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.
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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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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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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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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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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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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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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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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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L. Aravind Guilt by Association: Contextual Information in Genome Analysis Genome Res., August 1, 2000; 10(8): 1074 - 1077. [Full Text]
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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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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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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. [Abstract] [Full Text] [PDF]
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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. [Abstract] [Full Text] [PDF]
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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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 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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