedCrossRefGoogle Scholar
  34. Nandakumar J, Shuman S (2004) How an RNA ligase discriminates RNA versus DNA damage. Mol Cell 16:211–221PubMedCrossRefGoogle Scholar
  35. Nandakumar J, Shuman S (2005) Dual mechanisms whereby a broken RNA end assists the catalysis of its repair by T4 RNA ligase 2. J Biol Chem 280:23484–23489PubMedCrossRefGoogle Scholar
  36. Pascal JM, O’Brien PJ, Tomkinson AE, Ellenberger T (2004) Human DNA ligase I completely encircles and partially unwinds nicked DNA. Nature 432:473–478PubMedCrossRefGoogle Scholar
  37. Rolland JL, Gueguen Y, Persillon C, Masson JM, Dietrich J (2004) Characterization of a thermophilic DNA ligase from the archaeon Thermococcus fumicolans. FEMS Microbiol Lett 236:267–273PubMedCrossRefGoogle Scholar
  38. Ruepp A, Graml W, Santos-Martinez ML, Koretke KK, Volker C, Mewes HW, Frishman D, Stocker S, Lupas AN, Baumeister W (2000) The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum. Nature 407:508–513PubMedCrossRefGoogle Scholar
  39. Sambrook J, Russell D (2001) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring HarborGoogle Scholar
  40. Schleper C, Jurgens G, Jonuscheit M (2005) Genomic studies of uncultivated archaea. Nat Rev Micro 3:479–488CrossRefGoogle Scholar
  41. Searcy DG (1976) Thermoplasma acidophilum: intracellular pH and potassium concentration. Biochim Biophys Acta 451:278–286PubMedGoogle Scholar
  42. Sekiguchi J, Shuman S (1997) Ligation of RNA-containing duplexes by vaccinia DNA ligase. Biochemistry 36:9073–9079PubMedCrossRefGoogle Scholar
  43. She Q, Singh RK, Confalonieri F, Zivanovic Y, Allard G, Awayez MJ, Chan-Weiher CC, Clausen IG, Curtis BA, De Moors A, Erauso G, Fletcher C, Gordon PM, Heikamp-de Jong I, Jeffries AC, Kozera CJ, Medina N, Peng X, Thi-Ngoc HP, Redder P, Schenk ME, Theriault C, Tolstrup N, Charlebois RL, Doolittle WF, Duguet M, Gaasterland T, Garrett RA, Ragan MA, Sensen CW, Van der Oost J (2001) The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc Natl Acad Sci USA 98:7835–7840PubMedCrossRefGoogle Scholar
  44. Shuman S, Lima CD (2004) The polynucleotide ligase and RNA capping enzyme superfamily of covalent nucleotidyltransferases. Curr Opin Struct Biol 14:757–764PubMedCrossRefGoogle Scholar
  45. Sriskanda V, Kelman Z, Hurwitz J, Shuman S (2000) Characterisation of an ATP-dependent DNA ligase from the thermophilic archaeon Methanobacterium thermoautotrophicum. Nucleic Acids Res 28:2221–2228PubMedCrossRefGoogle Scholar
  46. Sriskanda V, Shuman S (1998) Specificity and fidelity of strand joining by Chlorella virus DNA ligase. Nucleic Acids Res 26:3536–3541PubMedCrossRefGoogle Scholar
  47. Timson DJ, Singleton MR, Wigley DB (2000) DNA ligases in the repair and replication of DNA. Mutat Res 460:301–318PubMedGoogle Scholar
  48. Tomkinson AE, Vijayakumar S, Pascal JM, Ellenberger T (2006) DNA ligases: structure, reaction mechanism, and function. Chem Rev 106:687–699PubMedCrossRefGoogle Scholar
  49. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:37–43PubMedCrossRefGoogle Scholar
  50. White MF (2003) Archaeal DNA repair: paradigms and puzzles. Biochem Soc Trans 31:690–693PubMedCrossRefGoogle Scholar
  51. Wilkinson A, Day J, Bowater R (2001) Bacterial DNA ligases. Mol Microbiol 40:1241–1248PubMedCrossRefGoogle Scholar
  52. Wilkinson A, Sayer H, Bullard D, Smith A, Day J, Kieser T, Bowater R (2003) NAD+-dependent DNA ligases of Mycobacterium tuberculosis and Streptomyces coelicolor. Proteins Struct Funct Genet 51:321–326PubMedCrossRefGoogle Scholar
  53. Wilkinson A, Smith A, Bullard D, Lavesa-Curto M, Sayer H, Bonner A, Hemmings AM, Bowater R (2005) Analysis of ligation and DNA binding by Escherichia coli DNA ligase (LigA). Biochim Biophys Acta 1749:113–122PubMedGoogle Scholar
  54. Yin S, Ho CK, Shuman S (2003) Structure-function analysis of T4 RNA ligase 2. J Biol Chem 278:17601–17608PubMedCrossRefGoogle Scholar
  55. Yin S, Kiong Ho C, Miller ES, Shuman S (2004) Characterization of bacteriophage KVP40 and T4 RNA ligase 2. Virology 319:141–151PubMedCrossRefGoogle Scholar
  56. Zhao A, Gray FC, MacNeill SA (2006) ATP- and NAD+-dependent DNA ligases share an essential function in the halophilic archaeon Haloferax volcanii. Mol Microbiol 59:743–752PubMedCrossRefGoogle Scholar

Copyright information

© Springer 2006

Authors and Affiliations

  • Brian R. Jackson
    • 1
  • Catherine Noble
    • 2
  • Manuel Lavesa-Curto
    • 1
  • Philip L. Bond
    • 3
  • Richard P. Bowater
    • 1
  1. 1.School of Biological SciencesUniversity of East AngliaNorwichUK
  2. 2.Department of BiochemistryUniversity of LeicesterLeicesterUK
  3. 3.Advanced Wastewater Management CentreUniversity of QueenslandBrisbaneAustralia

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