Nucleic Acids Research, Vol 27, Issue 5 1223-1242, Copyright © 1999 by Oxford University Press
L Aravind, DR Walker and EV Koonin
A detailed analysis of protein domains involved in DNA repair was performed
by comparing the sequences of the repair proteins from two well-studied
model organisms, the bacterium Escherichia coli and yeast Saccharomyces
cerevisiae, to the entire sets of protein sequences encoded in completely
sequenced genomes of bacteria, archaea and eukaryotes. Previously
uncharacterized conserved domains involved in repair were identified,
namely four families of nucleases and a family of eukaryotic repair
proteins related to the proliferating cell nuclear antigen. In addition, a
number of previously undetected occurrences of known conserved domains were
detected; for example, a modified helix- hairpin-helix nucleic acid-binding
domain in archaeal and eukaryotic RecA homologs. There is a limited
repertoire of conserved domains, primarily ATPases and nucleases, nucleic
acid-binding domains and adaptor (protein-protein interaction) domains that
comprise the repair machinery in all cells, but very few of the repair
proteins are represented by orthologs with conserved domain architecture
across the three superkingdoms of life. Both the external environment of an
organism and the internal environment of the cell, such as the chromatin
superstructure in eukaryotes, seem to have a profound effect on the layout
of the repair systems. Another factor that apparently has made a major
contribution to the composition of the repair machinery is horizontal gene
transfer, particularly the invasion of eukaryotic genomes by organellar
genes, but also a number of likely transfer events between bacteria and
archaea. Several additional general trends in the evolution of repair
proteins were noticed; in particular, multiple, independent fusions of
helicase and nuclease domains, and independent inactivation of enzymatic
domains that apparently retain adaptor or regulatory functions.
REVIEWS
Conserved domains in DNA repair proteins and evolution of repair systems
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  M. A. A. Castro, R. J. S. Dalmolin, J. C. F. Moreira, J. C. M. Mombach, and R. M. C. de Almeida Evolutionary origins of human apoptosis and genome-stability gene networks Nucleic Acids Res., October 2, 2008; (2008) gkn636v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. B. Christensen, S. A. Byrd, A. K. Walker, J. R. Strahler, P. C. Andrews, and M. J. Imperiale Presence of the Adenovirus IVa2 Protein at a Single Vertex of the Mature Virion J. Virol., September 15, 2008; 82(18): 9086 - 9093. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. Liveris, V. Mulay, S. Sandigursky, and I. Schwartz Borrelia burgdorferi vlsE Antigenic Variation Is Not Mediated by RecA Infect. Immun., September 1, 2008; 76(9): 4009 - 4018. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Frols, P. M. K. Gordon, M. A. Panlilio, I. G. Duggin, S. D. Bell, C. W. Sensen, and C. Schleper Response of the Hyperthermophilic Archaeon Sulfolobus solfataricus to UV Damage J. Bacteriol., December 1, 2007; 189(23): 8708 - 8718. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Z.-H. Zhong, W.-Q. Jiang, A. J. Cesare, A. A. Neumann, R. Wadhwa, and R. R. Reddel Disruption of Telomere Maintenance by Depletion of the MRE11/RAD50/NBS1 Complex in Cells That Use Alternative Lengthening of Telomeres J. Biol. Chem., October 5, 2007; 282(40): 29314 - 29322. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Trowbridge, K. McKim, S. J. Brill, and J. Sekelsky Synthetic Lethality of Drosophila in the Absence of the MUS81 Endonuclease and the DmBlm Helicase Is Associated With Elevated Apoptosis Genetics, August 1, 2007; 176(4): 1993 - 2001. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. L. Barnes and R. McCulloch Trypanosoma brucei homologous recombination is dependent on substrate length and homology, though displays a differential dependence on mismatch repair as substrate length decreases Nucleic Acids Res., May 11, 2007; 35(10): 3478 - 3493. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Y. Ha, H. K. Kim, D. J. Kim, K. H. Kim, S. J. Oh, H. H. Lee, H. J. Yoon, H. K. Song, and S. W. Suh The recombination-associated protein RdgC adopts a novel toroidal architecture for DNA binding Nucleic Acids Res., April 10, 2007; (2007) gkm144v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. J. Callegari and T. J. Kelly From the Cover: UV irradiation induces a postreplication DNA damage checkpoint PNAS, October 24, 2006; 103(43): 15877 - 15882. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Wagner, G. Price, and R. Rothstein The Absence of Top3 Reveals an Interaction Between the Sgs1 and Pif1 DNA Helicases in Saccharomyces cerevisiae Genetics, October 1, 2006; 174(2): 555 - 573. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Weiss Evidence for Mutagenesis by Nitric Oxide during Nitrate Metabolism in Escherichia coli J. Bacteriol., February 1, 2006; 188(3): 829 - 833. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. N. Guzder, C. H. Sommers, L. Prakash, and S. Prakash Complex Formation with Damage Recognition Protein Rad14 Is Essential for Saccharomyces cerevisiae Rad1-Rad10 Nuclease To Perform Its Function in Nucleotide Excision Repair In Vivo Mol. Cell. Biol., February 1, 2006; 26(3): 1135 - 1141. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Valenti, A. Napoli, M. C. Ferrara, M. Nadal, M. Rossi, and M. Ciaramella Selective degradation of reverse gyrase and DNA fragmentation induced by alkylating agent in the archaeon Sulfolobus solfataricus. Nucleic Acids Res., January 1, 2006; 34(7): 2098 - 2108. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Paz, V. Kirzhner, E. Nevo, and A. Korol Coevolution of DNA-Interacting Proteins and Genome "Dialect" Mol. Biol. Evol., January 1, 2006; 23(1): 56 - 64. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
O. V. Tsodikov, J. H. Enzlin, O. D. Scharer, and T. Ellenberger Crystal structure and DNA binding functions of ERCC1, a subunit of the DNA structure-specific endonuclease XPF-ERCC1 PNAS, August 9, 2005; 102(32): 11236 - 11241. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y.-J. Choi, K.-S. Ryu, Y.-M. Ko, Y.-K. Chae, J. G. Pelton, D. E. Wemmer, and B.-S. Choi Biophysical Characterization of the Interaction Domains and Mapping of the Contact Residues in the XPF-ERCC1 Complex J. Biol. Chem., August 5, 2005; 280(31): 28644 - 28652. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. N. Kinch, K. Ginalski, L. Rychlewski, and N. V. Grishin Identification of novel restriction endonuclease-like fold families among hypothetical proteins Nucleic Acids Res., June 22, 2005; 33(11): 3598 - 3605. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Akiba, N. Ishii, N. Rashid, M. Morikawa, T. Imanaka, and K. Harata Structure of RadB recombinase from a hyperthermophilic archaeon, Thermococcus kodakaraensis KOD1: an implication for the formation of a near-7-fold helical assembly Nucleic Acids Res., June 13, 2005; 33(10): 3412 - 3423. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Kanugula, G. T. Pauly, R. C. Moschel, and A. E. Pegg A bifunctional DNA repair protein from Ferroplasma acidarmanus exhibits O6-alkylguanine-DNA alkyltransferase and endonuclease V activities PNAS, March 8, 2005; 102(10): 3617 - 3622. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D.-Y. Chang and A-L. Lu Interaction of Checkpoint Proteins Hus1/Rad1/Rad9 with DNA Base Excision Repair Enzyme MutY Homolog in Fission Yeast, Schizosaccharomyces pombe J. Biol. Chem., January 7, 2005; 280(1): 408 - 417. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. J. Davison, B. L. Trus, N. Cheng, A. C. Steven, M. S. Watson, C. Cunningham, R.-M. L. Deuff, and T. Renault A novel class of herpesvirus with bivalve hosts J. Gen. Virol., January 1, 2005; 86(1): 41 - 53. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. I. Pyatkov, I. R. Arkhipova, N. V. Malkova, D. J. Finnegan, and M. B. Evgen'ev Reverse transcriptase and endonuclease activities encoded by Penelope-like retroelements PNAS, October 12, 2004; 101(41): 14719 - 14724. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. G. Beloglazova, O. O. Kirpota, K. V. Starostin, A. A. Ishchenko, V. I. Yamkovoy, D. O. Zharkov, K. T. Douglas, and G. A. Nevinsky Thermodynamic, kinetic and structural basis for recognition and repair of abasic sites in DNA by apurinic/apyrimidinic endonuclease from human placenta Nucleic Acids Res., September 30, 2004; 32(17): 5134 - 5146. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. P. Shanahan, M. A. Garcia, S. Jones, and J. M. Thornton Identifying DNA-binding proteins using structural motifs and the electrostatic potential Nucleic Acids Res., September 8, 2004; 32(16): 4732 - 4741. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Napoli, A. Valenti, V. Salerno, M. Nadal, F. Garnier, M. Rossi, and M. Ciaramella Reverse Gyrase Recruitment to DNA after UV Light Irradiation in Sulfolobus solfataricus J. Biol. Chem., August 6, 2004; 279(32): 33192 - 33198. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
O. Yildiz, H. Kearney, B. C. Kramer, and J. J. Sekelsky Mutational Analysis of the Drosophila DNA Repair and Recombination Gene mei-9 Genetics, May 1, 2004; 167(1): 263 - 273. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Liveris, V. Mulay, and I. Schwartz Functional Properties of Borrelia burgdorferi recA J. Bacteriol., April 15, 2004; 186(8): 2275 - 2280. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Constantinesco, P. Forterre, E. V. Koonin, L. Aravind, and C. Elie A bipolar DNA helicase gene, herA, clusters with rad50, mre11 and nurA genes in thermophilic archaea Nucleic Acids Res., February 27, 2004; 32(4): 1439 - 1447. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Wang, J. Guan, B. Hu, R. S. Weiss, G. Iliakis, and Y. Wang Involvement of Hus1 in the chain elongation step of DNA replication after exposure to camptothecin or ionizing radiation Nucleic Acids Res., February 3, 2004; 32(2): 767 - 775. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Ribar, T. Izumi, and S. Mitra The major role of human AP-endonuclease homolog Apn2 in repair of abasic sites in Schizosaccharomyces pombe Nucleic Acids Res., January 2, 2004; 32(1): 115 - 126. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Rodriguez, X. Yu, J. Chen, and Z. Songyang Phosphopeptide Binding Specificities of BRCA1 COOH-terminal (BRCT) Domains J. Biol. Chem., December 26, 2003; 278(52): 52914 - 52918. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Gao, X.-B. Chen, and C. H. McGowan Mus81 Endonuclease Localizes to Nucleoli and to Regions of DNA Damage in Human S-phase Cells Mol. Biol. Cell, December 1, 2003; 14(12): 4826 - 4834. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. A. Worthey, A. Schnaufer, I. S. Mian, K. Stuart, and R. Salavati Comparative analysis of editosome proteins in trypanosomatids Nucleic Acids Res., November 15, 2003; 31(22): 6392 - 6408. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. Salerno, A. Napoli, M. F. White, M. Rossi, and M. Ciaramella Transcriptional response to DNA damage in the archaeon Sulfolobus solfataricus Nucleic Acids Res., November 1, 2003; 31(21): 6127 - 6138. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Moe, J. Ringvoll, L. M. Nordstrand, L. Eide, M. Bjoras, E. Seeberg, T. Rognes, and A. Klungland Incision at hypoxanthine residues in DNA by a mammalian homologue of the Escherichia coli antimutator enzyme endonuclease V Nucleic Acids Res., July 15, 2003; 31(14): 3893 - 3900. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Lambert, S. J. Mason, L. J. Barber, J. A. Hartley, J. A. Pearce, A. M. Carr, and P. J. McHugh Schizosaccharomyces pombe Checkpoint Response to DNA Interstrand Cross-Links Mol. Cell. Biol., July 1, 2003; 23(13): 4728 - 4737. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Ogrunc and A. Sancar Identification and Characterization of Human MUS81-MMS4 Structure-specific Endonuclease J. Biol. Chem., June 6, 2003; 278(24): 21715 - 21720. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Higashibata, H. Kikuchi, Y. Kawarabayasi, and I. Matsui Helicase and Nuclease Activities of Hyperthermophile Pyrococcus horikoshii Dna2 Inhibited by Substrates with RNA Segments at 5'-End J. Biol. Chem., April 25, 2003; 278(18): 15983 - 15990. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Alani, J. Y. Lee, M. J. Schofield, A. W. Kijas, P. Hsieh, and W. Yang Crystal Structure and Biochemical Analysis of the MutS{middle dot}ADP{middle dot}Beryllium Fluoride Complex Suggests a Conserved Mechanism for ATP Interactions in Mismatch Repair J. Biol. Chem., April 25, 2003; 278(18): 16088 - 16094. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. F. Loughlin, F. M. Barnard, D. Jenkins, G. J. Sharples, and P. J. Jenks Helicobacter pylori Mutants Defective in RuvC Holliday Junction Resolvase Display Reduced Macrophage Survival and Spontaneous Clearance from the Murine Gastric Mucosa Infect. Immun., April 1, 2003; 71(4): 2022 - 2031. [Abstract] [Full Text]
|
|
|
|
|
|
M. Hori, S. Yonei, H. Sugiyama, K. Kino, K. Yamamoto, and Q.-M. Zhang Identification of high excision capacity for 5-hydroxymethyluracil mispaired with guanine in DNA of Escherichia coli MutM, Nei and Nth DNA glycosylases Nucleic Acids Res., February 15, 2003; 31(4): 1191 - 1196. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Defais, E. Phez, and N. P. Johnson Kinetic Mechanism for the Formation of the Presynaptic Complex of the Bacterial Recombinase RecA J. Biol. Chem., January 31, 2003; 278(6): 3545 - 3551. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Duncan, S. C. Trewick, P. Koivisto, P. A. Bates, T. Lindahl, and B. Sedgwick Reversal of DNA alkylation damage by two human dioxygenases PNAS, December 24, 2002; 99(26): 16660 - 16665. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. de Jager, C. Wyman, D. C. van Gent, and R. Kanaar DNA end-binding specificity of human Rad50/Mre11 is influenced by ATP Nucleic Acids Res., October 15, 2002; 30(20): 4425 - 4431. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Shor, S. Gangloff, M. Wagner, J. Weinstein, G. Price, and R. Rothstein Mutations in Homologous Recombination Genes Rescue top3 Slow Growth in Saccharomyces cerevisiae Genetics, October 1, 2002; 162(2): 647 - 662. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. P. Robinson, R. McCulloch, C. Conway, A. Browitt, and J. D. Barry Inactivation of Mre11 Does Not Affect VSG Gene Duplication Mediated by Homologous Recombination in Trypanosoma brucei J. Biol. Chem., July 12, 2002; 277(29): 26185 - 26193. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Hirai and H.-G. Wang A Role of the C-terminal Region of Human Rad9 (hRad9) in Nuclear Transport of the hRad9 Checkpoint Complex J. Biol. Chem., July 5, 2002; 277(28): 25722 - 25727. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. E. A. Verhoeven, M. van Kesteren, J. J. Turner, G. A. van der Marel, J. H. van Boom, G. F. Moolenaar, and N. Goosen The C-terminal region of Escherichia coli UvrC contributes to the flexibility of the UvrABC nucleotide excision repair system Nucleic Acids Res., June 1, 2002; 30(11): 2492 - 2500. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. Anantharaman, E. V. Koonin, and L. Aravind Comparative genomics and evolution of proteins involved in RNA metabolism Nucleic Acids Res., April 1, 2002; 30(7): 1427 - 1464. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 W. S. Joo, P. D. Jeffrey, S. B. Cantor, M. S. Finnin, D. M. Livingston, and N. P. Pavletich Structure of the 53BP1 BRCT region bound to p53 and its comparison to the Brca1 BRCT structure Genes & Dev., March 1, 2002; 16(5): 583 - 593. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. F. Moolenaar, S. van Rossum-Fikkert, M. van Kesteren, and N. Goosen Cho, a second endonuclease involved in Escherichia coli nucleotide excision repair PNAS, January 24, 2002; (2002) 32584099. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. S. Makarova, L. Aravind, N. V. Grishin, I. B. Rogozin, and E. V. Koonin A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis Nucleic Acids Res., January 15, 2002; 30(2): 482 - 496. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Narumi, K. Satoh, M. Kikuchi, T. Funayama, T. Yanagisawa, Y. Kobayashi, H. Watanabe, and K. Yamamoto The LexA Protein from Deinococcus radiodurans Is Not Involved in RecA Induction following gamma Irradiation J. Bacteriol., December 1, 2001; 183(23): 6951 - 6956. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. M. Iyer, L. Aravind, and E. V. Koonin Common Origin of Four Diverse Families of Large Eukaryotic DNA Viruses J. Virol., December 1, 2001; 75(23): 11720 - 11734. [Abstract] [Full Text]
|
|
|
|
|
|
R. Kaur, C. F. Kostrub, and T. Enoch Structure-Function Analysis of Fission Yeast Hus1-Rad1-Rad9 Checkpoint Complex Mol. Biol. Cell, December 1, 2001; 12(12): 3744 - 3758. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. W. Chang and D. A. Julin Structure and Function of the Escherichia coli RecE Protein, a Member of the RecB Nuclease Domain Family J. Biol. Chem., November 30, 2001; 276(49): 46004 - 46010. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Kondo, T. Wakayama, T. Naiki, K. Matsumoto, and K. Sugimoto Recruitment of Mec1 and Ddc1 Checkpoint Proteins to Double-Strand Breaks Through Distinct Mechanisms Science, October 26, 2001; 294(5543): 867 - 870. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. N. Hanna, R. J. Ferguson, Y.-H. Li, and D. G. Cvitkovitch uvrA Is an Acid-Inducible Gene Involved in the Adaptive Response to Low pH in Streptococcus mutans J. Bacteriol., October 15, 2001; 183(20): 5964 - 5973. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. Kaliraman, J. R. Mullen, W. M. Fricke, S. A. Bastin-Shanower, and S. J. Brill Functional overlap between Sgs1-Top3 and the Mms4-Mus81 endonuclease Genes & Dev., October 15, 2001; 15(20): 2730 - 2740. |