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Nucleic Acids Research, Vol 27, Issue 5 1223-1242, Copyright © 1999 by Oxford University Press


REVIEWS

Conserved domains in DNA repair proteins and evolution of repair systems

L Aravind, DR Walker and EV Koonin
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.

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.
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Nucleic Acids Res., July 15, 2001; 29(14): 3069 - 3079.
[Abstract] [Full Text] [PDF]


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A. Quiberoni, I. Biswas, M. El Karoui, L. Rezaiki, P. Tailliez, and A. Gruss
In Vivo Evidence for Two Active Nuclease Motifs in the Double-Strand Break Repair Enzyme RexAB of Lactococcus lactis
J. Bacteriol., July 1, 2001; 183(13): 4071 - 4078.
[Abstract] [Full Text] [PDF]


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Microbiol. Mol. Biol. Rev.Home page
K. S. Makarova, L. Aravind, Y. I. Wolf, R. L. Tatusov, K. W. Minton, E. V. Koonin, and M. J. Daly
Genome of the Extremely Radiation-Resistant Bacterium Deinococcus radiodurans Viewed from the Perspective of Comparative Genomics
Microbiol. Mol. Biol. Rev., March 1, 2001; 65(1): 44 - 79.
[Abstract] [Full Text] [PDF]


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ScienceHome page
R. D. Wood, M. Mitchell, J. Sgouros, and T. Lindahl
Human DNA Repair Genes
Science, February 16, 2001; 291(5507): 1284 - 1289.
[Abstract] [Full Text]


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Nucleic Acids ResHome page
P.-H. L. Gaillard and R. D. Wood
Activity of individual ERCC1 and XPF subunits in DNA nucleotide excision repair
Nucleic Acids Res., February 15, 2001; 29(4): 872 - 879.
[Abstract] [Full Text] [PDF]


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Genome ResHome page
E. V. Koonin, Y. I. Wolf, and L. Aravind
Prediction of the Archaeal Exosome and Its Connections with the Proteasome and the Translation and Transcription Machineries by a Comparative-Genomic Approach
Genome Res., February 1, 2001; 11(2): 240 - 252.
[Abstract] [Full Text]


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Mol. Cell. Biol.Home page
M. N. Boddy, A. Lopez-Girona, P. Shanahan, H. Interthal, W.-D. Heyer, and P. Russell
Damage Tolerance Protein Mus81 Associates with the FHA1 Domain of Checkpoint Kinase Cds1
Mol. Cell. Biol., December 1, 2000; 20(23): 8758 - 8766.
[Abstract] [Full Text]


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M.-J. Lombardo and S. M. Rosenberg
radC102 of Escherichia coli Is an Allele of recG
J. Bacteriol., November 15, 2000; 182(22): 6287 - 6291.
[Abstract] [Full Text]


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Nucleic Acids ResHome page
H. Daiyasu, K. Komori, S. Sakae, Y. Ishino, and H. Toh
Hjc resolvase is a distantly related member of the type II restriction endonuclease family
Nucleic Acids Res., November 15, 2000; 28(22): 4540 - 4543.
[Abstract] [Full Text] [PDF]


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K.-P. Hopfner, A. Karcher, D. Shin, C. Fairley, J. A. Tainer, and J. P. Carney
Mre11 and Rad50 from Pyrococcus furiosus: Cloning and Biochemical Characterization Reveal an Evolutionarily Conserved Multiprotein Machine
J. Bacteriol., November 1, 2000; 182(21): 6036 - 6041.
[Abstract] [Full Text]


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Genes Dev.Home page
C. D. Kaplan, J. R. Morris, C.-t. Wu, and F. Winston
Spt5 and Spt6 are associated with active transcription and have characteristics of general elongation factors in D. melanogaster
Genes & Dev., October 15, 2000; 14(20): 2623 - 2634.
[Abstract] [Full Text]


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Genes Dev.Home page
T.-F. Mah, K. Kuznedelov, A. Mushegian, K. Severinov, and J. Greenblatt
The alpha subunit of E. coli RNA polymerase activates RNA binding by NusA
Genes & Dev., October 15, 2000; 14(20): 2664 - 2675.
[Abstract] [Full Text]


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Nucleic Acids ResHome page
L. Aravind, K. S. Makarova, and E. V. Koonin
SURVEY AND SUMMARY: Holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories
Nucleic Acids Res., September 15, 2000; 28(18): 3417 - 3432.
[Abstract] [Full Text] [PDF]


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Nucleic Acids ResHome page
A. F. Neuwald and A. Poleksic
PSI-BLAST searches using hidden Markov models of structural repeats: prediction of an unusual sliding DNA clamp and of {beta}-propellers in UV-damaged DNA-binding protein
Nucleic Acids Res., September 15, 2000; 28(18): 3570 - 3580.
[Abstract] [Full Text] [PDF]


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Genes Dev.Home page
S. Dinglay, S. C. Trewick, T. Lindahl, and B. Sedgwick
Defective processing of methylated single-stranded DNA by E. coli alkB mutants
Genes & Dev., August 15, 2000; 14(16): 2097 - 2105.
[Abstract] [Full Text]


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Nucleic Acids ResHome page
K.-H. Lee, D. W. Kim, S.-H. Bae, J.-A. Kim, G.-H. Ryu, Y.-N. Kwon, K.-A. Kim, H.-S. Koo, and Y.-S. Seo
The endonuclease activity of the yeast Dna2 enzyme is essential in vivo
Nucleic Acids Res., August 1, 2000; 28(15): 2873 - 2881.
[Abstract] [Full Text] [PDF]


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Genome ResHome page
L. Aravind
Guilt by Association: Contextual Information in Genome Analysis
Genome Res., August 1, 2000; 10(8): 1074 - 1077.
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R. S. Weiss, T. Enoch, and P. Leder
Inactivation of mouse Hus1 results in genomic instability and impaired responses to genotoxic stress
Genes & Dev., August 1, 2000; 14(15): 1886 - 1898.
[Abstract] [Full Text]


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Nucleic Acids ResHome page
C. Venclovas and M. P. Thelen
Structure-based predictions of Rad1, Rad9, Hus1 and Rad17 participation in sliding clamp and clamp-loading complexes
Nucleic Acids Res., July 1, 2000; 28(13): 2481 - 2493.
[Abstract] [Full Text] [PDF]


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A.-S. Gourves, N. T. Le Gac, G. Villani, P. E. Boehmer, and N. P. Johnson
Equilibrium Binding of Single-stranded DNA with Herpes Simplex Virus Type I-coded Single-stranded DNA-binding Protein, ICP8
J. Biol. Chem., April 6, 2000; 275(15): 10864 - 10869.
[Abstract] [Full Text] [PDF]


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Nucleic Acids ResHome page
C. Saguez, G. Lecellier, and F. Koll
Intronic GIY-YIG endonuclease gene in the mitochondrial genome of Podospora curvicolla: evidence for mobility
Nucleic Acids Res., March 15, 2000; 28(6): 1299 - 1306.
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E. E. A. Verhoeven, M. van Kesteren, G. F. Moolenaar, R. Visse, and N. Goosen
Catalytic Sites for 3' and 5' Incision of Escherichia coli Nucleotide Excision Repair Are Both Located in UvrC
J. Biol. Chem., February 18, 2000; 275(7): 5120 - 5123.
[Abstract] [Full Text] [PDF]


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T. Caspari, M. Dahlen, G. Kanter-Smoler, H. D. Lindsay, K. Hofmann, K. Papadimitriou, P. Sunnerhagen, and A. M. Carr
Characterization of Schizosaccharomyces pombe Hus1: a PCNA-Related Protein That Associates with Rad1 and Rad9
Mol. Cell. Biol., February 15, 2000; 20(4): 1254 - 1262.
[Abstract] [Full Text]


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Q. Liu, W.-c. Choe, and J. L. Campbell
Identification of the Xenopus laevis Homolog of Saccharomyces cerevisiae DNA2 and Its Role in DNA Replication
J. Biol. Chem., January 21, 2000; 275(3): 1615 - 1624.
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J. Wang, R. Chen, and D. A. Julin
A Single Nuclease Active Site of the Escherichia coli RecBCD Enzyme Catalyzes Single-stranded DNA Degradation in Both Directions
J. Biol. Chem., January 7, 2000; 275(1): 507 - 513.
[Abstract] [Full Text] [PDF]


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Cold Spring Harb Symp Quant BiolHome page
K.-P. HOPFNER, S.S. PARIKH, and J.A. TAINER
Envisioning the Fourth Dimension of the Genetic Code: The Structural Biology of Macromolecular Recognition and Conformational Switching in DNA Repair
Cold Spring Harb Symp Quant Biol, January 1, 2000; 65(0): 113 - 126.
[Abstract] [PDF]



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