DNA binding proteins: Outline of functional classification

Biomolecular Concepts

Volumn 2, Issue 4, 2011, Pages 293-303

  Zheng, Zhiming ^a,b   Wang, Ya ^a  

^a EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b SHANDONG PROVINCIAL HOSPITAL AFFILIATED TO SHANDONG UNIVERSITY   (China)

Author keywords

DNA binding protein; DNA repair; DNA replication; Ku; p53; transcription

Indexed keywords

EID: 84901628057     PISSN: 18685021     EISSN: 1868503X     Source Type: Journal    
DOI: 10.1515/bmc.2011.023     Document Type: Review

References (94)

1. Harrison SC. A structural taxonomy of DNA-binding domains. Nature 1991; 353: 715-9.
2. Wolffe AP, Tafuri S, Ranjan M, Familari M. The Y-box factors: a family of nucleic acid binding proteins conserved from Escherichia coli to man. New Biol 1992; 4: 290-8.
3. Luscombe NM, Thornton JM. Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity. J Mol Biol 2002; 320: 991-1009.
4. Boch J, Bonas U. Xanthomonas AvrBs3 family-type III effectors: discovery and function. Annu Rev Phytopathol 2010; 48: 419-36.
5. Wold MS. Replication protein A: a heterotrimeric, singlestranded DNA-binding protein required for eukaryotic DNA metabolism. Annu Rev Biochem 1997; 66: 61-92.
6. Shereda RD, Kozlov AG, Lohman TM, Cox MM, Keck JL. SSB as an organizer/mobilizer of genome maintenance complexes. Crit Rev Biochem Mol Biol 2008; 43: 289-318.
7. Latchman DS. Transcription factors: an overview. Int J Biochem Cell Biol 1997; 29: 1305-12.
8. Lee T, Young R. Transcription of eukaryotic protein-coding genes. Annu Rev Genet 2000; 34: 77-137.
9. Stegmaier P, Kel AE, Wingender E. Systematic DNA-binding domain classification of transcription factors. Genome Inform 2004; 15: 276-86.
10. Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, Barre- Dirrie A, Reuter I, Chekmenev D, Krull M, Hornischer K, Voss N, Stegmaier P, Lewicki-Potapov B, Saxel H, Kel AE, Wingender E. TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res 2006; 34: D108-10.
11. Blackwood EM, Kadonaga JT. Going the distance: a current view of enhancer action. Science 1998; 281: 60-3.
12. Read D. The power of news: the history of Reuters, 2nd ed., Oxford: Oxford University Press, 1999.
13. Matlashewski G, Lamb P, Pim D, Peacock J, Crawford L, Benchimol S. Isolation and characterization of a human p53 cDNA clone: expression of the human p53 gene. EMBO J 1984; 3: 3257-62.
14. Isobe M, Emanuel BS, Givol D, Oren M, Croce CM. Localization of gene for human p53 tumour antigen to band 17p13. Nature 1986; 320: 84-5.
15. McBride OW, Merry D, Givol D. The gene for human p53 cellular tumor antigen is located on chromosome 17 short arm (17p13). Proc Natl Acad Sci USA 1986; 83: 130-4.
16. Kern SE, Kinzler KW, Baker SJ, Nigro JM, Rotter V, Levine AJ, Friedman P, Prives C, Vogelstein B. Mutant p53 proteins bind DNA abnormally in vitro. Oncogene 1991; 6: 131-6.
17. Vousden KH, Lane DP. p53 in health and disease. Nat Rev Mol Cell Biol 2007; 8: 275-83.
18. Menendez D, Inga A, Resnick MA. The expanding universe of p53 targets. Nat Rev Cancer 2009; 9: 724-37.
19. El-Deiry WF, Kern SE, Pietenpol JA, Kinzler KW, Vogelstein B. Definition of a consensus binding site for p53. Nat Genet 1992; 1: 45-9.
20. El-Deiry WS, Tokino T, Velculescu VE, Levy DB, Parsons R, Trent JM, Lin D, Mercer WE, Kinzler KW, Vogelstein B. WAF1, a potential mediator of p53 tumor suppression. Cell 1993; 75: 817-25.
21. Harper JW, Adami GR, Wei N, Keyomarsi K, Elledge SJ. The p21 Cdk-interacting protein Cip1 is a potent inhibitor of G1 cyclin-dependent kinases. Cell 1993; 75: 805-16.
22. Venot C, Maratrat M, Dureuil C, Conseiller E, Bracco L, Debussche L. The requirement for the p53 proline-rich functional domain for mediation of apoptosis is correlated with specific PIG3 gene transactivation and with transcriptional repression. EMBO J 1998; 17: 4668-79.
23. Harms KL, Chen X. The C terminus of p53 family proteins is a cell fate determinant. Mol Cell Biol 2005; 25: 2014-30.
24. Levrero M, De Laurenzi V, Costanzo A, Gong J, Wang JY, Melino G. The p53/p63/p73 family of transcription factors: overlapping and distinct functions. J Cell Sci 2000; 113: 1661-70.
25. Alberts B, Johnson AD, Lewis JA, Raff M, Roberts K, Walter P. DNA replication mechanisms: DNA topoisomerases prevent DNA tangling during replication. In: Molecular biology of the cell, 4th ed., New York: Garland Science, Chapter 5, 2002.
26. Weigel C, Schmidt A, Ruckert B, Lurz R, Messer W. DnaA protein binding to individual DnaA boxes in the Escherichia coli replication origin, oriC. EMBO J 1997; 16: 6574-83.
27. Berg J, Tymoczko J, Stryer L, Clarke N. DNA replication of both strands proceeds rapidly from specific start sites. In: Biochemistry, 5th ed., New York: W.H. Freeman and Company, Chapter 27, Section 4, 2002.
28. Lodish HF. Molecular cell biology, 4th ed., New York: W.H. Freeman, 2000.
29. Stillman BM, De Pamphilis L. Comparison of DNA replication in cells from prokarya and eukarya. New York: Cold Spring Harbor Laboratory Press, 1996.
30. Bell SP, Dutta A. DNA replication in eukaryotic cells. Annu Rev Biochem 2002; 71: 333-74.
31. Pursell ZF, Isoz I, Lundstrom EB, Johansson E, Kunkel TA. Yeast DNA polymerase epsilon participates in leading-strand DNA replication. Science 2007; 317: 127-30.
32. McCulloch SD, Kunkel TA. The fidelity of DNA synthesis by eukaryotic replicative and translesion synthesis polymerases. Cell Res 2008; 18: 148-61.
33. Barry ER, Bell SD. DNA replication in the archaea. Microbiol Mol Biol Rev 2006; 70: 876-87.
34. Weaver JR, Kugel JF, Goodrich JA. The sequence at specific positions in the early transcribed region sets the rate of transcript synthesis by RNA polymerase II in vitro. J Biol Chem 2005; 280: 39860-9.
35. Alberts B, Johnson AD, Lewis JA, Raff M, Roberts K, Walter P. DNA replication mechanisms. In: Molecular biology of the cell, 4th ed., New York: Garland Science, 2002.
36. Wang JC. Cellular roles of DNA topoisomerases: a molecular perspective. Nat Rev Mol Cell Biol 2002; 3: 430-40.
37. Miyata T, Oyama T, Mayanagi K, Ishino S, Ishino Y, Morikawa K. The clamp-loading complex for processive DNA replication. Nat Struct Mol Biol 2004; 11: 632-6.
38. Demple B, Herman T, Chen DS. Cloning and expression of APE, the cDNA encoding the major human apurinic endonuclease: definition of a family of DNA repair enzymes. Proc Natl Acad Sci USA 1991; 88: 11450-4.
39. Liu Y, Prasad R, Beard WA, Kedar PS, Hou EW, Shock DD, Wilson SH. Coordination of steps in single-nucleotide base excision repair mediated by apurinic/apyrimidinic endonuclease 1 and DNA polymerase b. J Biol Chem 2007; 282: 13532-41.
40. Braithwaite EK, Kedar PS, Lan L, Polosina YY, Asagoshi K, Poltoratsky VP, Horton JK, Miller H, Teebor GW, Yasui A, Wilson SH. DNA polymerase lambda protects mouse fibroblasts against oxidative DNA damage and is recruited to sites of DNA damage/repair. J Biol Chem 2005; 280: 31641-7.
41. Kao GD, Jiang Z, Fernandes AM, Gupta AK, Maity A. Inhibition of phosphatidylinositol-3-OH kinase/Akt signaling impairs DNA repair in glioblastoma cells following ionizing radiation. J Biol Chem 2007; 282: 21206-12.
42. Iyer RR, Pluciennik A, Burdett V, Modrich PL. DNA mismatch repair: functions and mechanisms. Chem Rev 2006; 106: 302-23.
43. Larrea AA, Lujan SA, Kunkel TA. SnapShot: DNA mismatch repair. Cell 2010; 141: 730.e1.
44. Griffiths AJF. Introduction to genetic analysis, 9th ed., New York: W.H. Freeman and Co., 2008.
45. de Waard H, de Wit J, Andressoo J-O, van Oostrom CTM, Riis B, Weimann A, Poulsen HE, van Steeg H, Hoeijmakers JHJ, van der Horst GTJ. Different effects of CSA and CSB deficiency on sensitivity to oxidative DNA damage. Mol Cell Biol 2004; 24: 7941-8.
46. DAmours D, Jackson SP. The Mre11 complex: at the crossroads of DNA repair and checkpoint signalling. Nat Rev Mol Cell Biol 2002; 3: 317-27.
47. Williams RS, Moncalian G, Williams JS, Yamada Y, Limbo O, Shin DS, Groocock LM, Cahill D, Hitomi C, Guenther G, Moiani D, Carney JP, Russell P, Tainer JA. Mre11 dimers coordinate DNA end bridging and nuclease processing in doublestrand- break repair. Cell 2008; 135: 97-109.
48. Mimitou EP, Symington LS. Sae2, Exo1 and Sgs1 collaborate in DNA double-strand break processing. Nature 2008; 455: 770-4.
49. Sung JH, Hong SS, Ahn SH, Li H, Seo SY, Park CH, Park BS, Chung SJ. Mechanism for increased bioavailability of tacrine in fasted rats. J Pharm Pharmacol 2006; 58: 643-9.
50. Helleday T, Lo J, van Gent DC, Engelward BP. DNA doublestrand break repair: from mechanistic understanding to cancer treatment. DNA Repair 2007; 6: 923-35.
51. Pfeiffer P, Thode S, Hancke J, Vielmetter W. Mechanisms of overlap formation in nonhomologous DNA end joining. Mol Cell Biol 1994; 14: 888-95.
52. Moore JK, Haber JE. Cell cycle and genetic requirements of two pathways of nonhomologous end-joining repair of doublestrand breaks in Saccharomyces cerevisiae. Mol Cell Biol 1996; 16: 2164-73.
53. Boulton SJ, Jackson SP. Saccharomyces cerevisiae Ku70 potentiates illegitimate DNA double-strand break repair and serves as a barrier to error-prone repair pathways. EMBO J 1996; 15: 5093-103.
54. Wilson TE, Lieber MR. Efficient processing of DNA ends during yeast nonhomologous end joining. Evidence for a DNA polymerase b (Pol4)-dependent pathway. J Biol Chem 1999; 274: 23599-609.
55. Budman J, Chu G. Processing of DNA for nonhomologous endjoining by cell-free extract. EMBO J 2005; 24: 849-60.
56. Espejel S, Franco S, Rodriguez-Perales S, Bouffler SD, Cigudosa JC, Blasco MA. Mammalian Ku86 mediates chromosomal fusions and apoptosis caused by critically short telomeres. EMBO J 2002; 21: 2207-19.
57. Guirouilh-Barbat J, Huck S, Bertrand P, Pirzio L, Desmaze C, Sabatier L, Lopez BS. Impact of the KU80 pathway on NHEJinduced genome rearrangements in mammalian cells. Mol Cell 2004; 14: 611-23.
58. Walker JR, Corpina RA, Goldberg J. Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair. Nature 2001; 412: 607-14.
59. Palmbos PL, Wu D, Daley JM, Wilson TE. Recruitment of Saccharomyces cerevisiae Dnl4-Lif1 complex to a doublestrand break requires interactions with Yku80 and the Xrs2 FHA domain. Genetics 2008; 180: 1809-19.
60. Yano K, Morotomi-Yano K, Wang SY, Uematsu N, Lee KJ, Asaithamby A, Weterings E, Chen DJ. Ku recruits XLF to DNA double-strand breaks. EMBO Rep 2008; 9: 91-6.
61. Ma Y, Pannicke U, Schwarz K, Lieber MR. Hairpin opening and overhang processing by an Artemis/DNA-dependent protein kinase complex in nonhomologous end joining and V(D)J recombination. Cell 2002; 108: 781-94.
62. Nick McElhinny SA, Ramsden DA. Sibling rivalry: competition between Pol X family members in V(D)J recombination and general double strand break repair. Immunol Rev 2004; 200: 156-64.
63. Daley JM, Laan RL, Suresh A, Wilson TE. DNA joint dependence of pol X family polymerase action in nonhomologous end joining. J Biol Chem 2005; 280: 29030-7.
64. Wilson TE, Grawunder U, Lieber MR. Yeast DNA ligase IV mediates non-homologous DNA end joining. Nature 1997; 388: 495-8.
65. Ahnesorg P, Smith P, Jackson SP. XLF interacts with the XRCC4-DNA ligase IV complex to promote DNA nonhomologous end-joining. Cell 2006; 124: 301-13.
66. Buck D, Malivert L, de Chasseval R, Barraud A, Fondaneche MC, Sanal O, Plebani A, Stephan JL, Hufnagel M, le Deist F, Fischer A, Durandy A, de Villartay JP, Revy P. Cernunnos, a novel nonhomologous end-joining factor, is mutated in human immunodeficiency with microcephaly. Cell 2006; 124: 287-99.
67. Callebaut I, Malivert L, Fischer A, Mornon JP, Revy P, de Villartay JP. Cernunnos interacts with the XRCC4 x DNA-ligase IV complex and is homologous to the yeast nonhomologous end-joining factor Nej1. J Biol Chem 2006; 281: 13857-60.
68. Riballo E, Woodbine L, Stiff T, Walker SA, Goodarzi AA, Jeggo PA. XLF-Cernunnos promotes DNA ligase IV-XRCC4 readenylation following ligation. Nucleic Acids Res 2009; 37: 482-92.
69. Wang M, Wu W, Rosidi B, Zhang L, Wang H, Iliakis G. PARP- 1 and Ku compete for repair of DNA double strand breaks by distinct NHEJ pathways. Nucleic Acids Res 2006; 34: 6170-82.
70. Mladenov E, Iliakis G. Induction and repair of DNA double strand breaks: the increasing spectrum of non-homologous end joining pathways. Mutat Res 2011; 711: 61-72.
71. Yan CT, Boboila C, Souza EK, Franco S, Hickernell TR, Murphy M, Gumaste S, Geyer M, Zarrin AA, Manis JP, Rajewsky K, Alt FW. IgH class switching and translocations use a robust non-classical end-joining pathway. Nature 2007; 449: 478-82.
72. Gilfillan S, Dierich A, Lemeur M, Benoist C, Mathis D. Mice lacking TdT: mature animals with an immature lymphocyte repertoire. Science 1993; 261: 1175-8.
73. Komori T, Okada A, Stewart V, Alt FW. Lack of N regions in antigen receptor variable region genes of TdT-deficient lymphocytes. Science 1993; 261: 1171-5.
74. Jung D, Alt FW. Unraveling V(D)J recombination; insights into gene regulation. Cell 2004; 116: 299-311.
75. Boulton SJ, Jackson SP. Components of the Ku-dependent nonhomologous end-joining pathway are involved in telomeric length maintenance and telomeric silencing. EMBO J 1998; 17: 1819-28.
76. Youngson RM. Collins dictionary of human biology. Glasgow: HarperCollins, 2006.
77. Cox M, Nelson D, Lehninger A. Principles of biochemistry. San Francisco, CA: W.H. Freeman, 2005.
78. Hartl D, Freifelder D, Snyder L. Basic genetics. Boston, MA: Jones and Bartlett Publishers, 1988.
79. Bhasin M, Reinherz EL, Reche PA. Recognition and classification of histones using support vector machine. J Comput Biol 2006; 13: 102-12.
80. Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 1997; 389: 251-60.
81. Farkas D. DNA simplified: the hitchhikers guide to DNA. Washington, DC: AACC Press, 1996.
82. Lennox RW, Oshima RG, Cohen LH. The H1 histones and their interphase phosphorylated states in differentiated and undifferentiated cell lines derived from murine teratocarcinomas. J Biol Chem 1982; 257: 5183-9.
83. Talasz H, Helliger W, Puschendorf B, Lindner H. In vivo phosphorylation of histone H1 variants during the cell cycle. Biochemistry 1996; 35: 1761-7.
84. Sarg B, Helliger W, Talasz H, Fog B, Lindner HH. Histone H1 phosphorylation occurs site-specifically during interphase and mitosis. J Biol Chem 2006; 281: 6573-80.
85. Bustin M. Regulation of DNA-dependent activities by the functional motifs of the high-mobility-group chromosomal proteins. Mol Cell Biol 1999; 19: 5237-46.
86. Laudet V, Stehelin D, Clevers H. Ancestry and diversity of the HMG box superfamily. Nucleic Acids Res 1993; 21: 2493-501.
87. Boonyaratanakornkit V, Melvin V, Prendergast P, Altmann M, Ronfani L, Bianchi ME, Taraseviciene L, Nordeen SK, Allegretto EA, Edwards DP. High-mobility group chromatin proteins 1 and 2 functionally interact with steroid hormone receptors to enhance their DNA binding in vitro and transcriptional activity in mammalian cells. Mol Cell Biol 1998; 18: 4471-87.
88. Pierantoni GM, Rinaldo C, Mottolese M, Di Benedetto A, Esposito F, Soddu S, Fusco A. High-mobility group A1 inhibits p53 by cytoplasmic relocalization of its proapoptotic activator HIPK2. J Clin Invest 2007; 117: 693-702.
89. van Gent DC, Hiom K, Paull TT, Gellert M. Stimulation of V(D)J cleavage by high mobility group proteins. EMBO J 1997; 16: 2665-70.
90. Zappavigna V, Falciola L, Helmer-Citterich M, Mavilio F, Bianchi ME. HMG1 interacts with HOX proteins and enhances their DNA binding and transcriptional activation. EMBO J 1996; 15: 4981-91.
91. Lotze MT, Tracey KJ. High-mobility group box 1 protein (HMGB1): nuclear weapon in the immune arsenal. Nat Rev Immunol 2005; 5: 331-42.
92. Rajeswari M, Jain A. High-mobility-group chromosomal proteins, HMGA1 as potential tumour markers. Curr Sci 2002; 82: 838-44.
93. Lu L, Wang Y. Immunoprecipitation alert: DNA binding proteins directly bind to protein A/G without any antibody as the bridge. Cell Cycle 2008; 7: 417-8.
94. Cho Y, Goprina S, Jeffrey PD, Pavletich NP. Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations. Science 1994; 265: 346-55.