Using the recognition code to swap homeodomain target specificity in cell culture

Molecular Biology Reports

Volumn 38, Issue 8, 2011, Pages 5349-5354

  Puppin, Cinzia ^a   Fabbro, Dora ^b   Pellizzari, Lucia ^b   Damante, Giuseppe ^a,b  

^a UNIVERSITY OF UDINE   (Italy)

^b SANTA MARIA DELLA MISERICORDIA UNIVERSITY HOSPITAL   (Italy)

Author keywords

DNA binding; Homeodomain; Recognition code

Indexed keywords

HOMEODOMAIN PROTEIN;

AMINO TERMINAL SEQUENCE; ARTICLE; BINDING KINETICS; BINDING SPECIFICITY; CHLORAMPHENICOL ACETYLTRANSFERASE GENE; CONTROLLED STUDY; DNA HELIX; DNA PROBE; DNA TRANSCRIPTION; DROSOPHILA; EXPRESSION VECTOR; GEL ELECTROPHORESIS; GEL RETARDATION ASSAY; GENE ACTIVITY; GENETIC TRANSFECTION; HELA CELL; HOMEODOMAIN; LUCIFERASE GENE; MOLECULAR RECOGNITION; NONHUMAN; PC5EIB GENE; PE1B GENE; PROTEIN DNA BINDING; PROTEIN DNA INTERACTION; PROTEIN DOMAIN; PROTEIN STRUCTURE; PTCBS GENE; PTK GENE; REPORTER GENE; TARGET CELL; TRANSACTIVATION;

AMINO ACID SEQUENCE; AMINO ACIDS; ANIMALS; BASE SEQUENCE; BIOLOGICAL ASSAY; CELL CULTURE TECHNIQUES; DROSOPHILA MELANOGASTER; ELECTROPHORETIC MOBILITY SHIFT ASSAY; GENES, REPORTER; HELA CELLS; HOMEODOMAIN PROTEINS; HUMANS; MOLECULAR SEQUENCE DATA; RECOMBINANT PROTEINS; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC; TRANSFECTION;

EID: 84855214456     PISSN: 03014851     EISSN: 15734978     Source Type: Journal    
DOI: 10.1007/s11033-011-0686-5     Document Type: Article

References (25)

1. Mitchell PJ, Tjian R (1989) Transcriptional regulation in mammalian cells by sequence-specific DNA binding proteins. Science 245(4916):371-378 (Pubitemid 19203358)
2. Gehring WJ, Qian YQ, Billeter M, Furukubo-Tokunaga K, Schier AF, Resendez-Perez D, Affolter M, Otting G, Wüthrich K (1994) Homeodomain-DNA recognition. Cell 78(2):211-223 (Pubitemid 24241090)
3. Pabo CO, Sauer RT (1992) Transcription factors: structural families and principles of DNA recognition. Annu Rev Biochem 61:1053-1095
4. Affolter M, Percival-Smith A, Müller M, Leupin W, Gehring WJ (1990) DNA binding properties of the purified Antennapedia homeodomain. Proc Natl Acad Sci USA 87(11):4093-4097
5. Hanes SD, Brent R (1989) DNA specificity of the bicoid activator protein is determined by homeodomain recognition helix residue 9. Cell 57:1275-1283 (Pubitemid 19169822)
6. Treisman J, Gönczy P, Vashishtha M, Harris E, Desplan C (1989) A single amino acid can determine the DNA binding specificity of homeodomain proteins. Cell 59:553-562 (Pubitemid 19284468)
7. Damante G, Pellizzari L, Esposito G, Fogolari F, Viglino P, Fabbro D, Tell G, Formisano S, Di Lauro R (1996) A molecular code dictates sequence-specific DNA recognition by homeodo-mains. EMBO J 15(18):4992-5000 (Pubitemid 26315809)
8. Baird-Titus JM, Clark-Baldwin K, Dave V, Caperelli CA, Ma J, Rance M (2006) The solution structure of the native K50 Bicoid homeodomain bound to the consensus TAATCC DNA-binding site. J Mol Biol 356:1137-1151 (Pubitemid 43199919)
9. Kissinger CR, Liu BS, Martin-Blanco E, Kornberg TB, Pabo CO (1990) Crystal structure of an engrailed homeodomain-DNA complex at 2.8 A resolution: a framework for understanding homeodomain-DNA interactions. Cell 63(3):579-590
10. Mann RS (1995) The specificity of homeotic gene function. Bi-oessays 17(10):855-863
11. Segil N, Roberts SB, Heintz N (1991) Mitotic phosphorylation of the Oct-1 homeodomain and regulation of Oct-1 DNA binding activity. Science 254(5039):1814-1816 (Pubitemid 21917536)
12. Dong J, Hung LH, Strome R, Krause HM (1998) A phosphory-lation site in the ftz homeodomain is required for activity. EMBO J 17(8):2308-2318 (Pubitemid 28171915)
13. Yang L, Yan D, Bruggeman M, Du H, Yan C (2004) Mutation of a lysine residue in a homeodomain generates dominant negative thyroid transcription factor 1. Biochemistry 43(39):12489-12497 (Pubitemid 39314710)
14. Tell G, Perrone L, Fabbro D, Pellizzari L, Pucillo C, De Felice M, Acquaviva R, Formisano S, Damante G (1998) Structural and functional properties of the N transcriptional activation domain of thyroid transcription factor-1: similarities with the acidic activation domains. Biochem J 329(Pt 2):395-403 (Pubitemid 28040805)
15. Zappavigna V, Sartori D, Mavilio F (1994) Specificity of HOX protein function depends on DNA-protein and protein-protein interactions, both mediated by the homeo domain. Genes Dev 8(6):732-744
16. Tell G, Scaloni A, Pellizzari L, Formisano S, Pucillo C, Damante G (1998) Redox potential controls the structure and DNA binding activity of the paired domain. J Biol Chem. 273(39):25062-25072 (Pubitemid 28443263)
17. 2 zinc finger proteins. Annu Rev Biophys Biomol Struct 3:183-212
18. Brennan RG, Matthews BW (1989) Structural basis of DNA-protein recognition. Trends Biochem Sci 14:286-290 (Pubitemid 19187258)
19. Maerkl SJ, Quake SR (2009) Experimental determination of the evolvability of a transcription factor. Proc Natl Acad Sci USA 106:18650-18655
20. Miller JC, Pabo CO (2001) Rearrangement of side-chains in a Zif268 mutant highlights the complexities of zinc finger-DNA recognition. J Mol Biol 313(2):309-315 (Pubitemid 33587190)
21. Wolfe SA, Grant RA, Elrod-Erickson M, Pabo CO (2001) Beyond the "recognition code": structures of two Cys2His2 zinc finger/TATA box complexes. Structure 9(8):717-723 (Pubitemid 32772894)
22. Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, Jaeger SA, Chan ET, Metzler G, Vedenko A, Chen X, Kuznetsov H, Wang CF, Coburn D, Newburger DE, Morris Q, Hughes TR, Bulyk ML (2009) Diversity and complexity in DNA recognition by transcription factors. Science 324(5935):1720-1723
23. Noyes MB, Christensen RG, Wakabayashi A, Stormo GD, Brodsky MH, Wolfe SA (2008) Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell 133(7):1277-1289 (Pubitemid 351852912)
24. Berger MF, Badis G, Gehrke AR, Talukder S, Philippakis AA, Peña-Castillo L, Alleyne TM, Mnaimneh S, Botvinnik OB, Chan ET, Khalid F, Zhang W, Newburger D, Jaeger SA, Morris QD, Bulyk ML, Hughes TR (2008) Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell 133(7):1266-1276 (Pubitemid 351852913)
25. Pellizzari L, Tell G, Fabbro D, Pucillo C, Damante G (1997) Functional interference between contacting amino acids of homeodomains. FEBS Lett 407(3):320-324 (Pubitemid 27199451)