Conserved domains in DNA repair proteins and evolution of repair systems

Nucleic Acids Research

Volumn 27, Issue 5, 1999, Pages 1223-1242

  Aravind, L ^a,b   Walker, D Roland ^a,c   Koonin, Eugene V ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b TEXAS A AND M UNIVERSITY   (United States)

^c JOHNS HOPKINS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLINE; DNA BINDING PROTEIN; HELICASE; HELIX LOOP HELIX PROTEIN; NUCLEASE; RECA PROTEIN;

AMINO ACID SEQUENCE; ARCHAEBACTERIUM; ARTICLE; CHROMATIN STRUCTURE; DNA REPAIR; ESCHERICHIA COLI; EVOLUTION; GENETIC CONSERVATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; SACCHAROMYCES CEREVISIAE;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; DNA REPAIR; DNA-BINDING PROTEINS; EVOLUTION, MOLECULAR; FUNGAL PROTEINS; GENE TRANSFER, HORIZONTAL; MOLECULAR SEQUENCE DATA; SEQUENCE HOMOLOGY, AMINO ACID;

ARCHAEA; BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; EUKARYOTA; NEGIBACTERIA; SACCHAROMYCES CEREVISIAE;

EID: 0033105094     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/27.5.1223     Document Type: Article

References (153)

1. Friedberg, E.C., Walker, G.C. and Siede, W. (1995) DNA Repair and Mutagenesis. ASM Press, Washington, DC.
2. Koonin, E.V., Mushegian, A.R. and Rudd, K.E. (1996) Curr. Biol., 6, 404-416.
3. Hanawalt, P.C. (1995) Mutat. Res., 336, 101-113.
4. Sancar, A. (1996) Annu. Rev. Biochem., 65, 43-81.
5. Modrich, P. and Lahue, R. (1996) Annu. Rev. Biochem., 65, 101-133.
6. Wood, R.D. (1996) Annu. Rev. Biochem., 65, 135-167.
7. Friedberg, E.C. (1996) Annu. Rev. Biochem., 65, 15-42.
8. Minnick, D.T. and Kunkel, T.A. (1996) Cancer Surv., 28, 3-20.
9. Wood, R. (1997) J. Biol. Chem., 272, 23465-23468.
10. Parikh, S.S., Mol, C.D. and Tainer, J.A. (1997) Structure, 5, 1543-1550.
11. Walker, D.R. and Koonin, E.V. (1997) ISMB, 5, 333-339.
12. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang,J., Zang,Z., Miller,W. and Lipman, D.J. (1997) Nucleic Acids Res., 25, 3389-3402.
13. Wootton, J.C. and Federhen, S. (1996) Methods Enzymol., 266, 554-571.
14. Tatusov, R.L., Altschul, S.F. and Koonin, E.V. (1994) Proc. Natl Acad. Sci. USA, 91, 12091-12095.
15. Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) Nucleic Acids Res., 22, 4673-4680.
16. Schuler, G.D., Altschul, S.F. and Lipman, D.J. (1991) Proteins, 9, 180-190.
17. Neuwald, A.F., Liu, J.S. and Lawrence, C.E. (1995) Protein Sci., 4, 1618-1632.
18. Rost, B. and Sander, C. (1994) Proteins, 19, 55-72.
19. Rost, B., Schneider, R. and Sander, C. (1997) J. Mol. Biol., 270, 471-480.
20. Fitch, W.M. (1970) System. Zool., 19, 99-106.
21. Fitch, W.M. (1995) Philos. Trans. R. Soc. Lond. B. Biol. Sci., 349, 93-102.
22. Tatusov, R.L., Koonin, E.V. and Lipman, D.J. (1997) Science, 278, 631-637.
23. Tatusov, R.L., Mushegian, A.R., Bork, P. Brown, N.P. Hayes, W.S., Borodovsky, M., Rudd, K.E. and Kooni, E.V. (1996) Curr. Biol., 6, 279-291.
24. Henikoff, S., Greene, E.A., Pietrokovski, S., Bork, P., Attwood, T.K. and Hood, L. (1997) Science, 278, 609-614.
25. Doolittle, R.F. (1995) Annu. Rev. Biochem., 64, 287-314.
26. Doolittle, R.F. and Bork, P. (1993) Sci. Am., 269, 50-56.
27. Harris, P.V., Mazina, O.M., Leonhardt, E.A., Case, R.B., Boyd, J.B. and Burtis, K.C. (1996) Mol. Cell Biol., 16, 5764-5771.
28. Gorbalenya, A.E. and Koonin, E.V. (1990) J. Mol. Biol. 213, 583-591.
29. Gorbalenya, A.E. and Koonin, E.V. (1993) Curr. Opin. Struct. Biol., 3, 419-429.
30. Braithwaite, D.K. and Ito, J. (1993) Nucleic Acids Res., 21, 787-802.
31. Doolittle, R.E. Johnson, M.S., Husain, I., Van Houten, B., Thomas, D.C. and Sancar, A. (1986) Nature, 323, 451-453.
32. Moser, M.J., Holley, W.R., Chanerjee, A. and Mian, I.S. (1997) Nucleic Acids Res., 25, 5110-5118.
33. Lieber, M.R. (1997) Bioessays, 19, 233-240.
34. Aravind, L. and Koonin, E.V. (1998) Nucleic Acids Res., 26, 3746-3752.
35. Ramotar, D. (1997) Biochem. Cell Biol., 75, 327-336.
36. Carrell, H.L. Glusker, J.P., Burger, V. Manfre, F., Tritsch, D. and Biellmann, J.F. (1989) Proc. Natl Acad. Sci. USA, 86, 4440-4444.
37. Lavie, A., Allen, K.N., Petsko, G.A. and Ringe, D. (1994) Biochemistry, 33, 5469-5480.
38. Holm, L. and Sander, C. (1997) Proteins, 28, 72-82.
39. Yajima, H., Takao, M. Yasuhira, S., Zhao, J.H., Ishii, C., Inoue, H. and Yasui, A. (1995) EMBO J., 14, 2393-2399.
40. Takao, M., Yonemasu, R., Yamamoto, K. and Yasui, A. (1996) Nucleic Acids Res., 24, 1267-1271.
41. Lin, J.J., Phillips, A.M., Hearst, J.E. and Sancar, A. (1992) J. Biol. Chem., 267, 17693-17700.
42. Lin, J.J. and Sancar, A. (1992) J. Biol. Chem., 267, 17688-17692.
43. Derbyshire, V., Kowalski, J.C., Dansereau, J.T. Hauer, C.R. and Belfort, M. (1997) J. Mol. Biol., 265, 494-506.
44. Sijbers, A.M., van der Spek, P.J., Odijk, H., van den Berg, J., van Duin, M., Westerveld, A., Jaspers, N.G., Bootsma, D. and Hoeijmakers, J.H (1996) Nucleic Acids Res., 24, 3370-3380.
45. Doherty, A.J., Serpell, L.C. and Ponting, C.P. (1996) Nucleic Acids Res., 24, 2488-2497.
46. Tomkinson, A.E., Bardwell, A.J., Tappe, N., Ramos, W. and Friedberg, E.C. (1994) Biochemistry, 33, 5305-5311.
47. Yu. M., Souaya, J. and Julin, D.A. (1998) Proc. Natl Acad. Sci. USA, 95, 981-986.
48. Haijema, B.J., Venema, G. and Kooistra, J. (1996) J. Bacteriol., 178, 5086-5091.
49. Champoux, J.J. (1998) Prog. Nucleic Acids Res. Mol. Biol., 60, 111-132.
50. Evans, B.R., Chen, J.W., Parsons, R.L., Bauer, T.K., Teplow, D.B. and Jayaram, M. (1990) J. Biol. Chem., 265, 18504-18510.
51. Tirumalai, R.S., Healey, E. and Landy, A. (1997) Proc. Natl Acad. Sci. USA, 94, 6104-6109.
52. Ilyina, T.V. and Koonin, E.V. (1992) Nucleic Acids Res., 20, 3279-3285.
53. Thayer, M.M., Ahern, H., Xing, D., Cunningham, R.P. and Tainer, J.A. (1995) EMBO J., 14, 4108-4120.
54. Morozov, V., Mushegian, A.R., Koonin, E.V. and Bork, P. (1997) Trends Biochem. Sci., 22, 417-418.
55. Moolenaar, G.F., Franken, K.L., Dijkstra, D.M., Thomas-Oates, J.E., Visse, R., van de Putte, P. and Goosen, N. (1995) J. Biol. Chem., 270, 30508-30515.
56. Callebaut, I. and Mornon, J.P. (1997) FEBS Lett., 400, 25-30.
57. Bork, P., Hofmann, K., Bucher, P., Neuwald, A.F., Altschul, S.F. and Koonin, E.V. (1997) FASEB J., 11, 68-76.
58. Masson, M., Niedergang, C., Schreiber, V., Muller, S., Menissier-de Murcia, J. and de Murcia, G. (1998) Mol. Cell Biol., 18, 3563-3571.
59. Tomkinson, A.E. and Mackey, Z.B. (1998) Mutat Res., 407, 1-9.
60. Yu, X., Wu, L.C., Bowcock, A.M., Aronheim, A. and Baer, R. (1998) J. Biol. Chem., 273, 25388-25392.
61. Hofmann, K. and Bucher, P. (1995) Trends Biochem. Sci., 20, 347-349.
62. Ohta, K., Nicolas, A., Furuse, M., Nabetani, A., Ogawa, H. and Shibata, T. (1998) Proc. Natl Acad. Sci. USA, 95, 646-651.
63. Sun, Z., Hsiao, J., Fay, D.S. and Stern, D.F. (1998) Science, 281, 272-274.
64. Aravind, L. and Koonin, E.V. (1998) Trends Biochem. Sci., 23, 284-286.
65. Jonsson, Z.O. and Hubscher, U. (1997) Bioessays, 19, 967-975.
66. Jonsson, Z.O., Hindges, R. and Hubscher, U. (1998) EMBO J., 17, 2412-2425.
67. Krishna, T.S., Kong, X.P., Gary, S., Burgers, P.M. and Kuriyan, J. (1994) Cell, 79, 1233-1243.
68. Thelen, M.P., Onel, K. and Holloman, W.K. (1994) J. Biol. Chem., 269, 747-754.
69. Parker, A.E., Van de Weyer, I., Laus, M.C., Oostveen, I., Yon, J., Verhasselt, P. and Luyten, W. (1998) J. Biol. Chem., 273, 18332-18339.
70. Kong, X.P., Onrust, R., O'Donnell, M. and Kuriyan, J. (1992) Cell, 69, 425-437.
71. Griffiths, D.J., Barbet, N.C. McCready, S., Lehmann, A.R. and Carr, A.M. (1995) EMBO J., 14, 5812-5823.
72. Oku, T., Ikeda, S., Sasaki, H., Fukuda, K., Morioka, H., Ohtsuka, E., Yoshikawa, H. and Tsurimoto, T. (1998) Genet Cells, 3, 357-369.
73. Roca, A.I. and Cox, M.M. (1997) Prog. Nucleic Acids Res. Mol. Biol., 56, 129-223.
74. Bianco, P.R., Tracy, R.B. and Kowalczykowski, S.C. (1998) Front. Biosci., 3, d570-d603.
75. Sargentini, N.J. and Smith, K.C. (1986) Radiat. Res., 107, 58-72.
76. Song, Y. and Sargentini, N.J. (1996) J. Bacteriol., 178, 5045-5048.
77. Koonin, E.V., Tatusov, R.L. and Rudd, K.E. (1996) In Neidhardt, F.C., III, R.C., Ingraham, J.L., Lin, E.C.C., Low, K.B., Magasanik, B., Resnikoff, W.S., Riley, M., Schaechter, M. and Umbarger, H.E. (eds), Escherichia coli and Salmonella typhimurium. ASM Press, Washington, DC, Vol. 2, pp. 2203-2217.
78. Harrington, J.J. and Lieber, M.R. (1994) Genes Dev., 8, 1344-1355.
79. Harrington, J.J. and Lieber, M.R. (1994) EMBO J., 13, 1235-1246.
80. Shen, B., Qiu, J., Hosfield, D. and Tainer, J.A. (1998) Trends Biochem. Sci., 23, 171-173.
81. Sharma, R.C. and Smith, K.C. (1987) J. Bacteriol., 169, 4559-4564.
82. Peterson, C.L. (1994) Cell, 79, 389-392.
83. Michaelis, C., Ciosk, R. and Nasmyth, K. (1997) Cell, 91, 35-45.
84. Koonin, E.V. (1994) Protein Sci., 3, 356-358.
85. Sharples, G.J. and Leach, D.R. (1995) Mol. Microbiol., 17, 1215-1217.
86. Connelly, J.C. Kirkham, L.A. and Leach, D.R.F. (1998) Proc. Natl Acad. Sci. USA, 95, 7969-7974.
87. West, S.C. (1997) Annu. Rev. Genet., 31, 213-244.
88. van Gool, A.J., Shah, R., Mezard, C. and West, S.C. (1998) EMBO J., 17, 1838-1845.
89. Eisen, J.A., Kaiser, D. and Myers, R.M. (1997) Nat. Med., 3, 1076-1078.
90. Bergerat, A., de Massy, B., Gadelle, D., Varoutas, P.C., Nicolas, A. and Forterre, P. (1997) Nature, 386, 414-417.
91. Mushegian, A.R., Bassett, D.E., Jr, Boguski, M.S., Bork, P. and Koonin, E.V. (1997) Proc. Natl Acad. Sci. USA, 94, 5831-5836.
92. Reenan, R.A. and Kolodner, R.D. (1992) Genetics, 132, 975-985.
93. Hanada, K., Ukita, T., Kohno, Y., Saito, K., Kato, J. and Ikeda, H. (1997) Proc. Natl Acad. Sci. USA, 94, 3860-3865.
94. Davey, S., Han, C.S., Ramer, S.A., Klassen, J.C., Jacobson, A., Eisenberger, A., Hopkins, K.M., Lieberman, H.B. and Freyer, G.A. (1998) Mol. Cell Biol., 18, 2721-2728.
95. Ellis, N.A., Groden, J., Ye, T.Z., Straughen, J., Lennon, D.J., Ciocci, S., Proytcheva, M. and German, J. (1995) Cell, 83, 655-666.
96. Lombard, D.B. and Guarente, L. (1996) Trends Genet., 12, 283-286.
97. Aravind, L. and Koonin, E.V. (1998) Trends Biochem. Sci., 23, 17-19.
98. Dianov, G. and Lindahl, T. (1994) Curr. Biol., 4, 1069-1076.
99. Dianov, G., Sedgwick, B., Daly, G., Olsson, M., Lovett, S. and Lindahl, T. (1994) Nucleic Acids Res., 22, 993-998.
100. Clark, A.J. (1991) Biochimie, 73, 523-532.
101. Webb, B.L. Cox, M.M. and Inman, R.B. (1997) Cell, 91, 347-356.
102. Aravind, L., Leipe, D.D. and Koonin, E.V. (1998) Nucleic Acids Res., 26, 4205-4213.
103. Little, J.W. (1993) J. Bacteriol., 175, 4943-4950.
104. Smith, B.T. and Walker, G.C. (1998) Genetics, 148, 1599-1610.
105. Selby, C.P. and Sancar, A. (1993) Science, 260, 53-58.
106. Selby, C.P. and Sancar, A. (1995) J. Biol. Chem., 270, 4882-4889.
107. Palmer, B.R. and Marinus, M.G. (1994) Gene, 143, 1-12.
108. Ban, C. and Yang, W. (1998) EMBO J., 17, 1526-1534.
109. Friedberg, E.C. (1991) Mol. Microbiol., 5, 2303-2310.
110. Lehmann, A.R. (1998) Bioessays, 20, 146-155.
111. Sung, P., Bailly, V., Weber, C., Thompson, L.H., Prakash, L. and Prakash, S. (1993) Nature, 365, 852-855.
112. Weeda, G., van Ham, R.C. Vermeulen, W., Bootsma, D., van der Eb, A.J. and Hoeijmakers, J.H. (1990) Cell, 62, 777-791.
113. Troelstra, C., van Gool, A., de Wit, J., Vermeulen, W., Bootsma, D. and Hoeijmakers, J.H. (1992) Cell, 71, 939-953.
114. Koonin, E.V. (1993) Nucleic Acids Res., 21, 1497.
115. Gerring, S.L., Spencer, F. and Hieter, P. (1990) EMBO J., 9, 4347-4358.
116. Poterszman, A., Lamour, V., Egly, J.M., Moras, D., Thierry, J.C. and Poch, O. (1997) Trends Biochem. Sci., 22, 418-419.
117. Eisen, J.A., Sweder, K.S. and Hanawalt, P.C. (1995) Nucleic Acids Res., 23, 2715-2723.
118. Bork, P. and Koonin, E.V. (1993) Nucleic Acids Res., 21, 751-752.
119. Muzzin, O., Campbell, E.A., Xia, L. Severinova, E., Darst, S.A. and Severinov, K. (1998) J. Biol. Chem., 273, 15157-15161.
120. Johnson, R.E., Henderson, S.T., Petes, T.D., Prakash, S., Bankmann, M. and Prakash, L. (1992) Mol. Cell Biol., 12, 3807-3818.
121. Bang, D.D., Verhage, R., Goosen, N., Brouwer, J. and van de Putte, P. (1992) Nucleic Acids Res., 20, 3925-3931.
122. Habraken, Y., Sung, P., Prakash, L. and Prakash, S. (1994) J. Biol. Chem., 269, 31342-31345.
123. Rapic Otrin, V., Kuraoka, I., Nardo, T., McLenigan, M., Eker, A.P., Stefanini, M., Levine, A.S. and Wood, R.D. (1998) Mol. Cell Biol., 18, 3182-3190.
124. Wolter, R., Siede, W. and Brendel, M. (1996) Mol. Gen. Genet., 250, 162-168.
125. Aravind, L. (1998) Silico Biol., 1, 8.
126. Borden, K.L. and Freemont, P.S. (1996) Curr. Opin. Struct. Biol., 6, 395-401.
127. Henning, K.A., Li, L., Iyer, N., McDaniel, L.D., Reagan, M.S., Legerski, R., Schultz, R.A., Stefanini, M., Lehmann, A.R., Mayne, L.V. et al. (1995) Cell, 82, 555-564.
128. Masutani, C., Sugasawa, K., Yanagisawa, J., Sonoyama, J., Ui, M., Enomoto, T., Takio, K., Tanaka, K., van der Spek, P.J., Bootsma, D. et al. (1994) EMBO J., 13, 1831-1843.
129. Allen, J.B., Zhou, Z., Siede, W., Friedberg, E.C. and Elledge, S.J. (1994) Genes Dev., 8, 2401-2415.
130. Zhou, Z. and Elledge, S.J. (1993) Cell, 75, 1119-1127.
131. Carr, A.M. (1997) Curr. Opin. Genet. Dev., 7, 93-98.
132. Sherr, C.J. (1996) Science, 274, 1672-1677.
133. Jeffrey, P.D., Gorina, S. and Pavletich, N.P. (1995) Science, 267, 1498-1502.
134. Gibson, T.J., Thompson, J.D., Blocker, A. and Kouzarides, T. (1994) Nucleic Acids Res., 22, 946-952.
135. Chow, T.Y., Perkins, E.L. and Resnick, M.A. (1992) Nucleic Acids Res., 20, 5215-5221.
136. Moore, P.D., Simon, J.R., Wallace, L.J. and Chow, T.Y. (1993) Curr. Genet. 23, 1-8.
137. Bailly, V., Lauder, S., Prakash, S. and Prakash, L. (1997) J. Biol. Chem., 272, 23360-23365.
138. Koomey, M. (1997) Curr. Biol., 7, R538-R540.
139. Bonner, C.A., Hays, S., McEntee, K. and Goodman, M.F (1990) Proc. Natl Acad. Sci. USA, 87, 7663-7667.
140. Lawrence, C.W. and Hinkle, D.C. (1996) Cancer Surv., 28, 21-31.
141. Hearst, J.E. (1995) Science, 268, 1858-1859.
142. Lamond, A.I. and Earnshaw, W.C. (1998) Science, 280, 547-553.
143. Scully, R., Chen, J., Plug, A., Xiao, Y., Weaver, D., Feunteun, J., Ashley, T. and Livingston, D.M. (1997) Cell, 88, 265-275.
144. Anderson, S.F., Schlegel, B.P., Nakajima, T., Wolpin, E.S. and Parvin, J.D. (1998) Nature Genet., 19, 254-256.
145. Chapman, M.S. and Verma, I.M. (1996) Nature, 382, 678-679.
146. Osada, M., Ohba, M., Kawahara, C., Ishioka, C., Kanamaru, R., Katoh, I., Ikawa, Y., Nimura, Y., Nakagawara, A., Obinata, M. and Ikawa, S. (1998) Nat. Med., 4, 839-843.
147. Buchhop, S., Gibson, M.K., Wang, X.W., Wagner, P., Sturzbecher, H.W. and Harris, C.C. (1997) Nucleic Acids Res., 25, 3868-3874.
148. Jayaraman, L., Murthy, K.G., Zhu, C., Curran, T., Xanthoudakis, S. and Prives, C. (1997) Genes Dev., 11, 558-570.
149. Ko, L.J. and Prives, C. (1996) Genes Dev., 10, 1054-1072.
150. Feng, Q., Moran, J.V., Kazazian, H.H., Jr and Boeke, J.D. (1996) Cell, 87, 905-916.
151. Ibba, M., Bono, J.L., Rosa, P.A. and Soll, D. (1997) Proc. Natl Acad. Sci. USA, 94, 14383-14388.
152. Koonin, E.V. and Aravind, L. (1998) Curr. Biol., 8, R266-R269.
153. Mushegian, A.R. and Koonin, E.V. (1996) Proc. Natl Acad. Sci. USA, 93, 10268-10273.