DNA repair systems in archaea: Mementos from the last universal common ancestor?

Journal of Molecular Evolution

Volumn 49, Issue 4, 1999, Pages 474-484

  DiRuggiero, Jocelyne ^a   Brown, James R ^b   Bogert, Allison P ^a   Robb, Frank T ^a  

^a UNIVERSITY OF MARYLAND   (United States)

^b GLAXOSMITHKLINE   (United Kingdom)

Author keywords

Archaea; DNA repair; Endonuclease; Hyperthermophile; Last universal common ancestor; Recombinase

Indexed keywords

DNA;

AMINO ACID SEQUENCE; ARCHAEBACTERIUM; ARTICLE; BIODIVERSITY; DNA DAMAGE; DNA REPAIR; DNA REPLICATION; DNA STRAND BREAKAGE; EUKARYOTE; GENE SEQUENCE; MOLECULAR BIOLOGY; MULTIGENE FAMILY; NONHUMAN; PHYLOGENY; PROKARYOTE; RECA GENE; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; ARCHAEA; DATABASES, FACTUAL; DNA REPAIR; DNA-BINDING PROTEINS; ENDONUCLEASES; EVOLUTION, MOLECULAR; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; RAD51 RECOMBINASE; REC A RECOMBINASES; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 0032863453     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/PL00006570     Document Type: Article

References (98)

1. Altschul SF, Gish W, Miller W, Lipman DJ (1990) Basic local alignment research tool. J Mol Biol 215:403-410
2. Aravind L, Walker DR, Koonin EV (1999) Conserved domains in DNA repair proteins and evolution of repair systems. Nucleic Acids Res 27:1223-1242
3. Ausubel FM, Brent R, Kingston RE, et al. (1987) Current protocols in molecular biology. Greene and Wiley-Interscience, New York
4. Barnes CJ, Wahl AF, Shen B, Park MS, Bambara RA (1996) Mechanism of tracking and cleveage of adduct-damaged DNA subtrates by mammalian 5′ to 3′-exo/endonuclease RAD2 homologue 1 or Flap endonuclease 1. J Biol Chem 217:29624-29631
5. Battista J (1998) DNA repair in Deinococcus radiodurans. In: Nickoloff JA, Hoekstra MF (eds) DNA damage and repair, Vol 1. Humana Press, Totowa, NJ, pp 287-303
6. Blochl E, Rachel R, Burgraf S, Hafenbradl D, Jannasch HW, Stetter KO (1997) Pyrolobus fumarii, gen. and sp. nov., represents a novel group of archaea, extending the upper limit temperature for life to 113°C. Extremophiles 1:14-21
7. Borges KM, Brummet SR, Bogert AP, et al. (1996) A survey of the genome of the hyperthermophilic Archaeon. Pyrococcus furiosus. Genome Sci Techn 2:37-46
8. Borges KM, Bergerat A, Bogert A, DiRuggiero J, Forterre P, Robb FT (1997) The reverse gyrase gene of an hyperthermophilic archaeon, Pyrococcus furiosus. J Bacteriol 179:1721-1726
9. Bouyoub A, Barbier G, Querellou J, Forterre P (1996) A putative SOS repair gene (dinF-like) in a hyperthermophic archaeon. Gene 167: 147-149
10. Brendel V, Brocchieri L, Sandler SJ, Clark AJ, Karlin S (1997) Evolutionary comparisons of RecA-like proteins across all major kingdoms of living organisms. J Mol Evol 44:528-541
11. Budd ME, Campbell JL (1997) A yeast replicative helicase, Dna2 helicase, interacts with yeast FEN-1 nuclease in carrying out its essential function. Mol Cell Biol 17:2136-2142
12. Bult CJ, White O, Olson GJ, et al. (1996) Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273:1058-1073
13. Cann IK, Komori K, Toh H, Kanai S, Ishino Y (1998). A heterodimeric DNA polymerase: Evidence that members of Euryarchaeota possess a distinct DNA polymerase. Proc Natl Acad Sci USA 95: 14250-14255
14. Ceska TA, Sayers JR, Stier G, Suck D (1996) A helical arch allowing single-stranded DNA to thread through T5 5′-exonuclease. Nature 382:90-93
15. Chui SK, Low KB, Yuan A, Radding CM (1997) Resolution of an early RecA-recombination intermediate by a junction-specific endonuclease. Proc Natl Acad Sci USA 94:6079-6083
16. Confalonieri F, Elie C, Nadal M, de La Tour C, Forterre P, Duguet M (1993) Reverse gyrase: A helicase-like domain and a type I topoisomerase in the same polypeptide. Proc Natl Acad Sci USA 90: 4753-4757
17. Corpet F (1988) Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res 16:10881-10890
18. DeMott MS, Shen B, Park MS, Bambara RA (1996) Human RAD2 homolog 1 5′- to 3′-exo/endonuclease can efficiently excise a displaced DNA fragment containing a 5′-terminal abasic lesion by endonuclease activity. J Biol Chem 271:30068-30076
19. DiRuggiero J, Robb FT (1996) Enzymes of central metabolism in hyperthermophiles: Biochemistry, regulation and genetics. In: Adams MWW (ed), Biocatalysis in hyperthermophiles. Adv Protein Chem. ACS Press, San Diego, CA, pp 311-339
20. DiRuggiero J, Santangelo N, Nackerdien Z, Ravel J, Robb FT (1997) Repair of extensive ionizing-radiation DNA damage at 95°C in the hyperthermophilic archaeon Pyrococcus furiosus. J Bacteriol 179: 4643-4645
21. Duguet M (1995) Reverse gyrase. In: Eckstein F, Lilley DMJ (eds) Nucleic acids and molecular biology. Springer-Verlag. Berlin/Heidelberg, pp 84-114
22. Felsenstein J (1993) PHYLIP (phylogeny inference package), version 3.57c. Department of Genetics, University of Washington, Seattle
23. Fitz-Gibbon S, Choi AJ, Miller JF, et al. (1997) A fosmid-based genomic map and identification of 474 genes of the hyperthermophilic archaeon Pyrobaculum aerophilum. Extremophiles 1:36-51
24. Fitt PS, Sharma N, Castellanos G (1983) A comparison of liquid-holding recovery and photoreactivtion in halophilic and non-halophilic bacteria. Biochim Biophys Acta 739:73-78
25. Forterre P (1995) Looking for the most "primitive" organism(s) on earth today: The state of the art. Planet Space Sci 43:167-177
26. Forterre P, Bergerat A, Lopez-Garcia P (1996) The unique DNA topology and DNA topoisomerases of hyperthermophilic Archaea. FEMS Microbiol Rev 18:237-248
27. Friedberg EC, Walker GC, Siede W (1995) DNA repair and mutagenesis. ASM Press, Washington, DC
28. Galtier N, Lobry JR (1997) Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes. J Mol Evol 44:632-636
29. Galtier N, Tourasse N, Gouy M (1999) A non hyperthermophilic common ancestor to extant life forms. Science 283:220-221
30. Gary R, Kim K, Cornelius HL, Park MS, Matsumoto Y (1999) Proliferating cell nuclear antigen facilitates excision in long-patch base excision repair. J Biol Chem 274:4354-4363
31. +-ATPase: Implication for the origin of eukaryotes. Proc Natl Acad Sci USA 86:6661-6665
32. Gottlich B, Reichenberger S, Feldmann E, Pfeiffer P (1998) Rejoining of DNA double-strand breaks in vitro by single-strand annealing. Eur J Biochem 258:387-395
33. Grogan DW (1997) Photoreactivation in an archaeon from geothermal environments. Microbiology 143:1071-1076
34. Grogan DW (1998) Hyperthermophiles and the problem of DNA instability. Mol Microbiol 28:1043-1049
35. Guipaud O, Marguet E, Noll KN, Bouthier De La Tour C, Forterre P (1997). Both DNA gyrase and reverse gyrase are present in the hyperthermophilic bacterium Thermotoga maritima, Proc Natl Acad Sci USA 94:10606-10611
36. Harrington JJ, Lieber MR (1994) Functional domains within FEN-1 and RAD2 define a family of structure-specific endonucleases: Implications for nucleotide excision repair. Genes Dev 8:1344-1355
37. Herzel H, Weiss O, Trifonov EN (1998) Sequence periodicity in complete genomes of archaea suggests positive supercoiling. J Biomol Struct Dyn 16:341-345
38. Hiller RZH, Zhou AMWW, Englender SW (1997) Stability and dynamics in a hyperthermophilic protein with melting temperature close to 200°C. Proc Natl Acad Sci USA 94:11329-11332
39. Holden JF, Baross JA (1993) Enhanced thermotolerance and temperature-induced changes in protein composition in the hyperthermophilic archaeon ES4. J Bacteriol 175:2839-2843
40. Horst JP, Fritz HJ (1996) Counteracting the mutagenic effect of hydrolytic deamination of DNA 5-methylcytosine residues at high temperature: DNA mismatch N-glycosylase Mig.Mth of the thermophilic archaeon Methanobacterium thermoautotrophicum THF. EMBO J 15:5459-5469
41. Hosfield DJ, Frank G, Weng Y, Tainer JA, Shen B (1998a) Newly discovered archaebacterial flap endonucleases show a structure-specific mechanism for DNA substrate binding and catalysis resembling human flap endonuclease-1. J Biol Chem 273:27154-27161
42. Hosfield DJ, Mol CD, Shen B, Tainer JA (1998b) Structure of the DNA repair and replication endonucleases and exonuclease FEN-1 : Coupling DNA and PCNA binding to FEN-1 activity. Cell 95:135-146
43. Hwang KY, Baek K, Kim HY, Cho Y (1998) The crystal structure of flap endonuclease-1 from Methanococcus jannaschii. Nat Struct Biol 5:707-713
44. Isabelle V, Franchet-Beuzit J, Sabattier R, Laine B, Spotheim-Maurizot M, Charlier M (1993) Radioprotection of DNA by a DNA-binding protein: MCI chromosomal protein from the archaebacterium Methanosarcina sp. CHTI55. Int J Radiat Biol 63:749-758
45. Ishino Y, Komori K, Cann IK, Koga Y (1998) A novel DNA polymerase family found in Archaea. J Bacteriol 180:2232-2236
46. Jacobs KL, Grogan DW (1997) Rates of spontaneous mutation in an archaeon from geothermal environments. J Bacteriol 179:3298-3303
47. Jaenicke R, Bohm G (1998) The stability of proteins in extreme environments. Curr Opin Struct Biol 8:738-748
48. Kawarabayasi Y, Sawasa M, Horikawa H, et al. (1998) Complete sequence and gene organization of the genome of a hyperthermophilic archaeon, Pyrococcus horikoshii. DNA Res 5:55-76
49. Kiener A, Gall R, Rechsteiner T, Leisinger T (1985) Photoreactivation in Methanobacterium thermoautotrophicum. Arch Microbiol 143: 147-150
50. Kiener A, Husain I, Sancar A, Walsh C (1989) Purification and properties of Methanobacterium thermoautotrophicum DNA photolyase. J Mol Biochem 264:13880-13887
51. Kim K, Biade S, Matsumoto Y (1998). Involvement of flap endonuclease 1 in base excision DNA repair. J Biol Chem 273:8842-8848
52. Klenk HP, Clayton RA, Tomb JF, et al. (1997) The complete genome sequence of the hyperthermophilic, sulfate-reducing archaeon Archaeoglobus fulgidus. Nature 390:364-370
53. Klungland A, Lindahl T (1997) Second pathway for complementation of human DNA base excision-repair: Reconstitution with purified proteins and requirement for DNase IV (FEN-1). EMBO J 16: 3341-3348
54. Kopylov VM, Bonch-Osmolovskaya EA, Svetlichnyi VA, Miroshnichenko ML, Skobkin VS (1993) g-Irradiation resistance and UV-sensitivity of extremely thermophilic archaebacteria and eubacteria. Mikrobiologika 62:90-95
55. Koulis A, Cowan DA, Pearl LH, Savva R (1996) Uracil-DNA glycosylase activities in hyperthermophilic micro-organisms. FEMS Microbiol Let 143:267-271
56. Krah R, Kozyavkin SA, Slesarev AI, Gellert M (1996) A two-subunit type I DNA topoisomerase (reverse gyrase) from an extreme hyperthermophile. Proc Natl Acad Sci USA 93:106-110
57. Krasin F, Hutchinson F (1977) Repair of DNA double-strand breaks in Escherichia coli, which requires recA function and the presence of a duplicate genome. J Mol Biol 166:81-98
58. Kulaeva OI, Koonin EV, McDonald JP, et al. (1996) Identification of a DinB/UmuC homolog in the archaeon Sulfolobus solfataricus. Mutat Res 357:245-253
59. Lazcano A, Miller SL (1996) The origin and early evolution of life: prebiotic chemistry, the pre-RNA world, and time. Cell 85:793-798
60. Lieber MR (1997) The FEN-1 family of structure-specific nucleases in eukaryotic DNA replication, recombination and repair. BioEssays 19:233-240
61. Lindahl T (1971) Excision of pyrimidine dimers from ultraviolet-irradiated DNA by exonucleases from mammalian tissues. Proc Natl Acad Sci USA 62:597-603
62. Lindahl T (1993) Instability and decay of the primary structure of DNA. Nature 362:709-715
63. Lindahl T, Nyberg B (1974) Heat-induced deamination of cytosine residues in deoxyribonucleic acid. Biochemistry 13:3405-3410
64. Lopez-Garcia P, Forterre P (1997) DNA topology in hyperthermophilic Archaea: Reference states and their variation with growth phase, growth temperature, and temperature. Mol Microbiol 23:1267-1279
65. Marguet E, Forterre P (1994) DNA stability at temperatures typical for hyperthermophiles. Nucleic Acids Res 22:1681-1686
66. McAfee JG, Edmondson SP, Zegar I, Shriver JW (1996) Equilibrium DNA-binding of Sac7d protein from the hyperthermophile Sulfolobus acidocaldarius: Fluorescence and circular dichroism studies. Biochemistry 35:4034-4045
67. McCready S (1996) The repair of ultraviolet light-induced DNA damage in the halophilic archaebacteria, Halobacterium cutirubrum, Halobacterium halobium and Haloferax volcanii. Mutat Res 364: 25-32
68. Michels PC, Clark DS (1997) Pressure-enhanced activity and stability of a hyperthermophilic protease from a deep-sea methanogen. Appl Environ Microbiol 63:3985-3991
69. Minton KW, Daly MJ (1995) A model for repair of radiation-induced DNA double-strand breaks in the extreme radiophile Deinococcus radiodurans. Bioessays 17:457-464
70. Ögrünç M, Becker DF, Ragsdale SW, Sancar A (1998) Nucleotide excision repair in the third kingdom. J Bacteriol 180:5796-5798
71. Peak MJ, Robb FT, Peak JG (1995) Extreme resistance to thermally induced DNA backbone breaks in the hyperthermophilic Archaeon Pyrococcus furiosus. J Bacteriol 177:6316-6318
72. Pereira SL, Reeve JN (1998) Histones and nucleosomes in archaea and eukarya - A comparative analysis. Extremophiles 2:141-148
73. Praul CA, Taylor WD (1997) Responses of Halobacterium halobium and Sulfolobus solfataricus to hydrogen peroxide and N-methyl-N-nitrosoguanidine exposure. Microbiol Res 152:257-260
74. Radman M (1975) SOS repair hypothesis: Phenomenology of an inducible DNA repair which is accompagnied by mutagenesis. In: Hanawalt AP. Setlow RB. (eds) Molecular mechanisms for repair of DNA. Plenum, New York, pp 355-367
75. Rao H, Rosenfeld A, Wetmur J (1998). Methanococcus jannaschii Flap endonuclease: Expression, purification and substrate requirements. I Bacteriol 180:5406-5412
76. Rashid N, Morikawa M, Imanaka T (1996) A RecA/RAD51 homologue from a hyperthermophilic archaeon retains the major RecA domain only. Mol Gen Genet 253:397-400
77. Rashid N, Morikawa M, Nagahisa K, Kanaya S, Imanaka T (1997) Characterization of a RecA/Rad51 homologue from the hyperthermophilic archaeon Pyrococcus sp. KOD1. Nucleic Acids Res 25: 719-726
78. Rashid N, Morikawa M, Kanaya S, Atomi H, Imanaka T (1999). A unique DNase activity shares the active site with ATPase activity of the recA/Rad51 homologue (Pk-REC) from a hyperthermophilic archaeon. FEBS Lett 445:111-114
79. Riera J, Robb FT, Weiss R, Fontecave M (1997) Ribonucleotide reductase in the archaeon Pyrococcus furiosus. A critical enzyme in the evolution of DNA genomes. Proc Natl Acad Sci USA 94:475-478
80. Robb FT, Maeder D (1998) Novel evolutionary histories and adaptative features of proteins from hyperthermophiles. Curr Opin Biotech 9:288-291
81. Robinson H, Gao YG, McCrary BS, Edmondson SP, Shriver JW, Wang AHJ (1998) The hyperthermophile chromosomal protein sac7d sharply kinks DNA. Nature 392:202-205
82. Sandler SJ, Hugenholtz P, Schleper C, DeLong EF, Pace NR, Clark AJ (1999) Diversity of radA genes from cultured and uncultured archaea: Comparative analysis of putative RadA proteins and their use as a phylogenetic marker. J Bacteriol 181:907-915
83. Sandler SJ, Satin LH, Samra HS, Clark AJ (1996) recA-like genes from three archaean species with putative protein products similar to Rad51 and Dmc1 proteins of the yeast Saccharomyces cerevisiae. Nucleic Acids Res 24:2125-2132
84. Sandman K, Reeve JN (1999) Archaeal nucleosome positioning by CTG repeats. J Bacteriol 181:1035-1038
85. Seitz EM, Brockmann JP, Sandler SJ, Clark AJ, Kowalczykowski SC (1998) RadA protein is an archaeal RecA protein homolog that catalyzes DNA strand exchange. Gen Dev 12:1248-1253
86. Skorvaga M, Raven ND, Margison GP (1998) Thermostable archaeal O6-alkylguanine-DNA alkyltransferases. Proc Natl Acad Sci USA 95:6711-6715
87. Smith DR, Doucette-Stamm LA, Deloughery C, et al. (1997) Complete genome sequence of Methanobacterium thermoautotrophicum ΔH: Functional analysis and comparative genomics. J Bacteriol 179: 7135-7155
88. Sommers CH, Miller EJ, Dujon B, Prakash S, Prakash L (1995) Conditional lethality of null mutations in RTH1 that encodes the yeast counterpart of a mammalian 5́ to 3́-exonuclease requires for lagging strand DNA synthesis in reconstituted systems. J Biol Chem 270:4193-4196
89. Stassen NY, Logsdon JM, Vora GJ, Offenberg HH, Palmer JD, Zolan ME (1997) Isolation and characterization of rad51 orthologs from Coprinus cinereus and Lycopersicon esculentum, and phylogenetic analysis of eukaryotic recA homologs. Curr Genet 31:144-157
90. Stetter KO, Fiala G, Huber R, Segerer A (1990) Hyperthermophilic microorganisms. FEMS Microbiol Rev 75:117-124
91. Swofford DL (1993) PAUP: Phylogenetic analysis using parsimony, version 3.1. Distributed by the Illinois Natural History Survey, Champaign
92. Trent JD, Nimmersgern E, Wall JS, Hartl FU, Horwich AL (1991) A molecular chaperone from a thermophilic archaebacterium is related to the eukaryotic protein t-complex polypeptide-1. Nature 354:490-493
93. Trent JD, Gabrielsen M, Jensen B, Neuhard J, Olsen J (1994) Acquired thermotolerance and heat shock proteins in thermophiles from the three phylogenetic domains. J Bacteriol 176:6148-6152
94. Uemori T, Sato Y, Kato I, Doi H, Ishino Y (1997). A novel DNA polymerase in the hyperthermophilic archaeon Pyrococcus furiosus: Gene cloning, expression and characterization. Genes Cells 2:499-512
95. Woese CR, Kandler O, Wheelis ML (1990) Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 87:4576-4579
96. Wood ER, Ghane F, Grogan DW (1997) Genetic responses of the thermophilic archaeon Sulfolobus acidocaldarius to short-wavelength UV light. J Bacteriol 179:5693-5698
97. Woods WG, Dyall-Smith ML (1997) Construction and analysis of a recombinant-deficient (radA) mutant of Haloferax volcanii. Mol Microbiol 23:791-797
98. Wu X, Wilson TE, Lieber MR (1999). A role for FEN-1 in nonhomologous DNA end joining: The order of strand annealing and nucleolytic processing events. Proc Natl Acad Sci USA 96:1303-1308